WorldWideScience

Sample records for bacterial microbiota profiling

  1. Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use.

    Directory of Open Access Journals (Sweden)

    Xiao-Xing Li

    Full Text Available Recent 16S ribosomal RNA gene (rRNA molecular profiling of the stomach mucosa revealed a surprising complexity of microbiota. Helicobacter pylori infection and non-steroidal anti-inflammatory drug (NSAID use are two main contributors to gastritis and peptic ulcer. However, little is known about the association between other members of the stomach microbiota and gastric diseases. In this study, cloning and sequencing of the 16S rRNA was used to profile the stomach microbiota from normal and gastritis patients. One hundred and thirty three phylotypes from eight bacterial phyla were identified. The stomach microbiota was found to be closely adhered to the mucosa. Eleven Streptococcus phylotypes were successfully cultivated from the biopsies. One to two genera represented a majority of clones within any of the identified phyla. We further developed two real-time quantitative PCR assays to quantify the relative abundance of the Firmicutes phylum and the Streptococcus genus. Significantly higher abundance of the Firmicutes phylum and the Streptococcus genus within the Firmicutes phylum was observed in patients with antral gastritis, compared with normal controls. This study suggests that the genus taxon level can largely represent much higher taxa such as the phylum. The clinical relevance and the mechanism underlying the altered microbiota composition in gastritis require further functional studies.

  2. Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

    OpenAIRE

    Bulgarelli, D.; Garrido Oter, R.; Muench, P.; Weiman, A.; Droege, J.; Pan, Y.; McHardy, A; Schulze-Lefert, P.

    2015-01-01

    Summary The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial f...

  3. Different Flavonoids Can Shape Unique Gut Microbiota Profile In Vitro.

    Science.gov (United States)

    Huang, Jiacheng; Chen, Long; Xue, Bin; Liu, Qianyue; Ou, Shiyi; Wang, Yong; Peng, Xichun

    2016-09-01

    The impact of flavonoids has been discussed on the relative viability of bacterial groups in human microbiota. This study was aimed to compare the modulation of various flavonoids, including quercetin, catechin and puerarin, on gut microbiota culture in vitro, and analyze the interactions between bacterial species using fructo-oligosaccharide (FOS) as carbon source under the stress of flavonoids. Three plant flavonoids, quercetin, catechin, and puerarin, were added into multispecies culture to ferment for 24 h, respectively. The bacterial 16S rDNA amplicons were sequenced, and the composition of microbiota community was analyzed. The results revealed that the tested flavonoids, quercetin, catechin, and puerarin, presented different activities of regulating gut microbiota; flavonoid aglycones, but not glycosides, may inhibit growth of certain species. Quercetin and catechin shaped unique biological webs. Bifidobacterium spp. was the center of the biological web constructed in this study.

  4. The Bacterial Microbiota in Inflammatory Lung Diseases

    Science.gov (United States)

    Huffnagle, Gary B.; Dickson, Robert P.

    2016-01-01

    Numerous lines of evidence, ranging from recent studies back to those in the 1920's, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined. PMID:26122174

  5. Structure and function of the bacterial root microbiota in wild and domesticated barley.

    Science.gov (United States)

    Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C; Weiman, Aaron; Dröge, Johannes; Pan, Yao; McHardy, Alice C; Schulze-Lefert, Paul

    2015-03-11

    The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface. PMID:25732064

  6. Cohabitation in the intestine: interactions between helminth parasites, bacterial microbiota and host immunity

    OpenAIRE

    Reynolds, Lisa A.; Finlay, B. Brett; Rick M Maizels

    2015-01-01

    Both intestinal helminth parasites and certain bacterial microbiota species have been credited with strong immunomodulatory effects. Recent studies have reported that the presence of helminth infection alters the composition of the bacterial intestinal microbiota, and conversely that the presence and composition of the bacterial microbiota affects helminth colonisation and persistence within mammalian hosts. This article reviews recent findings on these reciprocal relationships, in both human...

  7. Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation.

    Science.gov (United States)

    Boix-Amorós, Alba; Collado, Maria C; Mira, Alex

    2016-01-01

    Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 10(6) bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, "planktonic" state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system.

  8. Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation.

    Science.gov (United States)

    Boix-Amorós, Alba; Collado, Maria C; Mira, Alex

    2016-01-01

    Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 10(6) bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, "planktonic" state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system. PMID:27148183

  9. Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy.

    Directory of Open Access Journals (Sweden)

    Wataru Yamanaka

    Full Text Available Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.8 ± 2.6 months, and their bacterial composition was investigated using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis using the UniFrac distance metric revealed that the overall bacterial community composition of saliva is distinct from that of supragingival plaque, both pre- and post-therapy. Temporal variation following therapy in the salivary bacterial population was significantly smaller than in the plaque microbiota, and the post-therapy saliva sample was significantly more similar to that pre-therapy from the same individual than to those from other subjects. Following periodontal therapy, microbial richness and biodiversity were significantly decreased in the plaque microbiota, but not in the salivary bacterial population. The operational taxonomic units whose relative abundances changed significantly after therapy were not common to the two microbiotae. These results reveal the compositional stability of salivary bacterial populations against shifts in the supragingival microbiota, suggesting that the effect of the supragingival plaque microbiota on salivary bacterial population composition is limited.

  10. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

    Science.gov (United States)

    Ellegaard, Kirsten M.; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

  11. Distinct Patterns in Human Milk Microbiota and Fatty Acid Profiles Across Specific Geographic Locations

    Science.gov (United States)

    Kumar, Himanshu; du Toit, Elloise; Kulkarni, Amruta; Aakko, Juhani; Linderborg, Kaisa M.; Zhang, Yumei; Nicol, Mark P.; Isolauri, Erika; Yang, Baoru; Collado, Maria C.; Salminen, Seppo

    2016-01-01

    Breast feeding results in long term health benefits in the prevention of communicable and non-communicable diseases at both individual and population levels. Geographical location directly impacts the composition of breast milk including microbiota and lipids. The aim of this study was to investigate the influence of geographical location, i.e., Europe (Spain and Finland), Africa (South Africa), and Asia (China), on breast milk microbiota and lipid composition in samples obtained from healthy mothers after the 1 month of lactation. Altogether, 80 women (20 from each country) participated in the study, with equal number of women who delivered by vaginal or cesarean section from each country. Lipid composition particularly that of polyunsaturated fatty acids differed between the countries, with the highest amount of n-6 PUFA (25.6%) observed in the milk of Chinese women. Milk microbiota composition also differed significantly between the countries (p = 0.002). Among vaginally delivered women, Spanish women had highest amount of Bacteroidetes (mean relative abundance of 3.75) whereas Chinese women had highest amount of Actinobacteria (mean relative abundance 5.7). Women who had had a cesarean section had higher amount of Proteobacteria as observed in the milk of the Spanish and South African women. Interestingly, the Spanish and South African women had significantly higher bacterial genes mapped to lipid, amino acid and carbohydrate metabolism (p < 0.05). Association of the lipid profile with the microbiota revealed that monounsaturated fatty acids (MUFA) were negatively associated with Proteobacteria (r = -0.43, p < 0.05), while Lactobacillus genus was associated with MUFA (r = -0.23, p = 0.04). These findings reveal that the milk microbiota and lipid composition exhibit differences based on geographical locations in addition to the differences observed due to the mode of delivery. PMID:27790209

  12. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.

    Science.gov (United States)

    Bolaños, Luis M; Rosenblueth, Mónica; Castillo-Ramírez, Santiago; Figuier-Huttin, Gilles; Martínez-Romero, Esperanza

    2016-05-01

    Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species. PMID:26058415

  13. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life.

    Directory of Open Access Journals (Sweden)

    Laura Moles

    Full Text Available The establishment and succession of bacterial communities in infants may have a profound impact in their health, but information about the composition of meconium microbiota and its evolution in hospitalized preterm infants is scarce. In this context, the objective of this work was to characterize the microbiota of meconium and fecal samples obtained during the first 3 weeks of life from 14 donors using culture and molecular techniques, including DGGE and the Human Intestinal Tract Chip (HITChip analysis of 16S rRNA amplicons. Culture techniques offer a quantification of cultivable bacteria and allow further study of the isolate, while molecular techniques provide deeper information on bacterial diversity. Culture and HITChip results were very similar but the former showed lower sensitivity. Inter-individual differences were detected in the microbiota profiles although the meconium microbiota was peculiar and distinct from that of fecal samples. Bacilli and other Firmicutes were the main bacteria groups detected in meconium while Proteobacteria dominated in the fecal samples. Culture technique showed that Staphylococcus predominated in meconium and that Enterococcus, together with Gram-negative bacteria such as Escherichia coli, Escherichia fergusonii, Klebsiella pneumoniae and Serratia marcescens, was more abundant in fecal samples. In addition, HITChip results showed the prevalence of bacteria related to Lactobacillus plantarum and Streptococcus mitis in meconium samples whereas those related to Enterococcus, Escherichia coli, Klebsiella pneumoniae and Yersinia predominated in the 3(rd week feces. This study highlights that spontaneously-released meconium of preterm neonates contains a specific microbiota that differs from that of feces obtained after the first week of life. Our findings indicate that the presence of Serratia was strongly associated with a higher degree of immaturity and other hospital-related parameters, including

  14. Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity.

    Science.gov (United States)

    Reynolds, Lisa A; Finlay, B Brett; Maizels, Rick M

    2015-11-01

    Both intestinal helminth parasites and certain bacterial microbiota species have been credited with strong immunomodulatory effects. Recent studies reported that the presence of helminth infection alters the composition of the bacterial intestinal microbiota and, conversely, that the presence and composition of the bacterial microbiota affect helminth colonization and persistence within mammalian hosts. This article reviews recent findings on these reciprocal relationships, in both human populations and mouse models, at the level of potential mechanistic pathways and the implications these bear for immunomodulatory effects on allergic and autoimmune disorders. Understanding the multidirectional complex interactions among intestinal microbes, helminth parasites, and the host immune system allows for a more holistic approach when using probiotics, prebiotics, synbiotics, antibiotics, and anthelmintics, as well as when designing treatments for autoimmune and allergic conditions.

  15. Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity.

    Science.gov (United States)

    Reynolds, Lisa A; Finlay, B Brett; Maizels, Rick M

    2015-11-01

    Both intestinal helminth parasites and certain bacterial microbiota species have been credited with strong immunomodulatory effects. Recent studies reported that the presence of helminth infection alters the composition of the bacterial intestinal microbiota and, conversely, that the presence and composition of the bacterial microbiota affect helminth colonization and persistence within mammalian hosts. This article reviews recent findings on these reciprocal relationships, in both human populations and mouse models, at the level of potential mechanistic pathways and the implications these bear for immunomodulatory effects on allergic and autoimmune disorders. Understanding the multidirectional complex interactions among intestinal microbes, helminth parasites, and the host immune system allows for a more holistic approach when using probiotics, prebiotics, synbiotics, antibiotics, and anthelmintics, as well as when designing treatments for autoimmune and allergic conditions. PMID:26477048

  16. Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis.

    Science.gov (United States)

    Tanaka, Akiomi; Cho, Otomi; Saito, Chie; Saito, Mami; Tsuboi, Ryoji; Sugita, Takashi

    2016-08-01

    Seborrheic dermatitis (SD) is a chronic inflammatory dermatologic condition in which erythema and itching develop on areas of the body with sebaceous glands, such as the scalp, face and chest. The inflammation is evoked directly by oleic acid, which is hydrolyzed from sebum by lipases secreted by skin microorganisms. Although the skin fungal genus, Malassezia, is thought to be the causative agent of SD, analysis of the bacterial microbiota of skin samples of patients with SD is necessary to clarify any association with Malassezia because the skin microbiota comprises diverse bacterial and fungal genera. In the present study, bacterial microbiotas were analyzed at non-lesional and lesional sites of 24 patients with SD by pyrosequencing and qPCR. Principal coordinate analysis revealed clear separation between the microbiota of non-lesional and lesional sites. Acinetobacter, Corynebacterium, Staphylococcus, Streptococcus and Propionibacterium were abundant at both sites. Propionibacterium was abundant at non-lesional sites, whereas Acinetobacter, Staphylococcus and Streptococcus predominated at lesional sites; however, the extent of Propionibacterium colonization did not differ significantly between lesional and non-lesional sites according to qPCR. Given that these abundant bacteria hydrolyze sebum, they may also contribute to SD development. To the best of our knowledge, this is the first comprehensive analysis of the bacterial microbiotas of the skin of SD patients. PMID:27301664

  17. Diet and environment shape fecal bacterial microbiota composition and enteric pathogen load of grizzly bears.

    Directory of Open Access Journals (Sweden)

    Clarissa Schwab

    Full Text Available BACKGROUND: Diet and environment impact the composition of mammalian intestinal microbiota; dietary or health disturbances trigger alterations in intestinal microbiota composition and render the host susceptible to enteric pathogens. To date no long term monitoring data exist on the fecal microbiota and pathogen load of carnivores either in natural environments or in captivity. This study investigates fecal microbiota composition and the presence of pathogenic Escherichia coli and toxigenic clostridia in wild and captive grizzly bears (Ursus arctos and relates these to food resources consumed by bears. METHODOLOGY/PRINCIPAL FINDINGS: Feces were obtained from animals of two wild populations and from two captive animals during an active bear season. Wild animals consumed a diverse diet composed of plant material, animal prey and insects. Captive animals were fed a regular granulated diet with a supplement of fruits and vegetables. Bacterial populations were analyzed using quantitative PCR. Fecal microbiota composition fluctuated in wild and in captive animals. The abundance of Clostridium clusters I and XI, and of C. perfringens correlated to regular diet protein intake. Enteroaggregative E. coli were consistently present in all populations. The C. sordellii phospholipase C was identified in three samples of wild animals and for the first time in Ursids. CONCLUSION: This is the first longitudinal study monitoring the fecal microbiota of wild carnivores and comparing it to that of captive individuals of the same species. Location and diet affected fecal bacterial populations as well as the presence of enteric pathogens.

  18. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

    OpenAIRE

    Vandeputte, Doris; Falony, Gwen; Araujo Vieira Da Silva, Sara Manuel; Tito Tadeo, Raul Yhossef; Joossens, Marie; Raes, Jeroen

    2016-01-01

    Objective The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time. Design Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women,...

  19. Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type.

    Science.gov (United States)

    Zhong, Z; Hou, Q; Kwok, L; Yu, Z; Zheng, Y; Sun, Z; Menghe, B; Zhang, H

    2016-10-01

    Naturally fermented dairy products contain a rich microbial biodiversity. This study aimed to provide an overview on the bacterial microbiota biodiversity of 85 samples, previously collected across a wide region of China, Mongolia, and Russia. Data from these 85 samples, including 55 yogurts, 18 naturally fermented yak milks, 6 koumisses, and 6 cheeses, were retrieved and collectively analyzed. The most prevalent phyla shared across samples were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, which together accounted for 99% of bacterial sequences. The predominant genera were Lactobacillus, Lactococcus, Streptococcus, Acetobacter, Acinetobacter, Leuconostoc, and Macrococcus, which together corresponded to 96.63% of bacterial sequences. Further multivariate statistical analyses revealed significant differences in the microbiota structure across sample geographic origin and type. First, on the principal coordinate score plot, samples representing the 3 main sample collection regions (Russia, Xinjiang, and Tibet) were mostly located respectively in the upper left, lower right, and lower left quadrants, although slight overlapping occurred. In contrast, samples from the minor sampling areas (Inner Mongolia, Mongolia, Gansu, and Sichuan) were predominantly distributed in the lower left quadrant. These results suggest a possible association between sample geographical origin and microbiota composition. Second, bacterial microbiota structure was stratified by sample type. In particular, the microbiota of cheese was largely distinct from the other sample types due to its high abundances of Lactococcus and Streptococcus. The fermented yak milk microbiota was most like that of the yogurts. Koumiss samples had the lowest microbial diversity and richness. In conclusion, both geographic origin and sample type shape the microbial diversity of naturally fermented milk. PMID:27474988

  20. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  1. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  2. Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.).

    Science.gov (United States)

    Wang, Wenfeng; Zhai, Yanyan; Cao, Lixiang; Tan, Hongming; Zhang, Renduo

    2016-01-01

    The objective of this study was to elucidate the endophytic microbiota in rice sprouts, roots, and stems, and their transmission in the plant development. Prior to DNA extraction, roots and stems were treated with 36% formaldehyde and 0.1M NaOH solutions to remove epiphytic bacterial whole 16S rRNA genes. Bacterial and fungal taxa in the sprout, root, and stem samples were analyzed using Illumina-based sequencing of the V3-V4 hyper variable regions of bacterial 16S rRNA genes and the ITS2 regions of fungal rRNA genes, respectively. Results showed that more diverse bacterial OTUs were detected in roots than in stems, while more diverse fungal OTUs were detected in stems than in roots. Compared with the endophytic microbiota in sprouts, the bacterial OTUs increased in roots but decreased in stems, whereas the fungal OTUs in both stems and roots decreased. Sprout-borne bacterial genera Sphingomonas and Pseudomonus, and fungal genera Fusarium, Pestalotiopsis, and Penicillium were detected in stems and roots. The coexistence of these indigenous bacterial and fungal taxa in sprouts, roots, and stems indicated their transmission during the development from sprouts to mature plants. The results from this study should be useful to better understand the plant-microbe interactions and to select suitable microbial taxa for rice production. PMID:27296957

  3. Cultivable Bacterial Microbiota of Northern Bobwhite (Colinus virginianus): A New Reservoir of Antimicrobial Resistance?

    Science.gov (United States)

    Su, Hongwen; McKelvey, Jessica; Rollins, Dale; Zhang, Michael; Brightsmith, Donald J.; Derr, James; Zhang, Shuping

    2014-01-01

    The northern bobwhite (Colinus virginianus) is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57%) followed by Actinobacteria (24%), Proteobacteria (17%) and Bacteroidetes (0.02%). Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations. PMID:24937705

  4. Cultivable bacterial microbiota of northern bobwhite (Colinus virginianus: a new reservoir of antimicrobial resistance?

    Directory of Open Access Journals (Sweden)

    Hongwen Su

    Full Text Available The northern bobwhite (Colinus virginianus is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57% followed by Actinobacteria (24%, Proteobacteria (17% and Bacteroidetes (0.02%. Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations.

  5. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

    Energy Technology Data Exchange (ETDEWEB)

    Mahowald, Michael [Washington University, St. Louis; Rey, Frederico E. [Washington University, St. Louis; Seedorf, Henning [Washington University, St. Louis; Turnbaugh, Peter J. [Washington University, St. Louis; Fulton, Robert S. [Washington University, St. Louis; Wollam, Aye [Washington University, St. Louis; Shah, Neha [Washington University, St. Louis; Wang, Chunyan [Washington University, St. Louis; Magrini, Vincent [Washington University, St. Louis; Wilson, Richard K. [Washington University, St. Louis; Cantarel, Brandi L. [Centre National de la Recherche Scientifique, Unite Mixte de Recherche; Coutinho, Pedro M [Universite d' Aix-Marseille I & II; Henrissat, Bernard [Universite d' Aix-Marseille I & II; Crock, Lara W. [Washington University, St. Louis; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Erickson, Alison L [ORNL; Gordon, Jeffrey [Washington University, St. Louis

    2009-01-01

    The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial microbial and microbial host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

  6. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota.

    Science.gov (United States)

    Audebert, Christophe; Even, Gaël; Cian, Amandine; Loywick, Alexandre; Merlin, Sophie; Viscogliosi, Eric; Chabé, Magali

    2016-01-01

    Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract. PMID:27147260

  7. Culturable bacterial microbiota of the stomach of Helicobacter pylori positive and negative gastric disease patients.

    Science.gov (United States)

    Khosravi, Yalda; Dieye, Yakhya; Poh, Bee Hoon; Ng, Chow Goon; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna

    2014-01-01

    Human stomach is the only known natural habitat of Helicobacter pylori (Hp), a major bacterial pathogen that causes different gastroduodenal diseases. Despite this, the impact of Hp on the diversity and the composition of the gastric microbiota has been poorly studied. In this study, we have analyzed the culturable gastric microbiota of 215 Malaysian patients, including 131 Hp positive and 84 Hp negative individuals that were affected by different gastric diseases. Non-Hp bacteria isolated from biopsy samples were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry based biotyping and 16SrRNA sequencing. The presence of Hp did not significantly modify the diversity of the gastric microbiota. However, correlation was observed between the isolation of Streptococci and peptic ulcer disease. In addition, as a first report, Burkholderia pseudomallei was also isolated from the gastric samples of the local population. This study suggested that there may be geographical variations in the diversity of the human gastric microbiome. Geographically linked diversity in the gastric microbiome and possible interactions between Hp and other bacterial species from stomach microbiota in pathogenesis are proposed for further investigations.

  8. Culturable Bacterial Microbiota of the Stomach of Helicobacter pylori Positive and Negative Gastric Disease Patients

    Directory of Open Access Journals (Sweden)

    Yalda Khosravi

    2014-01-01

    Full Text Available Human stomach is the only known natural habitat of Helicobacter pylori (Hp, a major bacterial pathogen that causes different gastroduodenal diseases. Despite this, the impact of Hp on the diversity and the composition of the gastric microbiota has been poorly studied. In this study, we have analyzed the culturable gastric microbiota of 215 Malaysian patients, including 131 Hp positive and 84 Hp negative individuals that were affected by different gastric diseases. Non-Hp bacteria isolated from biopsy samples were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry based biotyping and 16SrRNA sequencing. The presence of Hp did not significantly modify the diversity of the gastric microbiota. However, correlation was observed between the isolation of Streptococci and peptic ulcer disease. In addition, as a first report, Burkholderia pseudomallei was also isolated from the gastric samples of the local population. This study suggested that there may be geographical variations in the diversity of the human gastric microbiome. Geographically linked diversity in the gastric microbiome and possible interactions between Hp and other bacterial species from stomach microbiota in pathogenesis are proposed for further investigations.

  9. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression

    Directory of Open Access Journals (Sweden)

    Handfield Martin

    2009-10-01

    Full Text Available Abstract Background Periodontitis is a chronic inflammatory disease caused by the microbiota of the periodontal pocket. We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis. A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4 from a maxillary posterior region. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each tissue sample. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total. Plaque samples were analyzed using checkerboard DNA-DNA hybridizations with respect to 11 bacterial species. Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories. Results Wide inter-species variation was noted in the number of differentially expressed gingival tissue genes according to subgingival bacterial levels: Using a Bonferroni correction (p -7, 9,392 probe sets were differentially associated with levels of Tannerella forsythia, 8,537 with Porphyromonas gingivalis, 6,460 with Aggregatibacter actinomycetemcomitans, 506 with Eikenella corrodens and only 8 with Actinomyces naeslundii. Cluster analysis identified commonalities and differences among tissue gene expression patterns differentially regulated according to bacterial levels. Conclusion Our findings suggest that the microbial content of the periodontal pocket is a determinant of gene expression in the gingival tissues and provide new insights into the differential ability of periodontal species to elicit a local host response.

  10. Cultivation-independent methods reveal differences among bacterial gut microbiota in triatomine vectors of Chagas disease.

    Directory of Open Access Journals (Sweden)

    Fabio Faria da Mota

    Full Text Available BACKGROUND: Chagas disease is a trypanosomiasis whose agent is the protozoan parasite Trypanosoma cruzi, which is transmitted to humans by hematophagous bugs known as triatomines. Even though insecticide treatments allow effective control of these bugs in most Latin American countries where Chagas disease is endemic, the disease still affects a large proportion of the population of South America. The features of the disease in humans have been extensively studied, and the genome of the parasite has been sequenced, but no effective drug is yet available to treat Chagas disease. The digestive tract of the insect vectors in which T. cruzi develops has been much less well investigated than blood from its human hosts and constitutes a dynamic environment with very different conditions. Thus, we investigated the composition of the predominant bacterial species of the microbiota in insect vectors from Rhodnius, Triatoma, Panstrongylus and Dipetalogaster genera. METHODOLOGY/PRINCIPAL FINDINGS: Microbiota of triatomine guts were investigated using cultivation-independent methods, i.e., phylogenetic analysis of 16s rDNA using denaturing gradient gel electrophoresis (DGGE and cloned-based sequencing. The Chao index showed that the diversity of bacterial species in triatomine guts is low, comprising fewer than 20 predominant species, and that these species vary between insect species. The analyses showed that Serratia predominates in Rhodnius, Arsenophonus predominates in Triatoma and Panstrongylus, while Candidatus Rohrkolberia predominates in Dipetalogaster. CONCLUSIONS/SIGNIFICANCE: The microbiota of triatomine guts represents one of the factors that may interfere with T. cruzi transmission and virulence in humans. The knowledge of its composition according to insect species is important for designing measures of biological control for T. cruzi. We found that the predominant species of the bacterial microbiota in triatomines form a group of low

  11. Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs.

    Directory of Open Access Journals (Sweden)

    Anne A M J Becker

    Full Text Available Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus, this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05, and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%. This observation may reflect the temporary impact of perturbations such as the animal's compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five

  12. Beyond the gut bacterial microbiota: The gut virome.

    Science.gov (United States)

    Columpsi, Paola; Sacchi, Paolo; Zuccaro, Valentina; Cima, Serena; Sarda, Cristina; Mariani, Marcello; Gori, Andrea; Bruno, Raffaele

    2016-09-01

    The gastrointestinal tract is colonized with a highly different population of bacterial, viral, ad fungal species; viruses are reported to be dominant. The composition of gut virome is closely related to dietary habits and surrounding environment. Host and their intestinal microbes live in a dynamic equilibrium and viruses stimulate a low degree of immune responses without causing symptoms (host tolerance). However, intestinal phages could lead to a rupture of eubiosis and may contribute to the shift from health to disease in humans and animals. Viral nucleic acids and other products of lysis of bacteria serve as pathogen-associated molecular patterns (PAMPs) and could trigger specific inflammatory modulations. At the same time, phages could elicit innate antiviral immune responses. Toll-like receptors (TLRs) operated as innate antiviral immune sensors and their activation triggers signaling cascades that lead to inflammatory response. J. Med. Virol. 88:1467-1472, 2016. © 2016 Wiley Periodicals, Inc. PMID:26919534

  13. Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs.

    Directory of Open Access Journals (Sweden)

    Marc A Sze

    Full Text Available Previous reports have shown that the gastrointestinal (GI bacterial microbiota can have profound effects on the lungs, which has been described as the "gut-lung axis". However, whether a "lung-gut" axis exists wherein acute lung inflammation perturbs the gut and blood microbiota is unknown.Adult C57/Bl6 mice were exposed to one dose of LPS or PBS instillation (n=3 for each group directly into lungs. Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR at 4 through 168 hours post-instillation. We then investigated the effects of oral neomycin and streptomycin (n=8 on the microbiota at 4 and 24 hours post LPS instillation versus control treatment (n=5 at baseline and 4 hours, n=7 at 24 hours.At 24 hours post LPS instillation, the total bacterial count was significantly increased in the cecum (P<0.05; whereas the total bacterial count in blood was increased at 4, 48, and 72 hours (P<0.05. Antibiotic treatment reduced the total bacteria in blood but not in the cecum. The increase in total bacteria in the blood correlated with Phyllobacteriaceae OTU 40 and was significantly reduced in the blood for both antibiotic groups (P<0.05.LPS instillation in lungs leads to acute changes in the bacterial microbiota in the blood and cecum, which can be modulated with antibiotics.

  14. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients.

    Directory of Open Access Journals (Sweden)

    Fabrice Armougom

    Full Text Available BACKGROUND: Studies of the bacterial communities of the gut microbiota have revealed a shift in the ratio of Firmicutes and Bacteroidetes in obese patients. Determining the variations of microbial communities in feces may be beneficial for the identification of specific profiles in patients with abnormal weights. The roles of the archaeon Methanobrevibacter smithii and Lactobacillus species have not been described in these studies. METHODS AND FINDINGS: We developed an efficient and robust real-time PCR tool that includes a plasmid-based internal control and allows for quantification of the bacterial divisions Bacteroidetes, Firmicutes, and Lactobacillus as well as the methanogen M. smithii. We applied this technique to the feces of 20 obese subjects, 9 patients with anorexia nervosa, and 20 normal-weight healthy controls. Our results confirmed a reduction in the Bacteroidetes community in obese patients (p<0.01. We found a significantly higher Lactobacillus species concentration in obese patients than in lean controls (p=0.0197 or anorexic patients (p=0.0332. The M. smithii concentration was much higher in anorexic patients than in the lean population (p=0.0171. CONCLUSIONS: Lactobacillus species are widely used as growth promoters in the farm industry and are now linked to obesity in humans. The study of the bacterial flora in anorexic patients revealed an increase in M. smithii. This increase might represent an adaptive use of nutrients in this population.

  15. Rye affects bacterial translocation, intestinal viscosity, microbiota composition and bone mineralization in Turkey poults.

    Directory of Open Access Journals (Sweden)

    Guillermo Tellez

    Full Text Available Previously, we have reported that rye significantly increased both viscosity and Clostridium perfringens proliferation when compared with corn in an in vitro digestive model. Two independent trials were conducted to evaluate the effect of rye as a source of energy on bacterial translocation, intestinal viscosity, gut microbiota composition, and bone mineralization, when compared with corn in turkey poults. In each experiment, day-of-hatch, turkey poults were randomly assigned to either a corn or a rye diet (n = 0 /group. At 10 d of age, in both experiments, 12 birds/group were given an oral gavage dose of fluorescein isothiocyanate dextran (FITC-d. After 2.5 h of oral gavage, blood and liver samples were collected to evaluate the passage of FITC-d and bacterial translocation (BT respectively. Duodenum, ileum and cecum gut sections were collected to evaluate intestinal viscosity and to enumerate gut microbiota. Tibias were collected for observation of bone parameters. Broilers fed with a rye diet showed increased (p<0.05 intestinal viscosity, BT, and serum FITC-d. Bacterial enumeration revealed that turkey poults fed with rye had increased the number of total lactic acid bacteria (LAB in all three sections of the gastrointestinal tract evaluated when compared to turkey poults fed with corn. Turkey poults fed with rye also had significantly higher coliforms in duodenum and ileum but not in the ceca, whereas the total number of anaerobes increased only in duodenum. A significant reduction in bone strength and bone mineralization was observed in turkey poults fed with rye when compared with corn fed turkey poults. In conclusion, rye evoked mucosal damage in turkey poults that increased intestinal viscosity, increased leakage through the intestinal tract, and altered the microbiota composition and bone mineralization. Studies to evaluate dietary inclusion of selected Direct-Fed Microbial (DFM candidates that produce exogenous enzymes in rye fed

  16. Comprehensive characterization of indoor airborne bacterial profile

    Institute of Scientific and Technical Information of China (English)

    P.L.Chan; P.H.F.Yu; Y.W.Cheng; C.Y.Chan; P.K.Wong

    2009-01-01

    This is the first detailed characterization of the air-borne bacterial profiles in indoor environments and two restaurants were selected for this study.Fifteen genera of bacteria were isolated from each restaurant and identified by three different bacterial identification systems including MIDI, Biolog and Riboprinter?.The dominant bacteria of both restaurants were Gram-positive bacteria in which Micrococcus and Bacillus species were the most abundant species.Most bacteria identified were representative species of skin and respiratory tract of human, and soil.Although the bacterial levels in these restaurants were below the limit of the Hong Kong Indoor Air Quality Objective (HKIAQO) Level 1 standard (i.e., < 500 cfu/m3), the majority of these bacteria were opportunistic pathogens.These results suggested that the identity of airborne bacteria should also be included in the IAQ to ensure there is a safety guideline for the public.

  17. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    Full Text Available BACKGROUND: Bacterial vaginosis (BV is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. METHODOLOGY/PRINCIPAL FINDINGS: Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel's clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs significantly associated with each of the four Amsel's criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. CONCLUSIONS/SIGNIFICANCE: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased

  18. The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand.

    Science.gov (United States)

    Reid, Nicola M; Addison, Sarah L; West, Mark A; Lloyd-Jones, Gareth

    2014-12-01

    Stolotermes ruficeps is a widespread, primitive, lower termite occupying dead and decaying wood of many tree species in New Zealand's temperate forests. We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies. Most family and many genus-level taxa were common to S. ruficeps colonies despite being sampled from different tree species. Major taxa identified were Spirochaetaceae, Elusimicrobiaceae and Porphyromonadaceae. Others less well known in termite guts were Synergistaceae, Desulfobacteraceae, Rhodocyclaceae, Lachnospiraceae and Ruminococcaceae. Synergistaceae, Lachnospiraceae and Spirochaetaceae were well represented in the RNA data set, indicating a high-protein synthesis potential. Using 130,800 sequences from nine S. ruficeps DNA and RNA data sets, we estimated a high level of bacterial richness (4024 phylotypes at 3% genetic distance). Very few abundant phylotypes were site-specific; almost all (95%) abundant phylotypes, representing 97% of data set sequences, were detected in at least two S. ruficeps colonies. This study of a little-researched phylogenetically basal termite identifies core bacteria taxa. These findings will extend inventories of termite gut microbiota and contribute to the understanding of the specificity of termite gut microbiota. PMID:25196080

  19. Nonstarch polysaccharides modulate bacterial microbiota, pathways for butyrate production, and abundance of pathogenic Escherichia coli in the pig gastrointestinal tract.

    Science.gov (United States)

    Metzler-Zebeli, Barbara U; Hooda, Seema; Pieper, Robert; Zijlstra, Ruurd T; van Kessel, Andrew G; Mosenthin, Rainer; Gänzle, Michael G

    2010-06-01

    The impact of nonstarch polysaccharides (NSP) differing in their functional properties on intestinal bacterial community composition, prevalence of butyrate production pathway genes, and occurrence of Escherichia coli virulence factors was studied for eight ileum-cannulated growing pigs by use of terminal restriction fragment length polymorphism (TRFLP) and quantitative PCR. A cornstarch- and casein-based diet was supplemented with low-viscosity, low-fermentability cellulose (CEL), with high-viscosity, low-fermentability carboxymethylcellulose (CMC), with low-viscosity, high-fermentability oat beta-glucan (LG), and with high-viscosity, high-fermentability oat beta-glucan (HG). Only minor effects of NSP fractions on the ileal bacterial community were observed, but NSP clearly changed the digestion in the small intestine. Compared to what was observed for CMC, more fermentable substrate was transferred into the large intestine with CEL, LG, and HG, resulting in higher levels of postileal dry-matter disappearance. Linear discriminant analysis of NSP and TRFLP profiles and 16S rRNA gene copy numbers for major bacterial groups revealed that CMC resulted in a distinctive bacterial community in comparison to the other NSP, which was characterized by higher gene copy numbers for total bacteria, Bacteroides-Prevotella-Porphyromonas, Clostridium cluster XIVa, and Enterobacteriaceae and increased prevalences of E. coli virulence factors in feces. The numbers of butyryl-coenzyme A (CoA) CoA transferase gene copies were higher than those of butyrate kinase gene copies in feces, and these quantities were affected by NSP. The present results suggest that the NSP fractions clearly and distinctly affected the taxonomic composition and metabolic features of the fecal microbiota. However, the effects were more linked to the individual NSP and to their effect on nutrient flow into the large intestine than to their shared functional properties.

  20. Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host†

    Science.gov (United States)

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-01-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic “termite clusters” comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites. PMID:16269686

  1. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.

    Science.gov (United States)

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-11-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

  2. Bacterial Diversity in Meconium of Preterm Neonates and Evolution of Their Fecal Microbiota during the First Month of Life

    NARCIS (Netherlands)

    Moles, L.; Gómez, M.; Heilig, G.H.J.; Bustos, G.; Fuentes Enriquez de Salamanca, S.; Vos, de W.M.; Fernandez, L.; Rodriguez, J.M.; Jimenez, E.

    2013-01-01

    The establishment and succession of bacterial communities in infants may have a profound impact in their health, but information about the composition of meconium microbiota and its evolution in hospitalized preterm infants is scarce. In this context, the objective of this work was to characterize t

  3. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health.

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  4. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  5. The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals

    DEFF Research Database (Denmark)

    Schoster, A; Guardabassi, L; Staempfli, H R;

    2016-01-01

    or class level between treatment groups at any age (all p>0.08) but some significant changes in relative abundance of families. Probiotic administration did not result in an increased relative abundance of lactobacilli or bifidobacteria at any age (Lactobacillus: p = 0.95, p = 0.1 and p = 0...... applied (all p>0.65). CONCLUSIONS: There were limited effects of probiotic treatment on the bacterial microbiota of foals. The studied probiotic based on lactobacilli and bifidobacteria has a limited potential for therapeutic modification of the gastrointestinal microbiota. This article is protected...

  6. Microbiota bacteriana da conjuntiva de doadores de córnea Bacterial microbiota of the conjunctiva of donor corneas

    Directory of Open Access Journals (Sweden)

    Maria Emília Xavier dos Santos Araújo

    2004-12-01

    Full Text Available OBJETIVOS: Quantificar e qualificar a microbiota aeróbia da conjuntiva de doadores de córnea segundo a interferência do intervalo de tempo entre o óbito e a colheita do espécime conjuntival, a causa do óbito e a idade do doador e avaliar a atividade biocida de determinados antibióticos aos microrganismos isolados. MÉTODOS: Entre janeiro e março de 1994 foram colhidos espécimes da conjuntiva de 242 olhos de doadores de córnea. O material transportado em meio de Stuart foi semeado em ágares sangue, chocolate, sangue azida, MacConkey e caldo tioglicolato. Foi registrada a idade do doador, hora e causa do óbito. A atividade biocida dos antibióticos foi avaliada pela metodologia de Kirby e Bauer. A análise estatística utilizou os testes do qui-quadrado, exato de Fisher e Mann-Whitney. RESULTADOS: A freqüência de cultura positiva da conjuntiva de doadores de córnea foi de 91,7%. A mediana da idade dos doadores foi de 62 anos e do intervalo de tempo entre o óbito e a colheita do espécime foi de 4,2 horas. A causa mais freqüente de óbito foi doença cardiovascular (26,4%. Não houve diferença significante entre a cultura positiva e as variáveis estudadas. A vancomicina inibiu 100% das cepas de bactérias Gram-positivas e a sensibilidade dos bacilos Gram-negativos à gentamicina variou de 36,7% a 92,3%. CONCLUSÕES: O estudo revelou freqüência elevada de cultura positiva da conjuntiva de doadores de córneas. Staphylococcus coagulase negativo foi a espécie com maior número de isolamentos positivos. Não foi encontrada associação entre os fatores de risco avaliados e cultura positiva. Os antibióticos tiveram atividade biocida variável sobre os Gram-negativos e 100% dos Gram-positivos foram sensíveis à vancomicina.PURPOSE: To identify and qualify bacterial organisms in conjunctival tissue of donor corneas. To correlate the frequency of positive cultures with donor age, cause of death, and time from death to collection of

  7. Genetic and metabolic signals during acute enteric bacterial infection alter the microbiota and drive progression to chronic inflammatory disease

    Energy Technology Data Exchange (ETDEWEB)

    Kamdar, Karishma; Khakpour, Samira; Chen, Jingyu; Leone, Vanessa; Brulc, Jennifer; Mangatu, Thomas; Antonopoulos, Dionysios A.; Chang, Eugene B; Kahn, Stacy A.; Kirschner, Barbara S; Young, Glenn; DePaolo, R. William

    2016-01-13

    Chronic inflammatory disorders are thought to arise due to an interplay between predisposing host genetics and environmental factors. For example, the onset of inflammatory bowel disease is associated with enteric proteobacterial infection, yet the mechanistic basis for this association is unclear. We have shown previously that genetic defiency in TLR1 promotes acute enteric infection by the proteobacteria Yersinia enterocolitica. Examining that model further, we uncovered an altered cellular immune response that promotes the recruitment of neutrophils which in turn increases metabolism of the respiratory electron acceptor tetrathionate by Yersinia. These events drive permanent alterations in anti-commensal immunity, microbiota composition, and chronic inflammation, which persist long after Yersinia clearence. Deletion of the bacterial genes involved in tetrathionate respiration or treatment using targeted probiotics could prevent microbiota alterations and inflammation. Thus, acute infection can drive long term immune and microbiota alterations leading to chronic inflammatory disease in genetically predisposed individuals.

  8. Microbiota bacteriana aeróbia da conjuntiva de doadores de córnea Aerobic bacterial microbiota of the conjunctiva of cornea donors

    Directory of Open Access Journals (Sweden)

    Paula Fontana Lorenzini

    2007-03-01

    Full Text Available OBJETIVOS: Determinar a microbiota bacteriana aeróbia da conjuntiva de doadores de córnea e seu padrão de suscetibilidade a antibióticos; verificar o número de córneas utilizadas para transplante e a média de tempo de preservação em solução preservante com gentamicina e estreptomicina; traçar o perfil dos doadores e receptores de córnea. MÉTODOS: Espécimes clínicos foram colhidos de saco inferior da conjuntiva de ambos os olhos, de 40 doadores de córnea. As amostras foram inoculadas em ágar sangue azida, ágar chocolate e ágar MacConkey e o antibiograma foi realizado pelo método de Kirby-Bauer. RESULTADOS: A freqüência de cultura positiva da conjuntiva de doadores de córnea foi de 72,5%, sendo que Gram-positivos totalizaram 81,6% e apenas 18,4% das amostras foram identificadas como Gram-negativos. Vancomicina inibiu 100% dos Gram-positivos, ao passo que a sensibilidade dos Gram-negativos à gentamicina foi de 53,8% e à estreptomicina foi de 30%. O sexo masculino predominou entre os doadores e receptores, a média de tempo entre o óbito e a enucleação foi de 2h e a de preservação em solução preservante com gentamicina e estreptomicina foi de 7 dias. Neoplasia e mais de uma causa associada foram as causas de óbito mais freqüentes. O ceratocone foi a principal indicação para transplante (51,7%. CONCLUSÕES: Staphylococcus coagulase negativo foi o microrganismo com o maior número de isolamentos, apresentando sensibilidade variada aos antimicrobianos. A quantidade de córneas utilizadas para transplante foi bastante inferior em relação ao total de captações. O perfil dos doadores e receptores de córnea mostrou-se heterogêneo para grande parte das variáveis analisadas.PURPOSE: To determine aerobic bacterial microbiota of the conjunctiva of cornea donors and its patterns of susceptibility to antibiotics; verify the number of corneas used for transplant and the average time of preservation in solutions with

  9. Gut microbiota can transfer fiber characteristics and lipid metabolic profiles of skeletal muscle from pigs to germ-free mice.

    Science.gov (United States)

    Yan, Honglin; Diao, Hui; Xiao, Yi; Li, Wenxia; Yu, Bing; He, Jun; Yu, Jie; Zheng, Ping; Mao, Xiangbing; Luo, Yuheng; Zeng, Benhua; Wei, Hong; Chen, Daiwen

    2016-01-01

    Obesity causes changes in microbiota composition, and an altered gut microbiota can transfer obesity-associated phenotypes from donors to recipients. Obese Rongchang pigs (RP) exhibited distinct fiber characteristics and lipid metabolic profiles in their muscle compared with lean Yorkshire pigs (YP). However, whether RP have a different gut microbiota than YP and whether there is a relationship between the microbiota and muscle properties are poorly understood. The present study was conducted to test whether the muscle properties can be transferred from pigs to germ-free (GF) mice. High-throughput pyrosequencing confirms the presence of distinct core microbiota between pig breeds, with alterations in taxonomic distribution and modulations in β diversity. RP displayed a significant higher Firmicutes/Bacteroidetes ratio and apparent genera differences compared with YP. Transplanting the porcine microbiota into GF mice replicated the phenotypes of the donors. RP and their GF mouse recipients exhibited a higher body fat mass, a higher slow-contracting fiber proportion, a decreased fiber size and fast IIb fiber percentage, and enhanced lipogenesis in the gastrocnemius muscle. Furthermore, the gut microbiota composition of colonized mice shared high similarity with their donor pigs. Taken together, the gut microbiota of obese pigs intrinsically influences skeletal muscle development and the lipid metabolic profiles. PMID:27545196

  10. MICROBIOTA AND GUT-LIVER AXIS: A MINI-REVIEW ON THEIR INFLUENCES ON OBESITY AND OBESITY RELATED LIVER DISEASE

    OpenAIRE

    Vajro, Pietro; Paolella, Giulia; Fasano, Alessio

    2013-01-01

    A specific bacterial gut microbiota profile with increased extraction of calories has recently been associated with obesity, which has been shown to be a transmissible phenotype by microbiota transplantation. At the same time, there is now increasing evidence that gut microbiota plays a role in the development of hepatic steatosis and its progression to non-alcoholic steatohepatitis, as well.

  11. Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.

    Science.gov (United States)

    Tong, Maomeng; Jacobs, Jonathan P; McHardy, Ian H; Braun, Jonathan

    2014-11-03

    Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.

  12. Microbiota and anthropic interference on antimicrobial resistance profile of bacteria isolated from Brazilian maned-wolf (Chrysocyon brachyurus

    Directory of Open Access Journals (Sweden)

    Olney Vieira-da-Motta

    2013-12-01

    Full Text Available Both the study of Brazilian wild mammal fauna and the conditions that foster the preservation of endangered species, such as Brazilian Maned-wolf (Chrysocyon brachyurus, in wild life are of extreme importance. In order to study the resistance profile of microbiota bacterial colonizing Brazilian Maned-wolf, this work investigated samples from eight male captive and free roaming animals originating from different Brazilian geographical regions. Samples for microbiological purposes were collected with swabs and kept in appropriate transport medium. Using routine microbiological techniques, the isolated bacteria were tested toward antimicrobial drugs by the agar disk diffusion method. Results showed that all samples from wild animals were sensitive toward all drugs tested. Conversely, the resistance profile of bacteria isolated from captive animals varied among strains and animal body site location. Escherichia coli samples from prepuce, anus and ear showed multi-resistance toward at least four drugs, especially against erythromycin and tetracycline, followed by Proteus mirabilis and P. vulgaris strains isolated from anus and ear. Among Gram-positive bacteria, strains of coagulase-negative staphylococci showed multi-resistance mainly toward erythromycin and amoxicillin. The work discusses these findings and suggests that profile of multi-resistance bacteria from captive subjects may be attributed to direct contact with human or through lifestyle factors such as feeding, predation or contact of animals with urban animals such as birds, rodents, and insects from surrounding environments.

  13. Microbiota and anthropic interference on antimicrobial resistance profile of bacteria isolated from Brazilian Maned-wolf (Chrysocyon brachyurus).

    Science.gov (United States)

    Vieira-da-Motta, Olney; Eckhardt-de-Pontes, Luiz Antonio; Petrucci, Melissa Paes; dos Santos, Israel Pereira; da Cunha, Isabel Candia Nunes; Morato, Ronaldo Gonçalves

    2013-12-01

    Both the study of Brazilian wild mammal fauna and the conditions that foster the preservation of endangered species, such as Brazilian Maned-wolf (Chrysocyon brachyurus), in wild life are of extreme importance. In order to study the resistance profile of microbiota bacterial colonizing Brazilian Maned-wolf, this work investigated samples from eight male captive and free roaming animals originating from different Brazilian geographical regions. Samples for microbiological purposes were collected with swabs and kept in appropriate transport medium. Using routine microbiological techniques, the isolated bacteria were tested toward antimicrobial drugs by the agar disk diffusion method. Results showed that all samples from wild animals were sensitive toward all drugs tested. Conversely, the resistance profile of bacteria isolated from captive animals varied among strains and animal body site location. Escherichia coli samples from prepuce, anus and ear showed multi-resistance toward at least four drugs, especially against erythromycin and tetracycline, followed by Proteus mirabilis and P. vulgaris strains isolated from anus and ear. Among Gram-positive bacteria, strains of coagulase-negative staphylococci showed multi-resistance mainly toward erythromycin and amoxicillin. The work discusses these findings and suggests that profile of multi-resistance bacteria from captive subjects may be attributed to direct contact with human or through lifestyle factors such as feeding, predation or contact of animals with urban animals such as birds, rodents, and insects from surrounding environments. PMID:24688529

  14. Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus.

    Science.gov (United States)

    Li, Hongjie; Dietrich, Carsten; Zhu, Na; Mikaelyan, Aram; Ma, Bin; Pi, Ruoxi; Liu, Yu; Yang, Mengyi; Brune, Andreas; Mo, Jianchu

    2016-05-01

    Fungus-cultivating termites (Macrotermitinae) possess an elaborate strategy of lignocellulose digestion. It involves a lignocellulose-degrading fungal symbiont (genus Termitomyces), a diverse gut microbiota and a characteristic labour division in food processing. In this study, using pyrotag sequencing and electron microscopy, we analysed the bacterial microbiota in the hindgut of Odontotermes formosanus and its fungus comb to investigate the spatial organization, establishment and temporal succession of the bacterial communities colonizing specific microhabitats. Our results document strong differences between the communities at the hindgut epithelium and the luminal fluid of newly moulted, young and old worker termites. The differences in community structure were consistent with the density, morphology and spatial distribution of bacterial cells and the pools of microbial metabolites in the hindgut compartment, underlining that both gut development and the age-specific changes in diet affect the composition and functional role of their gut microbiota. These findings provide strong support for the concept that changes in diet and gut environment are important determinants of community structure because they create new niches for microbial symbionts. PMID:26346907

  15. ANTAGONISM AGAINST VIBRIO CHOLERAE BY BACTERIAL DIFFUSIBLE COMPOUND IN THE FECAL MICROBIOTA OF RODENTS

    Directory of Open Access Journals (Sweden)

    Simone Helena da Silva

    1998-09-01

    Full Text Available In an ex vivo agar plate assay, we monitored the appearance of an inhibitory halo against Vibrio cholerae from the feces of Wistar and Fischer rats aged 10 to 42 days. The frequency of Wistar rats showing halo increased from 0% (10 days to a maximum of 80.0% (29 days and then decreased to 53.3% (42 days. A similar pattern was obtained with Fischer rats but with a lower intensity (maximum frequency of 50.0% by day 36. In a separate experiment, when Wistar rats were fed a low-protein diet for 7 days, the inhibitory halo decreased drastically. Three apparently different colony morphologies were isolated from the dominant fecal microbiota: a facultative anaerobe (FAN and two strict anaerobes (SAN. The ex vivo inhibitory test showed a halo around the feces of germfree mice monoassociated with the FAN bacterium or one of the SAN bacterium but not of the germfree ones. After oral challenge of all groups with V. cholerae, a permissive and a drastic barrier effects were observed in mice with FAN and SAN associated bacteria, respectively. The FAN and one SAN bacteria used in the in vivo challenges were identified as Escherichia coli and Streptococcus intermedius, respectively. The potent antagonism developed by the rat intestinal microbiota against V. cholerae seems to be due, in part, to diffusible compounds and this phenomenon depends apparently on age, strain and nutrition of the animals. These preliminary results also suggest that this effect was due to more than one bacterial component at any given moment.O aparecimento de halo de inibição contra o Vibrio cholerae a partir das fezes de ratos Wistar e Fischer nas idades de 10 a 42 dias foi observado usando um teste ex vivo em placa. A frequência de ratos Wistar apresentando halo aumentou de 0% (10 dias até um máximo de 80,0% (29 dias antes de decair para 53,3% (42 dias. Um perfil similar foi obtido com os ratos Fischer mas com valores inferiores (frequência máxima de 50,0% no dia 36. Num

  16. Quantitative and qualitative analyses of the bacterial microbiota of tilapia (Oreochromis niloticus) cultured in earthen ponds in the Philippines.

    Science.gov (United States)

    Pakingking, Rolando; Palma, Peter; Usero, Roselyn

    2015-02-01

    The quantity and composition of the bacterial microbiota in the rearing water, sediment, gills and intestines of tilapia Oreochromis niloticus collected every 2 weeks from Day 30 to Day 120 after stocking for grow-out culture in 6 earthen brackish water ponds in the Philippines were examined. The total heterotrophic aerobic bacterial counts obtained in the water, sediment, gills and intestines of tilapia ranged from 10(3) to 10(4) c.f.u. ml(-1), 10(3)-10(5), 10(5)-10(7) and 10(4)-10(7) c.f.u. g(-1), respectively. In terms of composition, a total of 20 bacterial genera and 31 species were identified with the preponderance of gram-negative bacteria constituting 84 % of all bacterial isolates examined. Aeromonas hydrophila, Bacillus spp., Plesiomonas shigelloides, Shewanella putrefaciens, Pseudomonas fluorescens, Staphylococcus spp. and Vibrio cholerae were the dominant bacteria identified in the gills and intestine of tilapia. These bacteria also dominated in the pond sediment and rearing water, except for the nil isolation of S. putrefaciens and V. cholerae in the water samples examined, indicating that resident bacteria in the pond water and sediment congruently typify the composition of bacterial microbiota in the gills and intestine of tilapia which under stressful conditions may propel the ascendance of disease epizootics. PMID:25555375

  17. Gut microbiota dysbiosis is associated with inflammation and bacterial translocation in mice with CCl4-induced fibrosis.

    Directory of Open Access Journals (Sweden)

    Isabel Gómez-Hurtado

    Full Text Available BACKGROUND: Gut is the major source of endogenous bacteria causing infections in advanced cirrhosis. Intestinal barrier dysfunction has been described in cirrhosis and account for an increased bacterial translocation rate. HYPOTHESIS AND AIMS: We hypothesize that microbiota composition may be affected and change along with the induction of experimental cirrhosis, affecting the inflammatory response. ANIMALS AND METHODS: Progressive liver damage was induced in Balb/c mice by weight-controlled oral administration of carbon tetrachloride. Laparotomies were performed at weeks 6, 10, 13 and 16 in a subgroup of treated mice (n = 6/week and control animals (n = 4/week. Liver tissue specimens, mesenteric lymph nodes, intestinal content and blood were collected at laparotomies. Fibrosis grade, pro-fibrogenic genes expression, gut bacterial composition, bacterial translocation, host's specific butyrate-receptor GPR-43 and serum cytokine levels were measured. RESULTS: Expression of pro-fibrogenic markers was significantly increased compared with control animals and correlated with the accumulated dose of carbon tetrachloride. Bacterial translocation episodes were less frequent in control mice than in treated animals. Gram-positive anaerobic Clostridia spp count was decreased in treated mice compared with control animals and with other gut common bacterial species, altering the aerobic/anaerobic ratio. This fact was associated with a decreased gene expression of GPR43 in neutrophils of treated mice and inversely correlated with TNF-alpha and IL-6 up-regulation in serum of treated mice along the study protocol. This pro-inflammatory scenario favoured blood bacterial translocation in treated animals, showing the highest bacterial translocation rate and aerobic/anaerobic ratio at the same weeks. CONCLUSIONS: Gut microbiota alterations are associated with the development of an inflammatory environment, fibrosis progression and bacterial translocation in

  18. Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins.

    Science.gov (United States)

    Cernada, María; Bäuerl, Christine; Serna, Eva; Collado, Maria Carmen; Martínez, Gaspar Pérez; Vento, Máximo

    2016-01-01

    Sepsis is a life-threatening condition in preterm infants. Neonatal microbiota plays a pivotal role in the immune system maturation. Changes in gut microbiota have been associated to inflammatory disorders; however, a link with sepsis in the neonatal period has not yet been established. We aimed to analyze gut microbiota and mucosal gene expression using non-invasively obtained samples to provide with an integrative perspective of host-microbe interactions in neonatal sepsis. For this purpose, a prospective observational case-control study was conducted in septic preterm dizygotic twins and their non-septic twin controls. Fecal samples were used for both microbiota analysis and host genome-wide expression using exfoliated intestinal cells. Gene expression of exfoliated intestinal cells in septic preterm showed an induction of inflammatory and oxidative stress pathways in the gut and pro-oxidant profile that caused dysbiosis in the gut microbiota with predominance of Enterobacteria and reduction of Bacteroides and Bifidobacterium spp.in fecal samples, leading to a global reduction of beneficial anaerobic bacteria. Sepsis in preterm infants induced low-grade inflammation and oxidative stress in the gut mucosa, and also changes in the gut microbiota. This study highlights the role of inflammation and oxidative stress in neonatal sepsis on gut microbial profiles. PMID:27180802

  19. Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins.

    Science.gov (United States)

    Cernada, María; Bäuerl, Christine; Serna, Eva; Collado, Maria Carmen; Martínez, Gaspar Pérez; Vento, Máximo

    2016-05-16

    Sepsis is a life-threatening condition in preterm infants. Neonatal microbiota plays a pivotal role in the immune system maturation. Changes in gut microbiota have been associated to inflammatory disorders; however, a link with sepsis in the neonatal period has not yet been established. We aimed to analyze gut microbiota and mucosal gene expression using non-invasively obtained samples to provide with an integrative perspective of host-microbe interactions in neonatal sepsis. For this purpose, a prospective observational case-control study was conducted in septic preterm dizygotic twins and their non-septic twin controls. Fecal samples were used for both microbiota analysis and host genome-wide expression using exfoliated intestinal cells. Gene expression of exfoliated intestinal cells in septic preterm showed an induction of inflammatory and oxidative stress pathways in the gut and pro-oxidant profile that caused dysbiosis in the gut microbiota with predominance of Enterobacteria and reduction of Bacteroides and Bifidobacterium spp.in fecal samples, leading to a global reduction of beneficial anaerobic bacteria. Sepsis in preterm infants induced low-grade inflammation and oxidative stress in the gut mucosa, and also changes in the gut microbiota. This study highlights the role of inflammation and oxidative stress in neonatal sepsis on gut microbial profiles.

  20. Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints

    Science.gov (United States)

    Mack, Isabelle; Cuntz, Ulrich; Grämer, Claudia; Niedermaier, Sabrina; Pohl, Charlotte; Schwiertz, Andreas; Zimmermann, Kurt; Zipfel, Stephan; Enck, Paul; Penders, John

    2016-01-01

    The gut microbiota not only influences host metabolism but can also affect brain function and behaviour through the microbiota-gut-brain axis. To explore the potential role of the intestinal microbiota in anorexia nervosa (AN), we comprehensively investigated the faecal microbiota and short-chain fatty acids in these patients before (n = 55) and after weight gain (n = 44) in comparison to normal-weight participants (NW, n = 55) along with dietary intake and gastrointestinal complaints. We show profound microbial perturbations in AN patients as compared to NW participants, with higher levels of mucin-degraders and members of Clostridium clusters I, XI and XVIII and reduced levels of the butyrate-producing Roseburia spp. Branched-chain fatty acid concentrations, being markers for protein fermentation, were elevated. Distinct perturbations in microbial community compositions were observed for individual restrictive and binge/purging AN-subtypes. Upon weight gain, microbial richness increased, however perturbations in intestinal microbiota and short chain fatty acid profiles in addition to several gastrointestinal symptoms did not recover. These insights provide new leads to modulate the intestinal microbiota in order to improve the outcomes of the standard therapy. PMID:27229737

  1. Gut microbiota and obesity.

    Science.gov (United States)

    Gérard, Philippe

    2016-01-01

    The human intestine harbors a complex bacterial community called the gut microbiota. This microbiota is specific to each individual despite the existence of several bacterial species shared by the majority of adults. The influence of the gut microbiota in human health and disease has been revealed in the recent years. Particularly, the use of germ-free animals and microbiota transplant showed that the gut microbiota may play a causal role in the development of obesity and associated metabolic disorders, and lead to identification of several mechanisms. In humans, differences in microbiota composition, functional genes and metabolic activities are observed between obese and lean individuals suggesting a contribution of the gut microbiota to these phenotypes. Finally, the evidence linking gut bacteria to host metabolism could allow the development of new therapeutic strategies based on gut microbiota modulation to treat or prevent obesity.

  2. The A0 blood group genotype modifies the jejunal glycomic binding pattern profile of piglets early associated with a simple or complex microbiota.

    Science.gov (United States)

    Priori, D; Colombo, M; Koopmans, S-J; Jansman, A J M; van der Meulen, J; Trevisi, P; Bosi, P

    2016-02-01

    The intestinal epithelium glycocalyx sugar motif is an important determinant of the bacterial-host interaction and may be affected in pigs by gut microbiota and by blood group genotype. The aim was to study the effect of intestinal association with different microbiota and A0 blood group genotypes on the expressed glycomic pattern in the small intestine. Twelve caesarean-derived pigs previously associated with a simple association (SA) or complex association (CA) microbiota were selected at 26 to 37 d of age. In each subject, different jejunal loops were perfused for 8 h with enterotoxigenic K88 (ETEC), ETEC fimbriae (F4), (LAM), or a saline control. The piglets were genotyped for A0 blood group and the glycomic profile was evaluated by microscopic screening of lectin binding: peanut agglutinin (PNA), which is galactose specific; agglutinin I (UEA), which is fucose specific; lectin II (MALii), which is sialic acid specific; concavalin A, which is mannose specific; soybean agglutinin (SBA), which is -acetyl-galactosamine specific; and wheat germ agglutinin (WGA), which is -acetyl-glucosamine specific. A0 pigs had fewer UEA-positive cells, MALii-positive cells ( < 0.001), and SBA-positive cells ( < 0.10) than 00 pigs. Simple association pigs had more SBA positive cells ( < 0.01) than CA pigs. Enterotoxigenic K88-perfused intestinal loops had fewer UEA-positive cells ( < 0.01) and WGA positive cells ( < 0.001) cells and more PNA positive cells (only in SA pigs, < 0.01). No effects of introduction of F4 and LAM in the intestinal lumen were observed. The porcine A0 blood group genotype and the luminal presence of ETEC strongly affected the jejunal mucosa glycomic pattern profile whereas an early oral simple or complex microbial association had limited effects. Pig genetic background has relevance on the cross talk between intestinal epithelium glycocalyx sugar motif and ETEC and, ultimately, on the gut microbial colonization in later life. PMID:27065129

  3. Bacterial spoilage profiles to identify irradiated fish

    International Nuclear Information System (INIS)

    Effects of low dose gamma-irradiation of fish product on spoilage potentials of bacteria (Aeromonas hydrophila, Salmonella typhimurium, Bacillus megaterium, and Pseudomonas marinoglutinosa) and mixed flora were examined for ability to proliferate in radurized fish and produce volatile acids (TVA) and bases (TVBN). Bacteria proliferated well in unirradiated and irradiated fish, but formation of VA and VB were lower in irradiated than unirradiated counterparts. This was found in Bombay duck, Indian mackerel, white pomfret, seer and shrimp gamma-irradiated at 0 to 5 kGy under ice. TVA and TVBN produced by the organisms or mixed flora from fish were only 30-50% those of controls. A method for identifying radiation-processed fish could evolve based on lower susceptibility of irradiated fish to bacterial spoilage

  4. Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

    Directory of Open Access Journals (Sweden)

    Ting-Chin David Shen

    Full Text Available We have recently reported that Altered Schaedler Flora (ASF can be used to durably engineer the gut microbiota to reduce ammonia production as an effective modality to reduce morbidity and mortality in the setting of liver injury. Here we investigated the effects of a low protein diet on ASF colonization and its ability to engineer the microbiota. Initially, ASF inoculation was similar between mice fed a normal protein diet or low protein diet, but the outgrowth of gut microbiota differed over the ensuing month. Notable was the inability of the dominant Parabacteroides ASF taxon to exclude other taxa belonging to the Bacteroidetes phylum in the setting of a low protein diet. Instead, a poorly classified yet highly represented Bacteroidetes family, S24-7, returned within 4 weeks of inoculation in mice fed a low protein diet, demonstrating a reduction in ASF resilience in response to dietary stress. Nevertheless, fecal ammonia levels remained significantly lower than those observed in mice on the same low protein diet that received a transplant of normal feces. No deleterious effects were observed in host physiology due to ASF inoculation into mice on a low protein diet. In total, these results demonstrate that low protein diet can have a pronounced effect on engineering the gut microbiota but modulation of ammonia is preserved.

  5. Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease

    Directory of Open Access Journals (Sweden)

    Ricanek P

    2012-09-01

    Full Text Available Petr Ricanek,1,2 Sheba M Lothe,1 Stephan A Frye,1 Andreas Rydning,2 Morten H Vatn,3,4 Tone Tønjum1,51Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, 2Department of Gastroenterology, Akershus University Hospital, Lørenskog and Faculty Division Akershus University Hospital, University of Oslo, Lørenskog, 3EpiGen Institute, Faculty Division Akershus University Hospital, University of Oslo, Lørenskog, 4Department of Medicine, Oslo University Hospital, Rikshospitalet, Oslo, 5Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, NorwayObjectives: The aim of this study was to define the composition of the gut bacterial flora in Norwegian patients with early stage Crohn's disease (CD. Methods: By using a nonselective metagenomics approach, the general bacterial composition in mucosal biopsies from the ileum and the colon of five subjects, four patients with different phenotypes of CD, and one noninflammatory bowel disease control, was characterized. After partial 16S ribosomal RNA (rRNA gene sequencing, BLAST homology searches for species identification and phylogenetic analysis were performed.Results: An overall biodiversity of 106 different bacterial operational taxonomic units (OTUs was detected in the cloned libraries. Nearly all OTUs belonged to the phylae Bacteroidetes (42% in CD, 71% in the control or Firmicutes (42% in CD, 28% in the control, except for some OTUs that belonged to the phylum Proteobacteria (15% in CD, 0% in the control and a few OTUs that could not be assigned to a phylum (2% in CD, 1% in the control.Conclusion: Based on the high incidence of inflammatory bowel disease (IBD in Norway, this pilot study represents a relevant determination of the gut microbiota in Norwegian patients compared to previous findings in other countries. The bacterial profile of Norwegian CD patients was found to be similar

  6. Altered Bacterial Profiles in Saliva from Adults with Caries Lesions

    DEFF Research Database (Denmark)

    Belstrøm, D; Fiehn, N-E; Nielsen, C H;

    2014-01-01

    The aim of this study was to learn whether presence of caries in an adult population was associated with a salivary bacterial profile different from that of individuals without untreated caries. Stimulated saliva samples from 621 participants of the Danish Health Examination Survey were analyzed...

  7. Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice.

    Directory of Open Access Journals (Sweden)

    Melissa K Friswell

    Full Text Available BACKGROUND: The gastrointestinal tract microbiota (GTM of mammals is a complex microbial consortium, the composition and activities of which influences mucosal development, immunity, nutrition and drug metabolism. It remains unclear whether the composition of the dominant GTM is conserved within animals of the same strain and whether stable GTMs are selected for by host-specific factors or dictated by environmental variables. METHODOLOGY/PRINCIPAL FINDINGS: The GTM composition of six highly inbred, genetically distinct strains of mouse (C3H, C57, GFEC, CD1, CBA nu/nu and SCID was profiled using eubacterial -specific PCR-DGGE and quantitative PCR of feces. Animals exhibited strain-specific fecal eubacterial profiles that were highly stable (c. >95% concordance over 26 months for C57. Analyses of mice that had been relocated before and after maturity indicated marked, reproducible changes in fecal consortia and that occurred only in young animals. Implantation of a female BDF1 mouse with genetically distinct (C57 and Agoutie embryos produced highly similar GTM profiles (c. 95% concordance between mother and offspring, regardless of offspring strain, which was also reflected in urinary metabolite profiles. Marked institution-specific GTM profiles were apparent in C3H mice raised in two different research institutions. CONCLUSION/SIGNIFICANCE: Strain-specific data were suggestive of genetic determination of the composition and activities of intestinal symbiotic consortia. However, relocation studies and uterine implantation demonstrated the dominance of environmental influences on the GTM. This was manifested in large variations between isogenic adult mice reared in different research institutions.

  8. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

    Science.gov (United States)

    Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

    2015-01-01

    In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples. PMID:26035837

  9. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

    Science.gov (United States)

    Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

    2015-01-01

    In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.

  10. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

    Directory of Open Access Journals (Sweden)

    Ilario Ferrocino

    Full Text Available In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE. The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.

  11. Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora.

    Science.gov (United States)

    Xiao, Bingbing; Niu, Xiaoxi; Han, Na; Wang, Ben; Du, Pengcheng; Na, Risu; Chen, Chen; Liao, Qinping

    2016-01-01

    Bacterial vaginosis (BV) is a highly prevalent disease in women, and increases the risk of pelvic inflammatory disease. It has been given wide attention because of the high recurrence rate. Traditional diagnostic methods based on microscope providing limited information on the vaginal microbiota increase the difficulty in tracing the development of the disease in bacteria resistance condition. In this study, we used deep-sequencing technology to observe dynamic variation of the vaginal microbiota at three major time points during treatment, at D0 (before treatment), D7 (stop using the antibiotics) and D30 (the 30-day follow-up visit). Sixty-five patients with BV were enrolled (48 were cured and 17 were not cured), and their bacterial composition of the vaginal microbiota was compared. Interestingly, we identified 9 patients might be recurrence. We also introduced a new measurement point of D7, although its microbiota were significantly inhabited by antibiotic and hard to be observed by traditional method. The vaginal microbiota in deep-sequencing-view present a strong correlation to the final outcome. Thus, coupled with detailed individual bioinformatics analysis and deep-sequencing technology, we may illustrate a more accurate map of vaginal microbial to BV patients, which provide a new opportunity to reduce the rate of recurrence of BV. PMID:27253522

  12. Oral bacterial microbiota and traumatic injuries of free-ranging Phrynops geoffroanus (Testudines, Chelidae in southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Bruno O. Ferronato

    2009-07-01

    Full Text Available During 2006 and 2007, we collected free-ranging Phrynops geoffroanus, from two anthropogenically altered rivers in southeastern Brazil. Oral microbiological samples were taken for isolation of aerobic and facultative anaerobic bacteria; a physical examination was performed;and we evaluated possible effects on the turtles’ health. Twenty-nine species of bacteria were isolated in Piracicaba River turtles (n=10, and twenty-four species in Piracicamirim stream turtles (n=8, most of them gram-negative. In both sites, potential pathogens for reptiles were: Escherichia coli, Klebsiella pneumoniae, Enterobacter agglomerans, Citrobacter freundii, and Bacillus sp. Although boatpropeller lesions were common on the carapace of the turtles, we have not found turtles with signs of clinical diseases. The oral bacterial microbiota of P. geoffroanus inhabiting the Piracicaba River basin are composed of a diverse microbe spectrum, and long-term studies of the effects of pollution and traumatic injuries on this population and its microbial flora are warranted.

  13. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

    DEFF Research Database (Denmark)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte;

    2016-01-01

    of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (mi...... species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization...

  14. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

  15. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  16. Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile.

    Science.gov (United States)

    Qi, Xiaozhe; Chen, Siyuan; Sheng, Yao; Guo, Mingzhang; Liu, Yifei; He, Xiaoyun; Huang, Kunlun; Xu, Wentao

    2015-02-01

    The genetically modified (GM) rice expressing human serum albumin (HSA) is used for non-food purposes; however, its food safety assessment should be conducted due to the probability of accidental mixture with conventional food. In this research, Sprague Dawley rats were fed diets containing 50% (wt/wt) GM rice expressing HSA or non-GM rice for 90 days. Urine metabolites were detected by (1)H NMR to examine the changes of the metabolites in the dynamic process of metabolism. Fecal bacterial profiles were detected by denaturing gradient gel electrophoresis to reflect intestinal health. Additionally, short chain fatty acids and fecal enzymes were investigated. The results showed that compared with rats fed the non-GM rice, some significant differences were observed in rats fed with the GM rice; however, these changes were not significantly different from the control diet group. Additionally, the gut microbiota was associated with blood indexes and urine metabolites. In conclusion, the GM rice diet is as safe as the traditional daily diet. Furthermore, urine metabonomics and fecal bacterial profiles provide a non-invasive food safety assessment rat model for genetically modified crops that are used for non-food/feed purposes. Fecal bacterial profiles have the potential for predicting the change of blood indexes in future.

  17. Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile.

    Science.gov (United States)

    Qi, Xiaozhe; Chen, Siyuan; Sheng, Yao; Guo, Mingzhang; Liu, Yifei; He, Xiaoyun; Huang, Kunlun; Xu, Wentao

    2015-02-01

    The genetically modified (GM) rice expressing human serum albumin (HSA) is used for non-food purposes; however, its food safety assessment should be conducted due to the probability of accidental mixture with conventional food. In this research, Sprague Dawley rats were fed diets containing 50% (wt/wt) GM rice expressing HSA or non-GM rice for 90 days. Urine metabolites were detected by (1)H NMR to examine the changes of the metabolites in the dynamic process of metabolism. Fecal bacterial profiles were detected by denaturing gradient gel electrophoresis to reflect intestinal health. Additionally, short chain fatty acids and fecal enzymes were investigated. The results showed that compared with rats fed the non-GM rice, some significant differences were observed in rats fed with the GM rice; however, these changes were not significantly different from the control diet group. Additionally, the gut microbiota was associated with blood indexes and urine metabolites. In conclusion, the GM rice diet is as safe as the traditional daily diet. Furthermore, urine metabonomics and fecal bacterial profiles provide a non-invasive food safety assessment rat model for genetically modified crops that are used for non-food/feed purposes. Fecal bacterial profiles have the potential for predicting the change of blood indexes in future. PMID:25478734

  18. Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis.

    Science.gov (United States)

    Aldunate, Muriel; Srbinovski, Daniela; Hearps, Anna C; Latham, Catherine F; Ramsland, Paul A; Gugasyan, Raffi; Cone, Richard A; Tachedjian, Gilda

    2015-01-01

    Lactic acid and short chain fatty acids (SCFAs) produced by vaginal microbiota have reported antimicrobial and immune modulatory activities indicating their potential as biomarkers of disease and/or disease susceptibility. In asymptomatic women of reproductive-age the vaginal microbiota is comprised of lactic acid-producing bacteria that are primarily responsible for the production of lactic acid present at ~110 mM and acidifying the vaginal milieu to pH ~3.5. In contrast, bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is characterized by decreased lactic acid-producing microbiota and increased diverse anaerobic bacteria accompanied by an elevated pH>4.5. BV is also characterized by a dramatic loss of lactic acid and greater concentrations of mixed SCFAs including acetate, propionate, butyrate, and succinate. Notably women with lactic acid-producing microbiota have more favorable reproductive and sexual health outcomes compared to women with BV. Regarding the latter, BV is associated with increased susceptibility to sexually transmitted infections (STIs) including HIV. In vitro studies demonstrate that lactic acid produced by vaginal microbiota has microbicidal and virucidal activities that may protect against STIs and endogenous opportunistic bacteria as well as immune modulatory properties that require further characterization with regard to their effects on the vaginal mucosa. In contrast, BV-associated SCFAs have far less antimicrobial activity with the potential to contribute to a pro-inflammatory vaginal environment. Here we review the composition of lactic acid and SCFAs in respective states of eubiosis (non-BV) or dysbiosis (BV), their effects on susceptibility to bacterial/viral STIs and whether they have inherent microbicidal/virucidal and immune modulatory properties. We also explore their potential as biomarkers for the presence and/or increased susceptibility to STIs.

  19. Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Muriel eAldunate

    2015-06-01

    Full Text Available Lactic acid and short chain fatty acids (SCFAs produced by vaginal microbiota have reported antimicrobial and immune modulatory activities indicating their potential as biomarkers of disease and/or disease susceptibility. In asymptomatic women of reproductive-age the vaginal microbiota is comprised of lactic acid-producing bacteria that are primarily responsible for the production of lactic acid present at ~110 mM and acidifying the vaginal milieu to pH ~3.5. In contrast, bacterial vaginosis (BV, a dysbiosis of the vaginal microbiota, is characterized by decreased lactic acid-producing microbiota and increased diverse anaerobic bacteria accompanied by an elevated pH>4.5. BV is also characterized by a dramatic loss of lactic acid and greater concentrations of mixed SCFAs including acetate, propionate, butyrate and succinate. Notably women with lactic acid-producing microbiota have more favorable reproductive and sexual health outcomes compared to women with BV. Regarding the latter, BV is associated with increased susceptibility to sexually transmitted infections (STIs including HIV. In vitro studies demonstrate that lactic acid produced by vaginal microbiota has microbicidal and virucidal activities that may protect against STIs and endogenous opportunistic bacteria as well as immune modulatory properties that require further characterization with regard to their effects on the vaginal mucosa. In contrast, BV-associated SCFAs have far less antimicrobial activity with the potential to contribute to a pro-inflammatory vaginal environment. Here we review the composition of lactic acid and SCFAs in respective states of eubiosis (non-BV or dysbiosis (BV, their effects on susceptibility to bacterial/viral STIs and whether they have inherent microbicidal/virucidal and immune modulatory properties. We also explore their potential as biomarkers for the presence and/or increased susceptibility to STIs.

  20. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.

    Directory of Open Access Journals (Sweden)

    Heather Maughan

    Full Text Available The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq: a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.

  1. Effect of various antibiotics on modulation of intestinal microbiota and bile acid profile in mice.

    Science.gov (United States)

    Zhang, Youcai; Limaye, Pallavi B; Renaud, Helen J; Klaassen, Curtis D

    2014-06-01

    Antibiotic treatments have been used to modulate intestinal bacteria and investigate the role of intestinal bacteria on bile acid (BA) homeostasis. However, knowledge on which intestinal bacteria and bile acids are modified by antibiotics is limited. In the present study, mice were administered various antibiotics, 47 of the most abundant bacterial species in intestine, as well as individual BAs in plasma, liver, and intestine were quantified. Compared to the two antibiotic combinations (vancomycin+imipenem and cephalothin+neomycin), the three single antibiotics (metronidazole, ciprofloxacin and aztreonam) have less effect on intestinal bacterial profiles, and thus on host BA profiles and mRNA expression of genes that are important for BA homeostasis. The two antibiotic combinations decreased the ratio of Firmicutes to Bacteroidetes in intestine, as well as most secondary BAs in serum, liver and intestine. Additionally, the two antibiotic combinations significantly increased mRNA of the hepatic BA uptake transporters (Ntcp and Oatp1b2) and canalicular BA efflux transporters (Bsep and Mrp2), but decreased mRNA of the hepatic BA synthetic enzyme Cyp8b1, suggesting an elevated enterohepatic circulation of BAs. Interestingly, the two antibiotic combinations tended to have opposite effect on the mRNAs of most intestinal genes, which tended to be inhibited by vancomycin+imipenem but stimulated by cephalothin+neomycin. To conclude, the present study clearly shows that various antibiotics have distinct effects on modulating intestinal bacteria and host BA metabolism.

  2. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores

    NARCIS (Netherlands)

    Boer, de P.; Caspers, M.; Sanders, J.W.; Kemperman, R.; Wijman, J.; Lommerse, G.; Roeselers, G.; Montijn, R.; Abee, T.; Kort, R.

    2015-01-01

    Background
    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon

  3. Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota

    NARCIS (Netherlands)

    Larsen, J.M.; Steen-Jensen, D.B.; Laursen, J.M.; Sondergaard, J.N.; Musavian, H.S.; Butt, T.M.; Brix, S.

    2012-01-01

    Recent studies using culture-independent methods have characterized the human airway microbiota and report microbial communities distinct from other body sites. Changes in these airway bacterial communities appear to be associated with inflammatory lung disease, yet the pro-inflammatory properties o

  4. Effect of various antibiotics on modulation of intestinal microbiota and bile acid profile in mice

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Youcai; Limaye, Pallavi B.; Renaud, Helen J.; Klaassen, Curtis D., E-mail: curtisklaassenphd@gmail.com

    2014-06-01

    Antibiotic treatments have been used to modulate intestinal bacteria and investigate the role of intestinal bacteria on bile acid (BA) homeostasis. However, knowledge on which intestinal bacteria and bile acids are modified by antibiotics is limited. In the present study, mice were administered various antibiotics, 47 of the most abundant bacterial species in intestine, as well as individual BAs in plasma, liver, and intestine were quantified. Compared to the two antibiotic combinations (vancomycin + imipenem and cephalothin + neomycin), the three single antibiotics (metronidazole, ciprofloxacin and aztreonam) have less effect on intestinal bacterial profiles, and thus on host BA profiles and mRNA expression of genes that are important for BA homeostasis. The two antibiotic combinations decreased the ratio of Firmicutes to Bacteroidetes in intestine, as well as most secondary BAs in serum, liver and intestine. Additionally, the two antibiotic combinations significantly increased mRNA of the hepatic BA uptake transporters (Ntcp and Oatp1b2) and canalicular BA efflux transporters (Bsep and Mrp2), but decreased mRNA of the hepatic BA synthetic enzyme Cyp8b1, suggesting an elevated enterohepatic circulation of BAs. Interestingly, the two antibiotic combinations tended to have opposite effect on the mRNAs of most intestinal genes, which tended to be inhibited by vancomycin + imipenem but stimulated by cephalothin + neomycin. To conclude, the present study clearly shows that various antibiotics have distinct effects on modulating intestinal bacteria and host BA metabolism. - Highlights: • Various antibiotics have different effects on intestinal bacteria. • Antibiotics alter bile acid composition in mouse liver and intestine. • Antibiotics influence genes involved in bile acid homeostasis. • Clostridia appear to be important for secondary bile acid formation.

  5. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota

    OpenAIRE

    Audebert, Christophe; Even, Gaël; Cian, Amandine; ,; Safadi, Dima El; Certad, Gabriela; Delhaes, Laurence; Pereira, Bruno; Nourrisson, Céline; Poirier, Philippe; Wawrzyniak, Ivan; Delbac, Frédéric; Morelle, Christelle; Bastien, Patrick; Lachaud, Laurence

    2016-01-01

    Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To ad...

  6. Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough "Masa Agria" (Maiz Añejo).

    Science.gov (United States)

    Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D; Paparella, Antonello

    2016-01-01

    Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential.

  7. Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough "Masa Agria" (Maiz Añejo).

    Science.gov (United States)

    Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D; Paparella, Antonello

    2016-01-01

    Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential. PMID:27524979

  8. Composition of the vaginal microbiota in women of reproductive age--sensitive and specific molecular diagnosis of bacterial vaginosis is possible?

    Directory of Open Access Journals (Sweden)

    Elena Shipitsyna

    Full Text Available BACKGROUND AND OBJECTIVE: Bacterial vaginosis (BV is the most common vaginal disorder, characterized by depletion of the normal lactobacillus-dominant microbiota and overgrowth of commensal anaerobic bacteria. This study aimed to investigate the composition of the vaginal microbiota in women of reproductive age (healthy women and women with BV, with the view of developing molecular criteria for BV diagnosis. MATERIALS AND METHODS: Vaginal samples from 163 women (79 control, 73 BV and 11 intermediate (Lactobacillary grade II flora cases were analyzed using 454 pyrosequencing of the hypervariable regions V3-V4 of the 16S rRNA gene and 16 quantitative bacterial species/genus-specific real-time PCR assays. Sensitivities and specificities of potential BV markers were computed using the Amsel criteria as reference standard for BV. The use of quantitative thresholds for prediction of BV, determined for both relative abundance measured with 454 pyrosequencing and bacterial load measured with qPCR, was evaluated. RESULTS: Relative to the healthy women, the BV patients had in their vaginal microbiota significantly higher prevalence, loads and relative abundances of the majority of BV associated bacteria. However, only Gardnerella vaginalis, Atopobium vaginae, Eggerthella, Prevotella, BVAB2 and Megasphaera type 1 detected at or above optimal thresholds were highly predictable for BV, with the best diagnostic accuracy shown for A. vaginae. The depletion of Lactobacillus species combined with the presence of either G. vaginalis or A. vaginae at diagnostic levels was a highly accurate BV predictor. CONCLUSIONS: Quantitative determination of the presence of G. vaginalis, A. vaginae, Eggerthella, Prevotella, BVAB2 and Megasphaera type 1 as well as the depletion of Lactobacillus was highly accurate for BV diagnosis. Measurements of abundance of normal and BV microbiota relative to total bacteria in vaginal fluid may provide more accurate BV diagnosis, and be

  9. Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis.

    Directory of Open Access Journals (Sweden)

    Christina A Muzny

    Full Text Available BACKGROUND: The pathogenesis of bacterial vaginosis (BV remains elusive. BV may be more common among women who have sex with women (WSW. The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM, and women who have sex with men (WSM with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV. METHODS: Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥ 2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon's Index implemented in QIIME and Unifrac analysis, respectively. RESULTS: 33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR=0.24; 95%CI 0.11-0.54 and Parvimonas (RR=0.33; 95%CI 0.11-0.93 were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86, and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88 was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa. CONCLUSION: The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest

  10. Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data

    Directory of Open Access Journals (Sweden)

    Leo Lahti

    2013-02-01

    Full Text Available Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae. These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes

  11. Microbiota bacteriana da conjuntiva no pré-operatório de injeção intravítrea de antiangiogênico por degeneração macular relacionada à idade comparada com a de cirurgia de catarata Preoperative conjunctival bacterial microbiota of antiangiogenic intravitreous injection for age-related macular degeneration compared to cataract surgery preoperative microbiota

    Directory of Open Access Journals (Sweden)

    José Ricardo Diniz

    2010-06-01

    pacientes no pré-operatório de cirurgia de catarata.Purpose: To evaluate the conjunctival bacterial microbiota and antibiogram profile in the preoperative of antiangiogenic intravitreous injection for age-related macular degeneration, and compare to the preoperative microbiota of patients submitted to cataract surgery. Methods: Cross-sectional, observational, case series study. Two groups were organized: group I (macular degeneration with 26 eyes from 26 patients (12 men/14 women with mean age of 69.2 ± 11.5 years; group II (cataract with 27 eyes from 27 patients (9 men/18 women with mean age of 67.6 ± 7.9 years. The groups were similar regarding age (p=0.538 and gender (p=0.787. The lower conjunctival sac was swabbed and the obtained material was immediately put in a tube filled with liquid culture media BHI ("brain heart infusion". Samples were processed according to standard laboratory techniques and antibiogram was determined for each bacterial colony. Results: Twenty-six bacterial colonies growth in group I, with 2 eyes showing no growth and 30 colonies growth in group II. Gram positive bacteria were more prevalent in both groups: 23/26 colonies (88.4% in group I and 29/30 colonies (96.7% in group II, with a Staphylococcus aureus predominance in both groups, with 16 samples (61.5% and 17 (56.7%, respectively. Coagulase negative Staphylococcus was the second most common identified bacteria, with 19.2% in group I and 20.0% in group II. No differences between the groups reached statistical significance. No statistically significant difference was noted on the antibiotic sensibility between both groups. Conclusions: There was no difference in the distribution of bacteria and antibiogram profile of the conjunctival microbiota in the preoperative of intravitreous injection of antiangiogenic for macular degeneration compared to the preoperative of cataract surgery.

  12. Plasmid profiling of bacterial isolates from confined environments

    Science.gov (United States)

    van Houdt, Rob; Provoost, Ann; Coninx, Ilse; Leys, Natalie; Mergeay, Max

    Plasmid profiling of bacterial isolates from confined environments R. Van Houdt, I. Coninx, A. Provoost, N. Leys, and M. Mergeay Expertise group for Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium. Human exploration of extreme and isolated hostile environments such as space requires special confined small volume habitats to protect and house the crew. However, human confinement in such small volume habitats has restrictions on waste disposal and personal hygiene and inevitably generates a particular community of microorganisms within the habitat. These microorganisms are mainly originating from the crew (skin, mucous membranes, upper respiratory tract, mouth, and gastrointestinal tract) but also include the residing environmental microorganisms. Earth-based confined habitats such as the Antarctic Research Station Concordia are used as test beds for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. The dynamics of the environmental microbial population in such a test bed could render additional insights in assessing the potential health risks in long-duration space missions. Not only total bacterial contamination levels are important, but it is essential to identify also the predominant microbial taxa and their mobile genetic elements (MGE). These MGEs could be exchanged between bacteria by horizontal gene transfer and may alter the pathogenic potential since they often carry antibiotic resistance or more in general adaptation-enhancing traits. In this study several bacterial strains isolated in the Concordia research station were examined for their plasmid content. An optimized protocol for extraction of large plasmids showed the present of at least one plasmid in 50% of the strains. For all strains the minimal inhibitory concentration of a range of antibiotics was determined indicating resistance to

  13. Altered colonic function and microbiota profile in a mouse model of chronic depression

    OpenAIRE

    Park, A J; Collins, J.; BLENNERHASSETT, P. A.; Ghia, J E; Verdu, E. F.; Bercik, P; COLLINS, S. M.

    2013-01-01

    Background Depression often coexists with the irritable bowel syndrome (IBS) which is characterized by alterations in gut function. There is emerging evidence that the microbial composition (microbiota) of the gut is altered in IBS, but the basis for this is poorly understood. The aim of this study was to determine whether the induction of chronic depression results in changes in the colonic function and in its microbial community, and to explore underlying mechanisms. Methods Bilateral olfac...

  14. Characterization of the bacterial gut microbiota in new neonatal porcine diarrhoea

    DEFF Research Database (Denmark)

    Hermann-Bank, Marie Louise

    was tested on DNA extracted from ileal or colonic contents from piglets with or without NNPD and verified via 454 next generation sequencing of the PCR amplicons. Bioinformatics was conducted using BION-meta customized for this specific setup. With the Gut Microbiotassay in place gut microbial profiles...... significantly up- or down-regulated reflecting the complex immunological response to being inoculated and/or infected with NNPD-material. Finally, a high abundance of genus Enterococcus (characteristic of case piglets) was associated with high expressions of several transcripts involved in epithelial integrity....... Altogether, the results of the studies included in this thesis reveal that NNPD is associated with a disturbed gut microbial composition, and all points towards members from the genus Enterococcus are involved in the pathogenesis of NNPD....

  15. Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Fiehn, Nils-Erik; Nielsen, Claus H;

    2015-01-01

    Bacterial profiles of saliva in subjects with periodontitis and dental caries have been demonstrated to differ from that of oral health. The aim of this comparative analysis of existing data generated by the Human Oral Microbe Identification Microarray (HOMIM) from 293 stimulated saliva samples...... was to compare bacterial profiles of saliva in subjects with periodontitis and dental caries....

  16. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants

    Science.gov (United States)

    Holman, Devin B.; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W.

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers’ grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills. PMID:27300323

  17. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Science.gov (United States)

    Holman, Devin B; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills. PMID:27300323

  18. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Science.gov (United States)

    Holman, Devin B; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills.

  19. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Directory of Open Access Journals (Sweden)

    Devin B Holman

    Full Text Available Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills.

  20. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    2014-04-01

    Full Text Available Background and objective: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. Design: Stimulated saliva samples from 292 participants with low levels of dental caries and periodontitis, enrolled in the Danish Health Examination Survey (DANHES, were analyzed for the presence of approximately 300 bacterial species by means of the Human Oral Microbe Identification Microarray (HOMIM. Using presence and levels (mean HOMIM-value of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann–Whitney tests with Benjamini–Hochberg's correction for multiple comparisons and principal component analysis. Results: Targets for 131 different probes were identified in 292 samples, with Streptococcus and Veillonella being the most predominant genera identified. Two bacterial taxa (Streptococcus sobrinus and Eubacterium [11][G-3] brachy were more associated with smokers than non-smokers (adjusted p-value<0.01. Stratification of the group based on extreme ends of the parameters age, gender, alcohol consumption, body mass index (BMI, and diet intake had no statistical influence on the composition of the bacterial profile of saliva. Conversely, differences in socioeconomic status were reflected by the bacterial profiles of saliva. Conclusions: The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status.

  1. [Irritable Bowel Syndrome, Emotion Regulation, and Gut Microbiota].

    Science.gov (United States)

    Fukudo, Shin

    2016-06-01

    Irritable bowel syndrome (IBS) is defined as a representative functional gastrointestinal disorder which is characterized by chronic or recurrent abdominal pain and/or abdominal discomfort associated with abnormal bowel movement. Gut microbiota are related to the pathophysiology of IBS. In the field of IBS, post-infectious etiology, stress-induced alteration of microbiota, increased mucosal permeability, bacterial overgrowth, disease-specific microbiota, microbial products, and brain-gut interactions are being investigated. In some individuals, IBS develops after recovery from acute gastroenteritis known as post-infectious IBS. Gut microbiota in IBS patients differ from those in healthy individuals, and the profiles of gut microbiota in IBS patients also vary among IBS patients with constipation, diarrhea, and mixed subtypes. In Japan, gut microbiota in IBS patients also differ from those observed in healthy individuals, and organic acid by-products observed in the patients correlated with symptoms, quality of life, and alexithymia. Further research on gut microbiota in IBS patients is warranted. PMID:27279158

  2. Effects on weight gain and gut microbiota in rats given bacterial supplements and a high-energy-dense diet from fetal life through to 6 months of age.

    Science.gov (United States)

    Karlsson, Caroline L J; Molin, Göran; Fåk, Frida; Johansson Hagslätt, Marie-Louise; Jakesevic, Maja; Håkansson, Åsa; Jeppsson, Bengt; Weström, Björn; Ahrné, Siv

    2011-09-01

    The aim of the present study was to assess the long-term effects of a high-energy-dense diet, supplemented with Lactobacillus plantarum (Lp) or Escherichia coli (Ec), on weight gain, fattening and the gut microbiota in rats. Since the mother's dietary habits can influence offspring physiology, dietary regimens started with the dams at pregnancy and throughout lactation and continued with the offspring for 6 months. The weight gain of group Lp was lower than that of groups C (control) and Ec (P = 0·086). More retroperitoneal adipose tissue (P = 0·030) and higher plasma leptin (P = 0·035) were observed in group Ec compared with group Lp. The viable count of Enterobacteriaceae was higher in group Ec than in group Lp (P = 0·019), and when all animals were compared, Enterobacteriaceae correlated positively with body weight (r 0·428, P = 0·029). Bacterial diversity was lower in group Ec than in groups C (P ≤ 0·05) and Lp (P ≤ 0·05). Firmicutes, Bacteroidetes and Verrucomicrobia dominated in all groups, but Bacteroidetes were more prevalent in group C than in groups Lp (P = 0·036) and Ec (P = 0·056). The same five bacterial families dominated the microbiota of groups Ec and C, and four of these were also present in group Lp. The other five families dominating in group Lp were not found in any of the other groups. Multivariate data analysis pointed in the same directions as the univariate statistics. The present results suggest that supplementation of L. plantarum or E. coli can have long-term effects on the composition of the intestinal microbiota, as well as on weight gain and fattening.

  3. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

    Science.gov (United States)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U; Meier-Kolthoff, Jan P; Kumar, Neeraj; Bresciani, Anne; Martínez, Inés; Just, Sarah; Ziegler, Caroline; Brugiroux, Sandrine; Garzetti, Debora; Wenning, Mareike; Bui, Thi P N; Wang, Jun; Hugenholtz, Floor; Plugge, Caroline M; Peterson, Daniel A; Hornef, Mathias W; Baines, John F; Smidt, Hauke; Walter, Jens; Kristiansen, Karsten; Nielsen, Henrik B; Haller, Dirk; Overmann, Jörg; Stecher, Bärbel; Clavel, Thomas

    2016-01-01

    Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC. PMID:27670113

  4. Clinical, Laboratory and Bacterial Profile of Spontaneous Bacterial Peritonitis in Chronic Liver Disease Patients

    International Nuclear Information System (INIS)

    Objective: To determine the clinical and laboratory features, bacterial profile and antibiotic sensitivity pattern of Spontaneous Bacterial Peritonitis (SBP) in Chronic Liver Disease (CLD) patients presenting at a tertiary care hospital of Karachi. Study Design: Cross-sectional study. Place and Duration of Study: PMRC Centre for Gastroenterology and Hepatology and Jinnah Postgraduate Medical Centre, Karachi, from April 2010 to March 2012. Methodology: CLD patients with ascites were recruited from PMRC Centre for Gastroenterology and Hepatology and Jinnah Postgraduate Medical Centre, Karachi. Basic demographics, symptoms and clinical signs of patients were recorded. Patients with the history of antibiotic use within last 3 days or any intra-abdominal source of infection were excluded. Diagnostic paracentesis was done for ascitic fluid detailed report (D/R) and culture. Blood sample was collected for total leukocyte count, serum proteins and billirubin levels. Results: Out of a total 152 CLD patients, 38 (25%) were diagnosed with SBP. Eight (24.2%) patients presented with classical SBP, 20 (52.6%) had culture negative neutrocytic ascites and 10 (26%) had bacterascites. Fever, abdominal tenderness and constipation were common in SBP patients. Ascitic fluid culture was positive in 19 (50%) patients. E. coli (65%) was the predominant pathogen followed by Enterococcus species (15%). Resistance was high against cephalosporins (78%) and fluoroquinolones (69.6%) and least against amikacin (13%) and meropenem (12%). Conclusion: Ascitic fluid D/R and culture together can lead to the accurate diagnosis of SBP and can guide for the right antibiotic choice as resistance to commonly prescribed antibiotic is common in such patients. (author)

  5. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

    Directory of Open Access Journals (Sweden)

    Mariat D

    2009-06-01

    Full Text Available Abstract Background In humans, the intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Applying current molecular methods is necessary to surmount the limitations of classical culturing techniques in order to obtain an accurate description of the microbiota composition. Results Here we report on the comparative assessment of human fecal microbiota from three age-groups: infants, adults and the elderly. We demonstrate that the human intestinal microbiota undergoes maturation from birth to adulthood and is further altered with ageing. The counts of major bacterial groups Clostridium leptum, Clostridium coccoides, Bacteroidetes, Bifidobacterium, Lactobacillus and Escherichia coli were assessed by quantitative PCR (qPCR. By comparing species diversity profiles, we observed age-related changes in the human fecal microbiota. The microbiota of infants was generally characterized by low levels of total bacteria. C. leptum and C. coccoides species were highly represented in the microbiota of infants, while elderly subjects exhibited high levels of E. coli and Bacteroidetes. We observed that the ratio of Firmicutes to Bacteroidetes evolves during different life stages. For infants, adults and elderly individuals we measured ratios of 0.4, 10.9 and 0.6, respectively. Conclusion In this work we have confirmed that qPCR is a powerful technique in studying the diverse and complex fecal microbiota. Our work demonstrates that the fecal microbiota composition evolves throughout life, from early childhood to old age.

  6. Aerobic bacterial microbiota of the conjunctiva in diabetic patients with normal and altered glycated hemoglobin levels in two regions in Brazil

    Directory of Open Access Journals (Sweden)

    Natalia Pimentel Moreno

    2014-12-01

    Full Text Available Purpose: To study the aerobic bacterial microbiota of the conjunctiva in diabetic patients with regard to the management of diabetes, assessed using glycated hemoglobin levels. Methods: A cross-sectional study was conducted using conjunctival smears of diabetic patients from both sexes and with different ages, residing in two different Brazilian cities (Sorocaba and Rio Branco. A control group of non-diabetic patients was also included. The diabetic patients were considered to have controlled diabetes when their glycated hemoglobin level was ≤7% and blood glucose level was ≤126 mg/dL. Patients with non-controlled diabetes were those with glycated hemoglobin levels >7% and blood glucose levels >126 mg/dL. The samples obtained were inoculated in Brain-Heart Infusion broth and in culture media for aerobic bacteria (blood and chocolate agars; bacterial growth was evaluated in a microbiology laboratory. Results: A total of 120 eyes of 120 patients were included in the present study. The percentage of cultures in which bacterial growth was observed was greater in diabetic patients, although the difference was not statistically significant (p=0.103. There was a greater trend toward bacterial growth in the conjunctiva of diabetic patients with altered fasting blood glucose. There was no difference in the frequency of bacterial growth on the conjunctiva between diabetic patients with normal or altered glycated hemoglobin levels. In Sorocaba, conjunctival bacterial growth was similar to that observed in Rio Branco. The microorganism most frequently detected in the present study was Staphylococcus epidermidis, followed by Staphylococcus aureus, Proteus mirabilis, and Escherichia coli. Conclusion: There was no difference between diabetic patients with normal or altered glycated hemoglobin levels. The microorganisms found were similar to those found in studies investigating the conjunctival bacterial flora of diabetic and non-diabetic patients.

  7. Utilization of rye as energy source affects bacterial translocation, intestinal viscosity, microbiota composition, and bone mineralization in broiler chickens

    Science.gov (United States)

    Two independent trials were conducted to evaluate the effect of two different dietary cereal types, corn versus rye, on digesta viscosity, gut integrity, and gut microbiota composition in commercial broiler chickens. In each experiment, day-of-hatch, off-sex broiler chickens were randomly assigned ...

  8. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Nielsen, Claus H;

    2014-01-01

    BACKGROUND AND OBJECTIVE: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. DESIGN......: Stimulated saliva samples from 292 participants with low levels of dental caries and periodontitis, enrolled in the Danish Health Examination Survey (DANHES), were analyzed for the presence of approximately 300 bacterial species by means of the Human Oral Microbe Identification Microarray (HOMIM). Using...... presence and levels (mean HOMIM-value) of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann-Whitney tests with Benjamini-Hochberg's correction for multiple comparisons and principal component analysis...

  9. Dose-dependent effects of dietary zinc oxide on bacterial communities and metabolic profiles in the ileum of weaned pigs.

    Science.gov (United States)

    Pieper, R; Vahjen, W; Neumann, K; Van Kessel, A G; Zentek, J

    2012-10-01

    Pharmacological levels of zinc oxide (ZnO) can improve the health of weaning piglets and influence the intestinal microbiota. This experiment aimed at studying the dose-response effect of five dietary concentrations of ZnO on small intestinal bacteria and metabolite profiles. Fifteen piglets, weaned at 25 ± 1 days of age, were allocated into five groups according to body weight and litter. Diets were formulated to contain 50 (basal diet), 150, 250, 1000 and 2500 mg zinc/kg by adding analytical-grade (>98% purity) ZnO to the basal diet and fed ad libitum for 14 days after a 7-day adaptation period on the basal diet. Ileal bacterial community profiles were analysed by denaturing gradient gel electrophoresis and selected bacterial groups quantified by real-time PCR. Concentrations of ileal volatile fatty acids (VFA), D- and L-lactate and ammonia were determined. Species richness, Shannon diversity and evenness were significantly higher at high ZnO levels. Quantitative PCR revealed lowest total bacterial counts in the 50 mg/kg group. Increasing ZnO levels led to an increase (p = 0.017) in enterobacteria from log 4.0 cfu/g digesta (50 mg/kg) to log 6.7 cfu/g digesta (2500 mg/kg). Lactic acid bacteria were not influenced (p = 0.687) and clostridial cluster XIVa declined (p = 0.035) at highest ZnO level. Concentration of total, D- and L-lactate and propionate was not affected (p = 0.736, p = 0.290 and p = 0.630), but concentrations of ileal total VFA, acetate and butyrate increased markedly from 50 to 150 mg/kg and decreased with further increasing zinc levels and reached low levels again at 2500 mg/kg (p = 0.048, p = 0.048 and p = 0.097). Ammonia decreased (p < 0.006) with increasing dietary ZnO level. In conclusion, increasing levels of dietary ZnO had strong and dose-dependent effects on ileal bacterial community composition and activity, suggesting taxonomic variation in metabolic response to ZnO. PMID:21929727

  10. Changes in vaginal microbiota following antimicrobial and probiotic therapy

    Directory of Open Access Journals (Sweden)

    Jean M. Macklaim

    2015-08-01

    Full Text Available Background: The composition of the vaginal microbiota is known to be important for health. When infections occur, antimicrobial therapy is often poorly efficacious. Objective and design: We used 16S rRNA gene sequencing to characterize changes in the bacterial microbiota following oral antimicrobial and probiotic interventions. Results: While the bacterial vaginal profiles of women with vulvovaginal candidiasis were dominated by lactobacilli as in healthy women, and unchanged by therapy, Gardnerella vaginalis, Prevotella, Atopobium, Sneathia, and Megasphaera dominated the vagina of women with bacterial vaginosis (BV, and treatment with tinidazole plus Lactobacillus reuteri RC-14+L. rhamnosus GR-1 resulted in an increased relative abundance of indigenous L. iners or L. crispatus. Conclusions: The ability to restore homeostasis provides a rationale for conjoint use of probiotics with antibiotic treatment of BV.

  11. Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum.

    Science.gov (United States)

    Ras, Refaat; Huynh, Kevin; Desoky, Enas; Badawy, Ahmed; Widmer, Giovanni

    2015-07-01

    Understanding the interaction between the intestinal microbiota (microbiome) and enteric pathogens is of interest in the development of alternative treatments that do not rely on chemotherapy and do not lead to drug resistance. We undertook research in a rodent model of cryptosporidiosis to assess whether the bacterial gut microbiota is impacted by infection with the protozoan pathogen Cryptosporidium parvum. The profile of the faecal bacterial microbiota in infected and uninfected animals was compared using 16S amplicon sequencing. In four independent experiments, the intestinal microbiota of infected mice differed from that of uninfected animals, regardless of the C. parvum isolate used to infect mice. The use of replicated treatment groups demonstrated that microbiota divergence between treatments was driven by the infection and did not result from spontaneous changes in the intestinal ecosystem unrelated to the infection. Microbiota perturbation induced by C. parvum appeared to be reversible, as we observed a tendency for the phylogenetic distance between infected and uninfected mice to diminish after mice cleared the infection. As mice infected with C. parvum do not develop diarrhoea, these observations indicate that microbiota perturbation results from other mechanisms than an accelerated movement of gut content. PMID:25913477

  12. Intestinal cytochromes P450 regulating the intestinal microbiota and its probiotic profile

    Directory of Open Access Journals (Sweden)

    Eugenia Elefterios Venizelos Bezirtzoglou

    2012-09-01

    Full Text Available Cytochromes P450 (CYPs enzymes metabolize a large variety of xenobiotic substances. In this vein, a plethora of studies were conducted to investigate their role, as cytochromes are located in both liver and intestinal tissues. The P450 profile of the human intestine has not been fully characterized. Human intestine serves primarily as an absorptive organ for nutrients, although it has also the ability to metabolize drugs. CYPs are responsible for the majority of phase I drug metabolism reactions. CYP3A represents the major intestinal CYP (80% followed by CYP2C9. CYP1A is expressed at high level in the duodenum, together with less abundant levels of CYP2C8-10 and CYP2D6. Cytochromes present a genetic polymorphism intra- or interindividual and intra- or interethnic. Changes in the pharmacokinetic profile of the drug are associated with increased toxicity due to reduced metabolism, altered efficacy of the drug, increased production of toxic metabolites, and adverse drug interaction. The high metabolic capacity of the intestinal flora is due to its enormous pool of enzymes, which catalyzes reactions in phase I and phase II drug metabolism. Compromised intestinal barrier conditions, when rupture of the intestinal integrity occurs, could increase passive paracellular absorption. It is clear that high microbial intestinal charge following intestinal disturbances, ageing, environment, or food-associated ailments leads to the microbial metabolism of a drug before absorption. The effect of certain bacteria having a benefic action on the intestinal ecosystem has been largely discussed during the past few years by many authors. The aim of the probiotic approach is to repair the deficiencies in the gut flora and establish a protective effect. There is a tentative multifactorial association of the CYP (P450 cytochrome role in the different diseases states, environmental toxic effects or chemical exposures and nutritional status.

  13. Characterisation of the bacterial microbiota of the vagina of dairy cows and isolation of pediocin-producing Pediococcus acidilactici

    Directory of Open Access Journals (Sweden)

    Wang Yvonne

    2013-01-01

    Full Text Available Abstract Background Uterine infections in dairy cows lower profitability of dairy operations. Infections of the reproductive tract are related to the overgrowth of pathogenic bacteria during the first three weeks after parturition. However, alterations in the vaginal microbiota composition in the first weeks after parturition remain poorly documented. Results In this study, bacteria isolated from the vagina of healthy pregnant, and infected postpartum cows were characterised by random amplification of polymorphic DNA (RAPD analysis and partial 16S ribosomal RNA (rDNA gene sequencing. Populations of bacilli and lactic acid bacteria of the genera Enterococcus, Lactobacillus, and Pediococcus were present in both healthy and infected cows. Infected cows had a significant increase in the vaginal enteric bacteria population which consisted mainly of Escherichia coli. Three E. coli isolates harboured the gene coding for Shiga-like-toxin (SLT I or II. Several isolates of the Pediococcus acidilactici were found to produce the bacteriocin pediocin AcH/PA-1. Quantitative PCR analyses of vaginal mucus samples collected from ten metritic cows before and after parturition confirmed the presence of the Lactobacillus group (Lactobacillus spp., Pediococcus spp., Leuconostoc spp., and Weissella spp.; Enterobacteriaceae, E. coli, and bacilli. The presence of the pediocin AcH/PA-1 structural gene and SLT genes were also confirmed with qPCR. Conclusions In conclusion, overgrowth of pathogenic bacteria, particularly E. coli, after parturition likely contributes to the development of metritis. Our microbiota analysis extends the information related to the composition of commensal bacteria in the bovine female reproductive tract and may facilitate the development of novel intervention strategies for prevention of uterine infections in dairy cows.

  14. Differences in bacterial saliva profile between periodontitis patients and a control cohort

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Fiehn, Nils-Erik; Nielsen, Claus H;

    2014-01-01

    the bacterial profile of saliva from subjects with chronic periodontitis with that of saliva from a control cohort. MATERIALS AND METHODS: Stimulated saliva samples from 139 chronic periodontitis patients and 447 samples from a control cohort were analysed using the Human Oral Microbe Identification Microarray...... in samples from periodontitis patients than in samples from the control cohort. These differences were independent of the individuals' smoking status. CONCLUSIONS: Periodontitis is associated with a characteristic bacterial profile of saliva different from that of a control cohort....

  15. Experimental study of the impact of antimicrobial treatments on Campylobacter, Enterococcus and PCR-capillary electrophoresis single-strand conformation polymorphism profiles of the gut microbiota of chickens.

    Science.gov (United States)

    Mourand, Gwenaëlle; Jouy, Eric; Bougeard, Stéphanie; Dheilly, Alexandra; Kérouanton, Annaëlle; Zeitouni, Salman; Kempf, Isabelle

    2014-11-01

    An experiment was conducted to compare the impact of antimicrobial treatments on the susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis, and on the diversity of broiler microbiota. Specific-pathogen-free chickens were first orally inoculated with strains of Campylobacter and Enterococcus faecium. Birds were then orally treated with recommended doses of oxytetracycline, sulfadimethoxine/trimethoprim, amoxicillin or enrofloxacin. Faecal samples were collected before, during and after antimicrobial treatment. The susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis strains isolated on supplemented or non-supplemented media was studied and PCR-capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) profiles of the gut microbiota were analysed. Enrofloxacin-resistant Campylobacter were selected in the enrofloxacin-treated group and showed the Thr86Ile mutation in the gyrA gene. Acquisition of the tetO gene in Campylobacter coli isolates was significantly more frequent in birds given oxytetracycline. No impact of amoxicillin treatment on the susceptibility of Campylobacter could be detected. Ampicillin- and sulfadimethoxine/trimethoprim-resistant Enterococcus faecium were selected in amoxicillin-treated broilers, but no selection of the inoculated vancomycin-resistant Enterococcus faecium could be detected, although it was also resistant to tetracycline and sulfadimethoxine/trimethoprim. PCR-CE-SSCP revealed significant variations in a few peaks in treated birds as compared with non-treated chickens. In conclusion, antimicrobial treatments perturbed chicken gut microbiota, and certain antimicrobial treatments selected or co-selected resistant strains of Campylobacter and Enterococcus.

  16. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.

    Directory of Open Access Journals (Sweden)

    Shun-Long Weng

    Full Text Available Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA, Atypical, and leukocytes. Computer-assisted semen analysis (CASA was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%, Pseudomonas (9.85%, Prevotella (8.51% and Gardnerella (4.21%. The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6% were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.

  17. Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough “Masa Agria” (Maiz Añejo)

    Science.gov (United States)

    Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D.; Paparella, Antonello

    2016-01-01

    Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1–3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential. PMID:27524979

  18. Exploring the bacterial microbiota of Colombian fermented maize dough “Masa Agria” (Maiz Añejo

    Directory of Open Access Journals (Sweden)

    Clemencia Chaves

    2016-07-01

    Full Text Available Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 Log CFU/g of presumptive lactic acid bacteria (LAB, 5.4 Log cfu/g for presumptive acetic bacteria and 5.6 Log CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7 registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by Lb. fermentum, Lb. vaccinostercus and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favour microbial biodiversity characterized by a useful technological potential.

  19. Terminal restriction fragment length polymorphism (T-RFLP) profiling of bacterial 16S rRNA genes.

    Science.gov (United States)

    Osborne, Catherine A

    2014-01-01

    T-RFLP profiling is a very effective method for comparing many samples in an environmental microbiology study, because fingerprints of microbial diversity can be generated in a sensitive, reproducible, and cost-effective manner. This protocol describes the steps required to generate T-RFLP profiles of the dominant members of a bacterial community, by PCR amplification of the bacterial 16S rRNA genes and three restriction endonuclease digests to generate three different profiles for each sample. The generation of multiple profiles per sample provides enough information to confidently differentiate rich environmental bacterial communities.

  20. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata

    KAUST Repository

    Closek, Collin J.

    2014-06-20

    Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD. © 2014 International Society for Microbial Ecology. All rights reserved.

  1. Differences in activity profile of bacterial cultures studied by dynamic speckle patterns

    Science.gov (United States)

    Ramírez-Miquet, E. E.; Otero, I.; Rodríguez, D.; Darias, J. G.; Combarro, A. M.; Contreras, O. R.

    2013-02-01

    We outline the main differences in the activity profile of bacterial cultures studied by dynamic laser speckle (or biospeckle) patterns. The activity is detected in two sorts of culture mediums. The optical setup and the experimental procedure are presented. The experimentally obtained images are processed by the temporal difference method and a qualitative assessment is made with the time history of speckle patterns of the sample. The main differences are studied after changing the culture medium composition. We conclude that the EC medium is suitable to detect the E. coli bacterial presence in early hours and that Mueller Hinton agar delays some additional hours to make possible the assessment of bacteria in time.

  2. Modulation of the Bifidobacterial Communities of the Dog Microbiota by Zeolite

    Science.gov (United States)

    Sabbioni, Alberto; Ferrario, Chiara; Milani, Christian; Mancabelli, Leonardo; Riccardi, Enzo; Di Ianni, Francesco; Beretti, Valentino; Superchi, Paola; Ossiprandi, Maria C.

    2016-01-01

    During last decades canine health and well being is becoming an important issue for human owners. In dogs, several factors including diet, pathogenic bacterial and stress conditions can affect the composition of the gut microbiota. In this study, we evaluated the effect of dietary chabazitic zeolitite (CZ) supplementation on the contribution of bifidobacteria to the fecal microbiota in training hunting dogs. Fecal microbiota cataloging based on 16S rRNA microbial profiling analyses highlighted an increase of Lactobacillus and Bifidobacterium in animals treated with CZ, with a simultaneous decrease of pathogens associated with dog gastrointestinal infections, such as Klebsiella and Enterobacter. A detailed profiling of the bifidobacterial population of dogs receiving CZ based on the ITS-based sequencing approach, revealed an enhancement bifidobacterial of species typical of animals such as Bifidobacterium animalis and B. pseudolongum. Moreover, these analyses identified the occurrence of putative new bifidobacterial taxa in both treated and untreated samples.

  3. Appropriate chicken sample size for identifying the composition of broiler intestinal microbiota affected by dietary antibiotics, using the polymerase chain reaction-denaturing gradient gel electrophoresis technique.

    Science.gov (United States)

    Zhou, H; Gong, J; Brisbin, J T; Yu, H; Sanei, B; Sabour, P; Sharif, S

    2007-12-01

    The bacterial microbiota in the broiler gastrointestinal tract are crucial for chicken health and growth. Their composition can vary among individual birds. To evaluate the composition of chicken microbiota in response to environmental disruption accurately, 4 different pools made up of 2, 5, 10, and 15 individuals were used to determine how many individuals in each pool were required to assess the degree of variation when using the PCR-denaturing gradient gel electrophoresis (DGGE) profiling technique. The correlation coefficients among 3 replicates within each pool group indicated that the optimal sample size for comparing PCR-DGGE bacterial profiles and downstream applications (such as identifying treatment effects) was 5 birds per pool for cecal microbiota. Subsequently, digesta from 5 birds was pooled to investigate the effects on the microbiota composition of the 2 most commonly used dietary antibiotics (virginiamycin and bacitracin methylene disalicylate) at 2 different doses by using PCR-DGGE, DNA sequencing, and quantitative PCR techniques. Thirteen DGGE DNA bands were identified, representing bacterial groups that had been affected by the antibiotics. Nine of them were validated. The effect of dietary antibiotics on the microbiota composition appeared to be dose and age dependent. These findings provide a working model for elucidating the mechanisms of antibiotic effects on the chicken intestinal microbiota and for developing alternatives to dietary antibiotics. PMID:18029800

  4. Oral microbiota and cancer

    OpenAIRE

    Meurman, Jukka

    2010-01-01

    Inflammation caused by infections may be the most important preventable cause of cancer in general. However, in the oral cavity the role of microbiota in carcinogenesis is not known. Microbial populations on mouth mucosa differ between healthy and malignant sites and certain oral bacterial species have been linked with malignancies but the evidence is still weak in this respect. Nevertheless, oral microorganisms inevitably up-regulate cytokines and other inflammatory mediators that affect the...

  5. Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling

    OpenAIRE

    Ilario Ferrocino; Raffaella Di Cagno; Maria De Angelis; Silvia Turroni; Lucia Vannini; Elena Bancalari; Kalliopi Rantsiou; Gianluigi Cardinali; Erasmo Neviani; Luca Cocolin

    2015-01-01

    In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal micr...

  6. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients.

    Science.gov (United States)

    de Steenhuijsen Piters, Wouter A A; Huijskens, Elisabeth G W; Wyllie, Anne L; Biesbroek, Giske; van den Bergh, Menno R; Veenhoven, Reinier H; Wang, Xinhui; Trzciński, Krzysztof; Bonten, Marc J; Rossen, John W A; Sanders, Elisabeth A M; Bogaert, Debby

    2016-01-01

    Bacterial pneumonia is a major cause of morbidity and mortality in elderly. We hypothesize that dysbiosis between regular residents of the upper respiratory tract (URT) microbiome, that is balance between commensals and potential pathogens, is involved in pathogen overgrowth and consequently disease. We compared oropharyngeal microbiota of elderly pneumonia patients (n=100) with healthy elderly (n=91) by 16S-rRNA-based sequencing and verified our findings in young adult pneumonia patients (n=27) and young healthy adults (n=187). Microbiota profiles differed significantly between elderly pneumonia patients and healthy elderly (PERMANOVA, Pdisease was less clear. A decision tree model based on the relative abundance of five bacterial community members in URT microbiota showed high specificity of 95% and sensitivity of 84% (89% and 73%, respectively, after cross-validation) for differentiating pneumonia patients from healthy individuals. These results suggest that pneumonia in elderly and young adults is associated with dysbiosis of the URT microbiome with bacterial overgrowth of single species and absence of distinct anaerobic bacteria. Whether the observed microbiome changes are a cause or a consequence of the development of pneumonia or merely coincide with disease status remains a question for future research.

  7. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    Science.gov (United States)

    Belstrøm, Daniel; Holmstrup, Palle; Bardow, Allan; Kokaras, Alexis; Fiehn, Nils-Erik; Paster, Bruce J.

    2016-01-01

    Background and objective The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial composition may not reflect the more natural, unstimulated state. The purpose of this study was to validate whether stimulated saliva is an adequate surrogate for unstimulated saliva in determining salivary microbiomes. Design Unstimulated (n=20) and stimulated (n=20) saliva samples were collected from 20 orally and systemically healthy, non-smoking participants. Salivary bacterial profiles were analyzed by means of the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using Mann–Whitney test with Benjamini–Hochberg's correction for multiple comparison, cluster analysis, principal component analysis, and correspondence analysis. Results From a total of 40 saliva samples, 496 probe targets were identified with a mean number of targets per sample of 203 (range: 146–303), and a mean number of probe targets of 206 and 200 in unstimulated and stimulated saliva samples, respectively (p=0.62). Based on all statistical methods used for this study, the microbial profiles of unstimulated and stimulated saliva samples collected from the same person were not statistically significantly different. Conclusions Analysis of bacterial salivary profiles in unstimulated and stimulated saliva samples collected from the same individual showed comparable results. Thus, the results verify that stimulated saliva is an adequate surrogate of unstimulated saliva for microbiome-related studies. PMID:26987356

  8. Influence of insoluble fibre and whole wheat inclusion on the performance, digestive tract development and ileal microbiota profile of broiler chickens.

    Science.gov (United States)

    Amerah, A M; Ravindran, V; Lentle, R G

    2009-05-01

    1. An experiment of 21-d duration was conducted to examine the effects of diluting wheat-based diets with insoluble fibre sources and whole wheat inclusion on the performance, nutrient utilisation, digestive tract development and ileal microbiota profile of broiler chickens. The treatments were as follows: Treatment 1, control diet based on ground wheat; Treatment 2, where 200 g/kg whole wheat replaced the ground wheat pre-pelleting; and Treatments 3 and 4 where the control diet was diluted with fine cellulose and wood shavings, respectively, at a ratio of 6 : 100 (w/w). 2. Weight gains and apparent metabolisable energy were unaffected by dietary treatment. Gain : feed ratio was not influenced by the inclusion of whole wheat or wood shavings, but decreased with cellulose inclusion. However, when gain:feed of birds was corrected by subtracting the amount of cellulose and wood shavings from the total feed consumption, it was found that the inclusion of wood shavings increased gain : feed, while cellulose inclusion had no effect. Similarly, AME(N) was unaffected by dietary treatment. However, when AME(N) was corrected for energy contribution from cellulose or wood shavings, improvements in AME(N) were observed in these two treatments. 3. Wood shavings increased the relative gizzard weights and improved ileal starch digestibility compared to other dietary treatments. All gut components were shorter in birds given diets containing cellulose and wood shavings compared to those receiving the control and whole wheat diets. 4. Ileal microbiota profiling, using denaturing gradient gel electrophoresis, showed that microbial composition was affected by dietary treatment and that the treatments were grouped into two main clusters. The two groupings showed similarity between birds receiving the control and cellulose diets and similarity between birds fed on the whole wheat and wood shavings diets. 5. The findings suggest that the effects of insoluble fibre on broiler performance

  9. Deep sequencing of the vaginal microbiota of women with HIV

    NARCIS (Netherlands)

    R.B.S. Hummelen (Ruben); A.D. Fernandes (Andrew); J.M. Macklaim (Jean); R.J. Dickson (Russell); J. Changalucha (John); G.B. Gloor (Gregory); G.K. Reid (Gregor)

    2010-01-01

    textabstractBackground:Women living with HIV and co-infected with bacterial vaginosis (BV) are at higher risk for transmitting HIV to a partner or newborn. It is poorly understood which bacterial communities constitute BV or the normal vaginal microbiota among this population and how the microbiota

  10. Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae.

    Directory of Open Access Journals (Sweden)

    Frank Po-Yen Lin

    Full Text Available The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence factors has not been fully examined. In this paper, we test this hypothesis and report a computational pipeline designed to identify previously unknown bacterial virulence genes using group B streptococcus (GBS as an example. Phylogenetic profiles of all GBS genes across 467 bacterial reference genomes were determined by candidate-against-all BLAST searches,which were then used to identify candidate virulence genes by machine learning models. Evaluation experiments with known GBS virulence genes suggested good functional and model consistency in cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively. Inspection of the top-10 genes in each of the 15 virulence functional groups revealed at least 15 (of 119 homologous genes implicated in virulence in other human pathogens but previously unrecognized as potential virulence genes in GBS. Among these highly-ranked genes, many encode hypothetical proteins with possible roles in GBS virulence. Thus, our approach has led to the identification of a set of genes potentially affecting the virulence potential of GBS, which are potential candidates for further in vitro and in vivo investigations. This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens.

  11. Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks.

    Directory of Open Access Journals (Sweden)

    Giovanna Carpi

    Full Text Available Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection

  12. Modulating the Gut Microbiota Improves Glucose Tolerance, Lipoprotein Profile and Atherosclerotic Plaque Development in ApoE-Deficient Mice.

    Directory of Open Access Journals (Sweden)

    Ida Rune

    Full Text Available The importance of the gut microbiota (GM in disease development has recently received increased attention, and numerous approaches have been made to better understand this important interplay. For example, metabolites derived from the GM have been shown to promote atherosclerosis, the underlying cause of cardiovascular disease (CVD, and to increase CVD risk factors. Popular interest in the role of the intestine in a variety of disease states has now resulted in a significant proportion of individuals without coeliac disease switching to gluten-free diets. The effect of gluten-free diets on atherosclerosis and cardiovascular risk factors is largely unknown. We therefore investigated the effect of a gluten-free high-fat cholesterol-rich diet, as compared to the same diet in which the gluten peptide gliadin had been added back, on atherosclerosis and several cardiovascular risk factors in apolipoprotein E-deficient (Apoe-/- mice. The gluten-free diet transiently altered GM composition in these mice, as compared to the gliadin-supplemented diet, but did not alter body weights, glucose tolerance, insulin levels, plasma lipids, or atherosclerosis. In parallel, other Apoe-/- mice fed the same diets were treated with ampicillin, a broad-spectrum antibiotic known to affect GM composition. Ampicillin-treatment had a marked and sustained effect on GM composition, as expected. Furthermore, although ampicillin-treated mice were slightly heavier than controls, ampicillin-treatment transiently improved glucose tolerance both in the absence or presence of gliadin, reduced plasma LDL and VLDL cholesterol levels, and reduced aortic atherosclerotic lesion area. These results demonstrate that a gluten-free diet does not seem to have beneficial effects on atherosclerosis or several CVD risk factors in this mouse model, but that sustained alteration of GM composition with a broad-spectrum antibiotic has beneficial effects on CVD risk factors and atherosclerosis

  13. Dietary supplementation with probiotics during late pregnancy: outcome on vaginal microbiota and cytokine secretion

    Directory of Open Access Journals (Sweden)

    Vitali Beatrice

    2012-10-01

    Full Text Available Abstract Background The vaginal microbiota of healthy women consists of a wide variety of anaerobic and aerobic bacterial genera and species dominated by the genus Lactobacillus. The activity of lactobacilli helps to maintain the natural healthy balance of the vaginal microbiota. This role is particularly important during pregnancy because vaginal dismicrobism is one of the most important mechanisms for preterm birth and perinatal complications. In the present study, we characterized the impact of a dietary supplementation with the probiotic VSL#3, a mixture of Lactobacillus, Bifidobacterium and Streptococcus strains, on the vaginal microbiota and immunological profiles of healthy women during late pregnancy. Results An association between the oral intake of the probiotic VSL#3 and changes in the composition of the vaginal microbiota of pregnant women was revealed by PCR-DGGE population profiling. Despite no significant changes were found in the amounts of the principal vaginal bacterial populations in women administered with VSL#3, qPCR results suggested a potential role of the probiotic product in counteracting the decrease of Bifidobacterium and the increase of Atopobium, that occurred in control women during late pregnancy. The modulation of the vaginal microbiota was associated with significant changes in some vaginal cytokines. In particular, the decrease of the anti-inflammatory cytokines IL-4 and IL-10 was observed only in control women but not in women supplemented with VSL#3. In addition, the probiotic consumption induced the decrease of the pro-inflammatory chemokine Eotaxin, suggesting a potential anti-inflammatory effect on the vaginal immunity. Conclusion Dietary supplementation with the probiotic VSL#3 during the last trimester of pregnancy was associated to a modulation of the vaginal microbiota and cytokine secretion, with potential implications in preventing preterm birth. Trial registration ClinicalTrials.gov NCT01367470

  14. Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

    Science.gov (United States)

    Kidd, Haack S.; Garchow, H.; Odelson, D.A.; Forney, L.J.; Klug, M.J.

    1994-01-01

    We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

  15. Evaluation and characterization of bacterial metabolic dynamics with a novel profiling technique, real-time metabolotyping.

    Directory of Open Access Journals (Sweden)

    Shinji Fukuda

    Full Text Available BACKGROUND: Environmental processes in ecosystems are dynamically altered by several metabolic responses in microorganisms, including intracellular sensing and pumping, battle for survival, and supply of or competition for nutrients. Notably, intestinal bacteria maintain homeostatic balance in mammals via multiple dynamic biochemical reactions to produce several metabolites from undigested food, and those metabolites exert various effects on mammalian cells in a time-dependent manner. We have established a method for the analysis of bacterial metabolic dynamics in real time and used it in combination with statistical NMR procedures. METHODOLOGY/PRINCIPAL FINDINGS: We developed a novel method called real-time metabolotyping (RT-MT, which performs sequential (1H-NMR profiling and two-dimensional (2D (1H, (13C-HSQC (heteronuclear single quantum coherence profiling during bacterial growth in an NMR tube. The profiles were evaluated with such statistical methods as Z-score analysis, principal components analysis, and time series of statistical TOtal Correlation SpectroScopY (TOCSY. In addition, using 2D (1H, (13C-HSQC with the stable isotope labeling technique, we observed the metabolic kinetics of specific biochemical reactions based on time-dependent 2D kinetic profiles. Using these methods, we clarified the pathway for linolenic acid hydrogenation by a gastrointestinal bacterium, Butyrivibrio fibrisolvens. We identified trans11, cis13 conjugated linoleic acid as the intermediate of linolenic acid hydrogenation by B. fibrisolvens, based on the results of (13C-labeling RT-MT experiments. In addition, we showed that the biohydrogenation of polyunsaturated fatty acids serves as a defense mechanism against their toxic effects. CONCLUSIONS: RT-MT is useful for the characterization of beneficial bacterium that shows potential for use as probiotic by producing bioactive compounds.

  16. Bacterial Cytological Profiling (BCP as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    D.T. Quach

    2016-02-01

    Full Text Available Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP, which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA and -resistant (MRSA clinical isolates of S. aureus (n = 71 within 1–2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS from daptomycin non-susceptible (DNS S. aureus strains (n = 20 within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice.

  17. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

    Directory of Open Access Journals (Sweden)

    Haas Brian J

    2012-12-01

    Full Text Available Abstract Background High-throughput sequencing of cDNA libraries (RNA-Seq has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. Results We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified. Conclusions Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species.

  18. Bacterial Cytological Profiling (BCP) as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus.

    Science.gov (United States)

    Quach, D T; Sakoulas, G; Nizet, V; Pogliano, J; Pogliano, K

    2016-02-01

    Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP), which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA) and -resistant (MRSA) clinical isolates of S. aureus (n = 71) within 1-2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS) from daptomycin non-susceptible (DNS) S. aureus strains (n = 20) within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice. PMID:26981574

  19. 结直肠癌患者肠道黏膜菌群多样性变化研究%Diversity of intestinal bacterial microbiota in patients with colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    丁平; 宋炳红; 朱利敏; 丁国军

    2011-01-01

    Objective To explore the intestinal bacterial diversity in patients with colorectal cancer by PCR-DGGE technique, which might provide new micro-ecological insights for the prevention and treatment of colorectal lesions. Method Three groups including the control group, colorectal polyps group and colorectal cancer group were enrolled in the study.After examination, the colorectal local anal swabs were collected, bacterial genomic DNA was extracted, and the diversity of intestinal microbiota was analyzed with PCR-DGGE. Result With PCR-DGGE fingerprinting analysis, the diversity of intestinal microbiota was significantly different among the three groups and showed a slight of shift of microbiota. Conclusion The diversity of intestinal microbiota from colorectal cancer patients with PCR-DGGE plays an important role in monitoring the development of colorectal lesions.%目的 应用PCR-DGGE技术对结直肠癌患者肠道黏膜局部菌群多样性进行研究,为结直肠病变的防治提供微生态调节思路.方法 收集正常对照组、结直肠息肉组及结直肠癌组患者各30例,采集结直肠黏膜局部肛拭子,提取细菌基因组DNA,采用PCR-DGGE对肠道黏膜局部菌群进行指纹图谱分析.结果 正常对照组、结直肠息肉组和结直肠癌组患者PCR-DGGE指纹图谱分析显示3组肠道黏膜局部菌群多样性发生了显著的变化,3组肠道黏膜局部菌群发生了显著的菌群变迁.结论 PCR-DGGE分析结直肠癌患者肠道黏膜局部菌群多样性变化对监测肠道局部微生态变化在结直肠癌的发生过程中的作用具有重要价值.

  20. Obesity and NAFLD: the role of bacteria and microbiota.

    Science.gov (United States)

    Duseja, Ajay; Chawla, Yogesh Kumar

    2014-02-01

    There are trillions of microorganisms in the human intestine collectively called gut microbiota. Obesity may be affected by the gut microbiota through energy harvesting and fat storage by the bacteria. Small intestinal bacterial overgrowth is also responsible for endotoxemia, systemic inflammation, and its consequences including obesity and nonalcoholic fatty liver disease (NAFLD). Relationship between gut microbiota and NAFLD is also dependent on altered choline and bile acid metabolism and endogenous alcohol production by gut bacteria. Further evidence linking gut microbiota with obesity and NAFLD comes from studies showing usefulness of probiotics in animals and patients with NAFLD. This article reviews the relationship among gut microbiota, obesity, and NAFLD.

  1. Feline gastrointestinal microbiota.

    Science.gov (United States)

    Minamoto, Yasushi; Hooda, Seema; Swanson, Kelly S; Suchodolski, Jan S

    2012-06-01

    The close relationship between gastrointestinal (GI) microbiota and its host has an impact on the health status of an animal that reaches beyond the GI tract. A balanced microbiome stimulates the immune system, aids in the competitive exclusion of transient pathogens and provides nutritional benefits to the host. With recent rapid advances in high-throughput sequencing technology, molecular approaches have become the routinely used tools for ecological studies of the feline microbiome, and have revealed a highly diverse and complex intestinal ecosystem in the feline GI tract. The major bacterial groups are similar to those found in other mammals, with Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria constituting more than 99% of intestinal microbiota. Several nutritional studies have demonstrated that the feline microbiota can be modulated by the amount of soluble fibers (i.e., prebiotics) and macronutrients (i.e., protein content) in the diet. Initial clinical studies have suggested the presence of a dysbiosis in feline inflammatory bowel disease (IBD). Recently, metagenomic approaches have attempted to characterize the microbial gene pool. However, more studies are needed to describe the phylogenetic and functional changes in the intestinal microbiome in disease states and in response to environmental and dietary modulations. This paper reviews recent studies cataloging the microbial phylotypes in the GI tract of cats.

  2. Impact of a probiotic, inulin, or their combination on the piglets' microbiota at different intestinal locations.

    Science.gov (United States)

    Sattler, V A; Bayer, K; Schatzmayr, G; Haslberger, A G; Klose, V

    2015-01-01

    Natural feed additives are used to maintain health and to promote performance of pigs without antibiotics. Effects of a probiotic, inulin, and their combination (synbiotic), on the microbial diversity and composition at different intestinal locations were analysed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and 16S rRNA gene pyrosequencing. Bacterial diversity assessed by DGGE and/or pyrosequencing was increased by inulin in all three gut locations and by the synbiotic in the caecum and colon. In contrast, the probiotic did only affect the microbiota diversity in the ileum. Shifts in the DGGE microbiota profiles of the caecum and colon were detected for the pro- and synbiotic fed animals, whereas inulin profiles were more similar to the ones of the control. 16S rRNA gene pyrosequencing revealed that all three additives could reduce Escherichia species in each gut location, indicating a potential beneficial effect on the gut microbiota. An increase of relative abundance of Clostridiaceae in the large intestine was found in the inulin group and of Enterococcaceae in the ileum of probiotic fed pigs. Furthermore, real-time PCR results showed that the probiotic and synbiotic increased bifidobacterial numbers in the ileum, which was supported by sequencing results. The probiotic and inulin, to different extents, changed the diversity, relative abundance of phylotypes, and community profiles of the porcine microbiota. However, alterations of the bacterial community were not uniformly between gut locations, demonstrating that functionality of feed additives is site specific. Therefore, gut sampling from various locations is crucial when investigations aim to identify the composition of a healthy gut microbiota after its manipulation through feed additives.

  3. Dynamic alteration of the colonic microbiota in intestinal ischemia-reperfusion injury.

    Directory of Open Access Journals (Sweden)

    Fan Wang

    Full Text Available BACKGROUND: Intestinal ischemia-reperfusion (I/R plays an important role in critical illnesses. Gut flora participate in the pathogenesis of the injury. This study is aimed at unraveling colonic microbiota alteration pattern and identifying specific bacterial species that differ significantly as well as observing colonic epithelium change in the same injury model during the reperfusion time course. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing gradient gel electrophoresis (DGGE was used to monitor the colonic microbiota of control rats and experimental rats that underwent 0.5 hour ischemia and 1, 3, 6, 12, 24, and 72 hours following reperfusion respectively. The microbiota similarity, bacterial diversity and species that characterized the dysbiosis were estimated based on the DGGE profiles using a combination of statistical approaches. The interested bacterial species in the gel were cut and sequenced and were subsequently quantified and confirmed with real-time PCR. Meanwhile, the epithelial barrier was checked by microscopy and D-lactate analysis. Colonic flora changed early and differed significantly at 6 hours after reperfusion and then started to recover. The shifts were characterized by the increase of Escherichia coli and Prevotella oralis, and Lactobacilli proliferation together with epithelia healing. CONCLUSION/SIGNIFICANCE: This study shows for the first time that intestinal ischemia-reperfusion results in colonic flora dysbiosis that follows epithelia damage, and identifies the bacterial species that contribute most.

  4. Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

    Science.gov (United States)

    Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

    2015-12-01

    Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of

  5. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota.

    Directory of Open Access Journals (Sweden)

    Kaarel Adamberg

    Full Text Available The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides and butyric acid-producing (e.g. Faecalibacterium taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses.

  6. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota.

    Science.gov (United States)

    Adamberg, Kaarel; Tomson, Katrin; Talve, Tiina; Pudova, Ksenia; Puurand, Marju; Visnapuu, Triinu; Alamäe, Tiina; Adamberg, Signe

    2015-01-01

    The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses. PMID:26629816

  7. Comparison of bacterial DNA profiles of footwear insoles and soles of feet for the forensic discrimination of footwear owners.

    Science.gov (United States)

    Goga, Haruhisa

    2012-09-01

    It is crucial to identify the owner of unattended footwear left at a crime scene. However, retrieving enough DNA for DNA profiling from the owner's foot skin (plantar skin) cells from inside the footwear is often unsuccessful. This is sometimes because footwear that is used on a daily basis contains an abundance of bacteria that degrade DNA. Further, numerous other factors related to the inside of the shoe, such as high humidity and temperature, can encourage bacterial growth inside the footwear and enhance DNA degradation. This project sought to determine if bacteria from inside footwear could be used for footwear trace evidence. The plantar skins and insoles of shoes of volunteers were swabbed for bacteria, and their bacterial community profiles were compared using bacterial 16S rRNA terminal restriction fragment length polymorphism analysis. Sufficient bacteria were recovered from both footwear insoles and the plantar skins of the volunteers. The profiling identified that each volunteer's plantar skins harbored unique bacterial communities, as did the individuals' footwear insoles. In most cases, a significant similarity in the bacterial community was identified for the matched foot/insole swabs from each volunteer, as compared with those profiles from different volunteers. These observations indicate the probability to discriminate the owner of footwear by comparing the microbial DNA fingerprint from inside footwear with that of the skin from the soles of the feet of the suspected owner. This novel strategy will offer auxiliary forensic footwear evidence for human DNA identification, although further investigations into this technique are required.

  8. Diet, microbiota, and colorectal cancer.

    Science.gov (United States)

    Akin, Hakan; Tözün, Nurdan

    2014-01-01

    Colorectal cancer (CRC) is the third most common cancer in the world causing nearly 500,000 deaths every year. In addition to genetic background, environmental factors including diet and lifestyle are accepted as major contributors to adenoma and CRC development. Lifestyle factors include high BMI, obesity, and reduced physical activity. Growing interest and accumulating data on human microbiota implicate that host-microbe interplay has an important role in the development of metabolic, neoplastic, and inflammatory diseases. Findings from recent studies suggest that colon cancer risk is determined by the interaction between diet and gut microbiota. Dietary changes affect gut microbiota and conversely microbiota mediates the generation of dietary factors triggering colon cancer. Identification of the microbial communities associated with carcinogenesis is of crucial importance. Nowadays, with the evolvement of culture-independent molecular techniques, it has become possible to identify main bacterial species in healthy individuals, inflammatory conditions, and CRC. Some recent studies have shown the differences in intestinal microbiota between colon cancer patients and healthy individuals. Animal studies have provided a better understanding of interaction between pathobionts and symbionts in the development of colon cancer. There is no single causative organism identified in CRC; however, there is strong evidence that reduction of protective bacteria, increase in some bacteria (ie, fusobacterium members; Bacteroides/Prevotella), and age-related changes in microbiota have an impact on adenoma or cancer development. Future studies will enable us to understand procarcinogenic and anticarcinogenic mechanisms and give insights to rational manipulation of the microbiota with prebiotics, probiotics, or dietary modifications. PMID:25291132

  9. Determination of Contamination Profiles of Human Bacterial Pathogens in Shrimp Obtained from Java, Indonesia

    International Nuclear Information System (INIS)

    Shrimp continues to be an important export commodity for Indonesia and contributed significantly to the country’s revenue. However, shrimp exports have been frequently rejected by importing countries due to filth, Salmonella and insanitary conditions. This study was conducted to evaluate the profiles of bacterial contamination of ocean and aquaculture shrimp obtained from the area of West, Central and East Java; frozen shrimp and shrimp during industry production of frozen shrimp. The study indicated that both ocean and aquaculture shrimp obtained from the study area were heavily contaminated. On the average, shrimp obtained from West Java were more contaminated than those obtained from East and Central Java. The total bacterial counts were generally higher in ocean shrimp than those of aquaculture ones. Salmonella was present in two of 32 samples of ocean shrimp and in four of 32 samples of aquaculture shrimp obtained from the study area. Vibrio cholerae was not detected in shrimp from West Java, but was found in three out of 16 samples obtained from East and Central Java. V. parahaemolyticus was frequently identified in aquaculture shrimp but absent in fresh ocean shrimp. Studies on shrimp collected from six sampling points during frozen shrimp production revealed that processing will reduce the number of total bacterial, E. coli, and Staphylococal counts. However, the processing did not effectively reduce the incidence of Salmonella or V. parahaemolyticus when the raw material has been contaminated with the pathogens. Sizing and grading as well as arrangement of shrimp before freezing were considered as the critical points where bacteria should be controlled to inhibit growth and cross contamination with bacteria such as Listeria. Implementation of Good Agricultural Practices in production of raw shrimp as well as Hazard Analysis Critical Control Point at the line processing are expected to improve the quality of fresh and frozen shrimp. (author)

  10. Gut Microbiota: Its Role in Hepatic Encephalopathy

    OpenAIRE

    Rai, Rahul; Saraswat, Vivek A.; Dhiman, Radha K.

    2014-01-01

    Ammonia, a key factor in the pathogenesis of hepatic encephalopathy (HE), is predominantly derived from urea breakdown by urease producing large intestinal bacteria and from small intestine and kidneys, where the enzyme glutaminases releases ammonia from circulating glutamine. Non-culture techniques like pyrosequencing of bacterial 16S ribosomal ribonucleic acid are used to characterize fecal microbiota. Fecal microbiota in patients with cirrhosis have been shown to alter with increasing Chil...

  11. Metagenomic Surveys of Gut Microbiota

    Directory of Open Access Journals (Sweden)

    Rahul Shubhra Mandal

    2015-06-01

    Full Text Available Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.

  12. Metagenomic Surveys of Gut Microbiota

    Institute of Scientific and Technical Information of China (English)

    Rahul Shubhra Mandal; Sudipto Saha; Santasabuj Das

    2015-01-01

    Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax-onomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti-mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac-tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe inter-action networks.

  13. An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease?

    Science.gov (United States)

    Burman, S; Hoedt, E C; Pottenger, S; Mohd-Najman, N-S; Ó Cuív, P; Morrison, Mark

    2016-01-01

    While it is now accepted that the gut microbiota contribute to the genotype-environment-lifestyle interactions triggering inflammatory bowel disease (IBD) episodes, efforts to identify the pathogen(s) that cause these diseases have met with limited success. The advent of culture-independent techniques for characterizing the structure and/or function of microbial communities (hereafter referred to as metagenomics) has provided new insights into the events associated with the onset, remission and recurrence of IBD. A large number of observational and/or case-control studies of IBD patients have confirmed substantive changes in gut bacterial profiles (dysbiosis) associated with disease. These types of studies have been augmented by new profiling approaches that support the identification of more 'colitogenic' bacteria from numerically predominant taxa. Evidence of alterations in lesser abundant taxa such as the methanogenic archaea, to favor types that are more immunogenic, has also been forthcoming. Several recent longitudinal studies of patients with Crohn's disease have produced additional insights, including evidence for the role of 'anti-inflammatory' microbiota in providing a protective effect and/or promoting remission. In summation, the implications of dysbiosis and restoration of a 'healthy microbiota' in IBD patients requires definition beyond a taxonomic assessment of the changes in the gut microbiota during disease course. The available evidence does suggest that specific members of the gut microbiota can contribute either pro- or anti-inflammatory effects, and their ecological fitness in the large bowel affects the onset and recurrence of IBD. While metagenomics and related approaches offer the potential to provide novel and important insights into these microbiota and thereby the pathophysiology of IBD, we also need to better understand factors affecting the ecological fitness of these microbes, if new treatment of IBD patients are to be delivered. PMID

  14. Diversified microbiota of meconium is affected by maternal diabetes status.

    Directory of Open Access Journals (Sweden)

    Jianzhong Hu

    Full Text Available This study was aimed to assess the diversity of the meconium microbiome and determine if the bacterial community is affected by maternal diabetes status.The first intestinal discharge (meconium was collected from 23 newborns stratified by maternal diabetes status: 4 mothers had pre-gestational type 2 diabetes mellitus (DM including one mother with dizygotic twins, 5 developed gestational diabetes mellitus (GDM and 13 had no diabetes. The meconium microbiome was profiled using multi-barcode 16S rRNA sequencing followed by taxonomic assignment and diversity analysis.All meconium samples were not sterile and contained diversified microbiota. Compared with adult feces, the meconium showed a lower species diversity, higher sample-to-sample variation, and enrichment of Proteobacteria and reduction of Bacteroidetes. Among the meconium samples, the taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the DM group showing higher alpha-diversity than that of no-diabetes or GDM groups. No global difference was found between babies delivered vaginally versus via Cesarean-section. Regression analysis showed that the most robust predictor for the meconium microbiota composition was the maternal diabetes status that preceded pregnancy. Specifically, Bacteroidetes (phyla and Parabacteriodes (genus were enriched in the meconium in the DM group compared to the no-diabetes group.Our study provides evidence that meconium contains diversified microbiota and is not affected by the mode of delivery. It also suggests that the meconium microbiome of infants born to mothers with DM is enriched for the same bacterial taxa as those reported in the fecal microbiome of adult DM patients.

  15. Target Product Profile for a Diagnostic Assay to Differentiate between Bacterial and Non-Bacterial Infections and Reduce Antimicrobial Overuse in Resource-Limited Settings: An Expert Consensus

    Science.gov (United States)

    Dittrich, Sabine; Tadesse, Birkneh Tilahun; Moussy, Francis; Chua, Arlene; Zorzet, Anna; Tängdén, Thomas; Dolinger, David L.; Page, Anne-Laure; Crump, John A.; D’Acremont, Valerie; Bassat, Quique; Lubell, Yoel; Newton, Paul N.; Heinrich, Norbert; Rodwell, Timothy J.; González, Iveth J.

    2016-01-01

    Acute fever is one of the most common presenting symptoms globally. In order to reduce the empiric use of antimicrobial drugs and improve outcomes, it is essential to improve diagnostic capabilities. In the absence of microbiology facilities in low-income settings, an assay to distinguish bacterial from non-bacterial causes would be a critical first step. To ensure that patient and market needs are met, the requirements of such a test should be specified in a target product profile (TPP). To identify minimal/optimal characteristics for a bacterial vs. non-bacterial fever test, experts from academia and international organizations with expertise in infectious diseases, diagnostic test development, laboratory medicine, global health, and health economics were convened. Proposed TPPs were reviewed by this working group, and consensus characteristics were defined. The working group defined non-severely ill, non-malaria infected children as the target population for the desired assay. To provide access to the most patients, the test should be deployable to community health centers and informal health settings, and staff should require 90% and >80% for sensitivity and specificity, respectively. Other key characteristics, to account for the challenging environment at which the test is targeted, included: i) time-to-result <10 min (but maximally <2 hrs); ii) storage conditions at 0–40°C, ≤90% non-condensing humidity with a minimal shelf life of 12 months; iii) operational conditions of 5–40°C, ≤90% non-condensing humidity; and iv) minimal sample collection needs (50–100μL, capillary blood). This expert approach to define assay requirements for a bacterial vs. non-bacterial assay should guide product development, and enable targeted and timely efforts by industry partners and academic institutions. PMID:27559728

  16. Target Product Profile for a Diagnostic Assay to Differentiate between Bacterial and Non-Bacterial Infections and Reduce Antimicrobial Overuse in Resource-Limited Settings: An Expert Consensus.

    Science.gov (United States)

    Dittrich, Sabine; Tadesse, Birkneh Tilahun; Moussy, Francis; Chua, Arlene; Zorzet, Anna; Tängdén, Thomas; Dolinger, David L; Page, Anne-Laure; Crump, John A; D'Acremont, Valerie; Bassat, Quique; Lubell, Yoel; Newton, Paul N; Heinrich, Norbert; Rodwell, Timothy J; González, Iveth J

    2016-01-01

    Acute fever is one of the most common presenting symptoms globally. In order to reduce the empiric use of antimicrobial drugs and improve outcomes, it is essential to improve diagnostic capabilities. In the absence of microbiology facilities in low-income settings, an assay to distinguish bacterial from non-bacterial causes would be a critical first step. To ensure that patient and market needs are met, the requirements of such a test should be specified in a target product profile (TPP). To identify minimal/optimal characteristics for a bacterial vs. non-bacterial fever test, experts from academia and international organizations with expertise in infectious diseases, diagnostic test development, laboratory medicine, global health, and health economics were convened. Proposed TPPs were reviewed by this working group, and consensus characteristics were defined. The working group defined non-severely ill, non-malaria infected children as the target population for the desired assay. To provide access to the most patients, the test should be deployable to community health centers and informal health settings, and staff should require 90% and >80% for sensitivity and specificity, respectively. Other key characteristics, to account for the challenging environment at which the test is targeted, included: i) time-to-result targeted and timely efforts by industry partners and academic institutions.

  17. Target Product Profile for a Diagnostic Assay to Differentiate between Bacterial and Non-Bacterial Infections and Reduce Antimicrobial Overuse in Resource-Limited Settings: An Expert Consensus.

    Science.gov (United States)

    Dittrich, Sabine; Tadesse, Birkneh Tilahun; Moussy, Francis; Chua, Arlene; Zorzet, Anna; Tängdén, Thomas; Dolinger, David L; Page, Anne-Laure; Crump, John A; D'Acremont, Valerie; Bassat, Quique; Lubell, Yoel; Newton, Paul N; Heinrich, Norbert; Rodwell, Timothy J; González, Iveth J

    2016-01-01

    Acute fever is one of the most common presenting symptoms globally. In order to reduce the empiric use of antimicrobial drugs and improve outcomes, it is essential to improve diagnostic capabilities. In the absence of microbiology facilities in low-income settings, an assay to distinguish bacterial from non-bacterial causes would be a critical first step. To ensure that patient and market needs are met, the requirements of such a test should be specified in a target product profile (TPP). To identify minimal/optimal characteristics for a bacterial vs. non-bacterial fever test, experts from academia and international organizations with expertise in infectious diseases, diagnostic test development, laboratory medicine, global health, and health economics were convened. Proposed TPPs were reviewed by this working group, and consensus characteristics were defined. The working group defined non-severely ill, non-malaria infected children as the target population for the desired assay. To provide access to the most patients, the test should be deployable to community health centers and informal health settings, and staff should require 90% and >80% for sensitivity and specificity, respectively. Other key characteristics, to account for the challenging environment at which the test is targeted, included: i) time-to-result development, and enable targeted and timely efforts by industry partners and academic institutions. PMID:27559728

  18. Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection.

    Science.gov (United States)

    Muturi, Ephantus J; Bara, Jeffrey J; Rooney, Alejandro P; Hansen, Allison K

    2016-08-01

    Understanding how midgut microbial communities of field-collected mosquitoes interact with pathogens is critical for controlling vector infection and disease. We used 16S rRNA and internal transcribed spacer sequencing to characterize the midgut bacterial and fungal communities of adult females of Aedes triseriatus and Aedes japonicus collected as pupae in tree holes, plastic bins and waste tires and their response to La Crosse virus (LACV) infection. For both mosquito species and across all habitat and virus treatments, a total of 62 bacterial operational taxonomic units (OTUs) from six phyla and 21 fungal OTUs from two phyla were identified. The majority of bacterial (92%) and fungal (71%) OTUs were shared between the mosquito species; however, several OTUs were unique to each species. Bacterial and fungal communities of individuals that took either infectious or noninfectious bloodmeals were less diverse and more homogeneous compared to those of newly emerged adults. Interestingly, LACV-infected A. triseriatus and A. japonicus had higher bacterial richness and lower fungal richness compared to individuals that took a noninfectious bloodmeal, suggesting that viral infection was associated with an increase in bacterial OTUs and a decrease in fungal OTUs. For both mosquito species, several OTUs were identified that had both high fidelity and specificity to mosquito midguts that were infected with LACV. Overall, these findings demonstrate that bacterial and fungal communities that reside in mosquito midguts respond to host diet and viral infection and could play a role in modulating vector susceptibility to LACV. PMID:27357374

  19. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems.

    Science.gov (United States)

    Luo, Xia; Jellison, Kristen L; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community.

  20. Metabolite profiles of rice cultivars containing bacterial blight-resistant genes are distinctive from susceptible rice

    Institute of Scientific and Technical Information of China (English)

    Jiao Wu; Haichuan Yu; Haofu Dai; Wenli Mei; Xin Huang; Shuifang Zhu; Ming Peng

    2012-01-01

    The metabolic changes of bacterial blight-resistant line C418/Xa23 generated by molecular marker-assisted selection (n =12),transgenic variety C418-Xa21 generated by using the Agrobacterium-mediated system (n =12),and progenitor cultivar C418 (n =12) were monitored using gas chromatography/mass spectrometry.The validation,discrimination,and establishment of correlative relationships between metabolite signals were performed by cluster analysis,principal component analysis,and partial least squares-discriminant analysis.Significant and unintended changes were observed in 154 components in C418/Xa23 and 48 components in C418-Xa21 compared with C418 (P < 0.05,Fold change > 2.0).The most significant decreases detected (P< 0.001) in both C418/Xa23 and C418-Xa21 were in three amino acids: glycine,tyrosine,and alanine,and four identified metabolites: malic acid,ferulic acid,succinic acid,and glycerol.Linoleic acid was increased specifically in C418/Xa23 which was derived from traditional breeding.This line,possessing a distinctive metabolite profile as a positive control,shows more differences vs.the parental than the transgenic line.Only succinic acid that falls outside the boundaries of natural variability between the two non-transgenic varieties C418 and C418/Xa23 should be further investigated with respect to safety or nutritional impact.

  1. Whole blood gene expression profiling of neonates with confirmed bacterial sepsis

    Directory of Open Access Journals (Sweden)

    Paul Dickinson

    2015-03-01

    Full Text Available Neonatal infection remains a primary cause of infant morbidity and mortality worldwide and yet our understanding of how human neonates respond to infection remains incomplete. Changes in host gene expression in response to infection may occur in any part of the body, with the continuous interaction between blood and tissues allowing blood cells to act as biosensors for the changes. In this study we have used whole blood transcriptome profiling to systematically identify signatures and the pathway biology underlying the pathogenesis of neonatal infection. Blood samples were collected from neonates at the first clinical signs of suspected sepsis alongside age matched healthy control subjects. Here we report a detailed description of the study design, including clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO data sets (GSE25504. Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis.

  2. Profiling a gut microbiota-generated catechin metabolite's fate in human blood cells using a metabolomic approach.

    Science.gov (United States)

    Mülek, Melanie; Fekete, Agnes; Wiest, Johannes; Holzgrabe, Ulrike; Mueller, Martin J; Högger, Petra

    2015-10-10

    The microbial catechin metabolite δ-(3,4-dihydroxy-phenyl)-γ-valerolactone (M1) has been found in human plasma samples after intake of maritime pine bark extract (Pycnogenol). M1 has been previously shown to accumulate in endothelial and blood cells in vitro after facilitated uptake and to exhibit anti-inflammatory activity. The purpose of the present research approach was to systematically and comprehensively analyze the metabolism of M1 in human blood cells in vitro and in vivo. A metabolomic approach that had been successfully applied for drug metabolite profiling was chosen to detect 19 metabolite peaks of M1 which were subsequently further analyzed and validated. The metabolites were categorized into three levels of identification according to the Metabolomics Standards Initiative with six compounds each confirmed at levels 1 and 2 and seven putative metabolites at level 3. The predominant metabolites were glutathione conjugates which were rapidly formed and revealed prolonged presence within the cells. Although a formation of an intracellular conjugate of M1 and glutathione (M1-GSH) was already known two GSH conjugate isomers, M1-S-GSH and M1-N-GSH were observed in the current study. Additionally detected organosulfur metabolites were conjugates with oxidized glutathione and cysteine. Other biotransformation products constituted the open-chained ester form of M1 and a methylated M1. Six of the metabolites determined in in vitro assays were also detected in blood cells in vivo after ingestion of the pine bark extract by two volunteers. The present study provides the first evidence that multiple and structurally heterogeneous polyphenol metabolites can be generated in human blood cells. The bioactivity of the M1 metabolites and their contribution to the previously determined anti-inflammatory effects of M1 now need to be elucidated. PMID:26025814

  3. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia

    OpenAIRE

    Schuijt, T. J.; Lankelma, J.M.; Scicluna, B.P.; Melo, E; Roelofs, J.J.; Boer, de, J.W.; Hoogendijk, A.J.; Beer, de, VHJ Vincent; De Vos; Belzer, C.; Poll, van der, T.; Wiersinga, W.J.

    2015-01-01

    OBJECTIVE: Pneumonia accounts for more deaths than any other infectious disease worldwide. The intestinal microbiota supports local mucosal immunity and is increasingly recognised as an important modulator of the systemic immune system. The precise role of the gut microbiota in bacterial pneumonia, however, is unknown. Here, we investigate the function of the gut microbiota in the host defence against Streptococcus pneumoniae infections. DESIGN: We depleted the gut microbiota in C57BL/6 mice ...

  4. Intestinal microbiota and HIV-1 infection

    Directory of Open Access Journals (Sweden)

    E. B. S. M. Trindade

    2007-01-01

    Full Text Available The intestinal microbiota consists of a qualitatively and quantitatively diverse range of microorganisms dynamically interacting with the host. It is remarkably stable with regard to the presence of microorganisms and their roles which, however, can be altered due to pathological conditions, diet composition, gastrointestinal disturbances and/or drug ingestion. The present review aimed at contributing to the discussion about changes in the intestinal microbiota due to HIV-1 infection, focusing on the triad infection-microbiota-nutrition as factors that promote intestinal bacterial imbalance. Intestinal microbiota alterations can be due to the HIV-1 infection as a primary factor or the pharmacotherapy employed, or they can be one of the consequences of the disease.

  5. Rhizosphere bacterial communities of potato cultivars evaluated through PCR-DGGE profiles Comunidades bacterianas associadas à rizosfera de cultivares de batata avaliadas por perfis de PCR-DGGE

    Directory of Open Access Journals (Sweden)

    Enderson Petrônio de Brito Ferreira

    2008-05-01

    Full Text Available The objective of this work was to determine the shifts on the PCR-DGGE profiles of bacterial communities associated to the rhizosphere of potato cultivars, in order to generate baseline information for further studies of environmental risk assessment of genetically modified potato plants. A greenhouse experiment was carried out with five potato cultivars (Achat, Bintje, Agata, Monalisa and Asterix, cultivated in pots containing soil from an integrated system for agroecological production. The experiment was conducted in a split plot randomized block design with five cultivars, three sampling periods and five replicates. Rhizosphere samples were collected in three sampling dates during plant development. DNA of rhizosphere microorganisms was extracted, amplified by PCR using bacterial universal primers, and analyzed through DGGE. Shifts on the rhizosphere bacterial communities associated to rhizosphere of different cultivars were related to both cultivar and plant age. Differences among rhizosphere bacterial communities were clearest at the earliest plant age, tending to decrease in later stages. This variation was detected among bacterial communities of the five tested cultivars. The characterization of soil microbial communities can be part of plant breeding programs to be used on studies of environmental risk assessment of genetically modified potatoes.O objetivo deste trabalho foi determinar as alterações nos perfis de PCR-DGGE das comunidades bacterianas associadas à rizosfera de cultivares de batata, para obter informações para futuros estudos de avaliação de risco ambiental de plantas de batatas geneticamente modificadas. Foi conduzido experimento em casa de vegetação com cinco cultivares de batata (Achat, Bintje, Ágata, Monalisa e Asterix, cultivadas em vasos com solo de um sistema integrado de produção agroecológica. O delineamento experimental foi o de blocos ao acaso, em parcelas subdivididas, com cinco cultivares, tr

  6. Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota

    DEFF Research Database (Denmark)

    Larsen, Jeppe Madura; Steen-Jensen, Daniel Bisgaard; Laursen, Janne Marie;

    2012-01-01

    of individual bacterial species are unknown. In this study, we compared the immune stimulatory capacity on human monocyte-derived dendritic cells (DCs) of selected airway commensal and pathogenic bacteria predominantly associated with lungs of asthma or COPD patients (pathogenic Haemophillus spp. and Moraxella...... spp.), healthy lungs (commensal Prevotella spp.) or both (commensal Veillonella spp. and Actinomyces spp.). All bacteria were found to induce activation of DCs as demonstrated by similar induction of CD83, CD40 and CD86 surface expression. However, asthma and COPD-associated pathogenic bacteria...... provoked a 3-5 fold higher production of IL-23, IL-12p70 and IL-10 cytokines compared to the commensal bacteria. Based on the differential cytokine production profiles, the studied airway bacteria could be segregated into three groups (Haemophilus spp. and Moraxella spp. vs. Prevotella spp. and Veillonella...

  7. Medición de cambios cuantitativos de la microbiota subgingival posterior a la remoción de placa bacteriana supragingival Measurement of quantitative changes of the microbiota subgingival after to removal of bacterial plaque supragingival

    Directory of Open Access Journals (Sweden)

    C Godoy

    2010-04-01

    possible that the microorganisms responsible for the origin and progression of the disease periodontal that live on the margin gingival (supragingival and under this (subgingival they have a direct relation that allows to support influential interactions in the growth and development of the different bacterial species that they live in the tissue periodontal.Therefore having removed the microorganisms that are located supragingivalmente would be possible to find changes in the way subgingival when an exchange not to exist between the aerobic environments (supragingival and anaerobic (subgingival once disorganized the bacterial plate supragingival. To demonstrate this relation 7 individuals selected with diagnosis of periodontitis chronicle moderate and severe to which they there was realized a destartraje supragingival of complete mouth to achieve supragingival to disorganize the bacterial plate. In turn microbiological samples of the sacks took periodontales deeper of every quadrant of these individuals, being the first taken sample before the destartraje supragingival considered as sample basal (the 0th, then they took at to 1, 7 and 21 days of removed the bacterial plate supragingival anaerobios (subgingival once disorganized the bacterial plate supragingival Of the results of the present study we could conclude that on having disorganized the biofilm supragingival a decrease is observed in the total quantity of microorganisms subgingivales, as well as also it diminishes in a considerable way the proportion of present Porphyoromona gingivalis in the way subgingival. Which would lead to thinking that there exists a direct and dependent relation between the microorganisms that live the way supragingival and subgingival.

  8. The gut microbiota, obesity and insulin resistance.

    Science.gov (United States)

    Shen, Jian; Obin, Martin S; Zhao, Liping

    2013-02-01

    The human gut is densely populated by commensal and symbiotic microbes (the "gut microbiota"), with the majority of the constituent microorganisms being bacteria. Accumulating evidence indicates that the gut microbiota plays a significant role in the development of obesity, obesity-associated inflammation and insulin resistance. In this review we discuss molecular and cell biological mechanisms by which the microbiota participate in host functions that impact the development and maintenance of the obese state, including host ingestive behavior, energy harvest, energy expenditure and fat storage. We additionally explore the diverse signaling pathways that regulate gut permeability and bacterial translocation to the host and how these are altered in the obese state to promote the systemic inflammation ("metabolic endotoxemia") that is a hallmark of obesity and its complications. Fundamental to our discussions is the concept of "crosstalk", i.e., the biochemical exchange between host and microbiota that maintains the metabolic health of the superorganism and whose dysregulation is a hallmark of the obese state. Differences in community composition, functional genes and metabolic activities of the gut microbiota appear to distinguish lean vs obese individuals, suggesting that gut 'dysbiosis' contributes to the development of obesity and/or its complications. The current challenge is to determine the relative importance of obesity-associated compositional and functional changes in the microbiota and to identify the relevant taxa and functional gene modules that promote leanness and metabolic health. As diet appears to play a predominant role in shaping the microbiota and promoting obesity-associated dysbiosis, parallel initiatives are required to elucidate dietary patterns and diet components (e.g., prebiotics, probiotics) that promote healthy gut microbiota. How the microbiota promotes human health and disease is a rich area of investigation that is likely to generate

  9. Epidemiological, Clinical and Prognostic Profile of Acute Bacterial Meningitis among Children in Alexandria, Egypt

    Directory of Open Access Journals (Sweden)

    Farag HF

    2005-01-01

    Full Text Available Purpose: To address the epidemiological characteristics and clinical indices that may predict the prognostic profile of meningitis among children. Methods: Children admitted to Alexandria fever hospital with clinical diagnosis of meningitis/meningoencephalitis during the period 2002-2003 were recruited for the study. They were subjected to clinical examination as well as CSF bacteriological and serological investigations Results: Three hundred and ten patients (195 males and 115 females were included. About 65.2% of them were infected with acute bacterial meningitis (ABM and 34.8% were infected with aseptic meningitis. In this study, ABM was caused by Haemophilus influenzae (21%, Streptococcus pneumoniae (13.9%, Neisseria meningitidis (14.2% and other undetermined bacteria (16.1%. ABM showed significant association with age group 1-9 years (66.3%, low socio-economic class (96%, working mother (83.2%, more than two smokers in the family (62.9% and cold seasons(fall 35.1% and winter 48.5%. Aseptic meningitis showed significant association with age group 3-15 months (100% and previous immunization(81.5%. The overall case fatality rate was 10.3%; 13.9% for ABM and 3.4% for aseptic meningitis. 7.1% of all survivors developed epileptic attacks. Predictors for death or epilepsy events were high WHO meningitis score (> 9, decreased CSF glucose level (Conclusion: This study highlights the importance of several predictors of the outcome of meningitis in children. It is concluded that quick and simple scoring scales, such as the WHO scale, are not only applicable but valuable prognostic tools for meningitis in children.

  10. Deviations in human gut microbiota

    DEFF Research Database (Denmark)

    Casén, C; Vebø, H C; Sekelja, M;

    2015-01-01

    BACKGROUND: Dysbiosis is associated with many diseases, including irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD), obesity and diabetes. Potential clinical impact of imbalance in the intestinal microbiota suggests need for new standardised diagnostic methods to facilitate...... microbiome profiling. AIM: To develop and validate a novel diagnostic test using faecal samples to profile the intestinal microbiota and identify and characterise dysbiosis. METHODS: Fifty-four DNA probes targeting ≥300 bacteria on different taxonomic levels were selected based on ability to distinguish......, and potential clinically relevant deviation in the microbiome from normobiosis. This model was tested in different samples from healthy volunteers and IBS and IBD patients (n = 330) to determine the ability to detect dysbiosis. RESULTS: Validation confirms dysbiosis was detected in 73% of IBS patients, 70...

  11. Bacterial adaptation to the gut environment favors successful colonization

    Science.gov (United States)

    Rezzonico, Enea; Mestdagh, Renaud; Delley, Michèle; Combremont, Séverine; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy; Bibiloni, Rodrigo

    2011-01-01

    Rodent models harboring a simple yet functional human intestinal microbiota provide a valuable tool to study the relationships between mammals and their bacterial inhabitants. In this study, we aimed to develop a simplified gnotobiotic mouse model containing 10 easy-to-grow bacteria, readily available from culture repositories, and of known genome sequence, that overall reflect the dominant commensal bacterial makeup found in adult human feces. We observed that merely inoculating a mix of fresh bacterial cultures into ex-germ free mice did not guarantee a successful intestinal colonization of the entire bacterial set, as mice inoculated simultaneously with all strains only harbored 3 after 21 d. Therefore, several inoculation procedures were tested and levels of individual strains were quantified using molecular tools. Best results were obtained by inoculating single bacterial strains into individual animals followed by an interval of two weeks before allowing the animals to socialize to exchange their commensal microbes. Through this procedure, animals were colonized with almost the complete bacterial set (9/10). Differences in the intestinal composition were also reflected in the urine and plasma metabolic profiles, where changes in lipids, SCFA, and amino acids were observed. We conclude that adaptation of bacterial strains to the host’s gut environment (mono-colonization) may predict a successful establishment of a more complex microbiota in rodents. PMID:22157236

  12. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

    Science.gov (United States)

    De Filippis, Francesca; Vannini, Lucia; La Storia, Antonietta; Laghi, Luca; Piombino, Paola; Stellato, Giuseppina; Serrazanetti, Diana I; Gozzi, Giorgia; Turroni, Silvia; Ferrocino, Ilario; Lazzi, Camilla; Di Cagno, Raffaella; Gobbetti, Marco; Ercolini, Danilo

    2014-01-01

    The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1)H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis. PMID:25372853

  13. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

    Science.gov (United States)

    De Filippis, Francesca; Vannini, Lucia; La Storia, Antonietta; Laghi, Luca; Piombino, Paola; Stellato, Giuseppina; Serrazanetti, Diana I; Gozzi, Giorgia; Turroni, Silvia; Ferrocino, Ilario; Lazzi, Camilla; Di Cagno, Raffaella; Gobbetti, Marco; Ercolini, Danilo

    2014-01-01

    The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1)H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.

  14. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

    Directory of Open Access Journals (Sweden)

    Francesca De Filippis

    Full Text Available The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.

  15. Production of immune response mediators by HT-29 intestinal cell-lines in the presence of Bifidobacterium-treated infant microbiota.

    Science.gov (United States)

    Arboleya, S; Bahrami, B; Macfarlane, S; Gueimonde, M; Macfarlane, G T; de los Reyes-Gavilán, C G

    2015-01-01

    The colonisation and establishment of the intestinal microbiota starts immediately at birth and is essential for the development of the intestine and the immune system. This microbial community gradually increases in number and diversity until the age of two or three years when it becomes a stable ecosystem resembling that of adults. This period constitutes a unique window of opportunity to modulate it through probiotic action, with a potential impact in later health. In the present work we have investigated how putative bifidobacterial probiotics modify the metabolic profiles and immune-modulatory properties of faecal microbiotas. An in vitro pH-controlled single-stage continuous-culture system (CCS) inoculated with infant faeces was employed to characterise the effects of two Bifidobacterium species on the intestinal microbiotas in three children, together with the effects of these modified microbiotas on cytokine production by HT-29 cells. Intestinal bacterial communities, production of short-chain fatty acids and lactate were determined by quantitative PCR and gas chromatography, respectively. Cytokines production by HT-29 cells was measured by ELISA. The combination of CCS with infant faeces and human intestinal cells provided a suitable model to evaluate the specific modulation of the intestinal microbiota and immune system by probiotics. In the CCS, infant faecal microbiotas were influenced by the addition of bifidobacteria, resulting in changes in their ability to induce the production of immune mediators by HT-29 cells. The different metabolic and immunological responses induced by the bifidobacterial species tested indicate the need to assess potential probiotics in model systems including complex intestinal microbiotas. Potential probiotic bifidobacteria can modulate the infant microbiota and its ability to induce the production of mediators of the immune response by intestinal cells. PMID:25691102

  16. Metabolomic analysis of human fecal microbiota: a comparison of feces-derived communities and defined mixed communities.

    Science.gov (United States)

    Yen, Sandi; McDonald, Julie A K; Schroeter, Kathleen; Oliphant, Kaitlyn; Sokolenko, Stanislav; Blondeel, Eric J M; Allen-Vercoe, Emma; Aucoin, Marc G

    2015-03-01

    The extensive impact of the human gut microbiota on its human host calls for a need to understand the types of communication that occur among the bacteria and their host. A metabolomics approach can provide a snapshot of the microbe-microbe interactions occurring as well as variations in the microbes from different hosts. In this study, metabolite profiles from an anaerobic continuous stirred-tank reactors (CSTR) system supporting the growth of several consortia of bacteria representative of the human gut were established and compared. Cell-free supernatant samples were analyzed by 1D (1)H nuclear magnetic resonance (NMR) spectroscopy, producing spectra representative of the metabolic activity of a particular community at a given time. Using targeted profiling, specific metabolites were identified and quantified on the basis of NMR analyses. Metabolite profiles discriminated each bacterial community examined, demonstrating that there are significant differences in the microbiota metabolome between each cultured community. We also found unique compounds that were identifying features of individual bacterial consortia. These findings are important because they demonstrate that metabolite profiles of gut microbial ecosystems can be constructed by targeted profiling of NMR spectra. Moreover, examination of these profiles sheds light on the type of microbes present in the gut and their metabolic interactions.

  17. The Gastrointestinal Tract Microbiota and Allergic Diseases.

    Science.gov (United States)

    Kyburz, Andreas; Müller, Anne

    2016-01-01

    The gastrointestinal (GI) tract microbiota is required for optimal digestion of foods, for the development of resistance against pathogens (termed colonization resistance), for the development of mucosa-associated lymphoid tissue, and for local as well as systemic immune homeostasis. Certain constituents of the GI tract microbiota are widely recognized as critical regulators and modulators of their host's immune response. These include bacterial members of the microbiota as well as parasitic nematodes. Immune regulation by immunomodulatory members of the GI microbiota primarily serves to subvert host antimicrobial immune defenses and promote persistent colonization, but as a side effect may prevent or suppress immunological disorders resulting from inappropriate responses to harmless antigens, such as allergy, colitis or autoimmunity. Many of the best understood GI-resident immunomodulatory species have co-evolved with their mammalian hosts for tens of thousands of years and masterfully manipulate host immune responses. In this review, we discuss the epidemiological evidence for the role of the GI tract microbiota as a whole, and of specific members, in protection against allergic and other immunological disorders. We then focus on the mechanistic basis of microbial immunomodulation, which is presented using several well-understood paradigmatic examples, that is, helminths, Helicobacter pylori, Bifidobacteria and Lactobacilli. In a final chapter, we highlight past and ongoing attempts at harnessing the immunomodulatory properties of GI microbiota species and their secreted products for intervention studies and describe the promises and limitations of these experimental approaches. The effects of pro- and prebiotics, bacterial lysates, as well as of fecal microbiota transplantation are presented and compared. PMID:27028536

  18. Metabolic and phylogenetic profile of bacterial community in Guishan coastal water (Pearl River Estuary), South China Sea

    Science.gov (United States)

    Hu, Xiaojuan; Liu, Qing; Li, Zhuojia; He, Zhili; Gong, Yingxue; Cao, Yucheng; Yang, Yufeng

    2014-10-01

    Characteristics of a microbial community are important as they indicate the status of aquatic ecosystems. In the present study, the metabolic and phylogenetic profile of the bacterioplankton community in Guishan coastal water (Pearl River Estuary), South China Sea, at 12 sites (S1-S12) were explored by community-level physiological profiling (CLPP) with BIOLOG Eco-plate and denaturing gradient gel electrophoresis (DGGE). Our results showed that the core mariculture area (S6, S7 and S8) and the sites associating with human activity and sewage discharge (S11 and S12) had higher microbial metabolic capability and bacterial community diversity than others (S1-5, S9-10). Especially, the diversity index of S11 and S12 calculated from both CLPP and DGGE data ( H>3.2) was higher than that of others as sewage discharge may increase water nitrogen and phosphorus nutrient. The bacterial community structure of S6, S8, S11 and S12 was greatly influenced by total phosphorous, salinity and total nitrogen. Based on DGGE fingerprinting, proteobacteria, especially γ- and α-proteobacteria, were found dominant at all sites. In conclusion, the aquaculture area and wharf had high microbial metabolic capability. The structure and composition of bacterial community were closely related to the level of phosphorus, salinity and nitrogen.

  19. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    Denaturing gradient gel electrophoresis (DGGE) was used to elucidate spatial and temporal variations in bacterial community composition (BCC) from four locations along the central west coast of India. DNA extracts from 36 water samples collected...

  20. Dominant culturable bacterial microbiota in the digestive tract of the American black vulture (Coragyps atratus Bechstein 1793 and search for antagonistic substances Microbiota bacteriana dominante cultivável no trato digestivo do urubu (Coragyps atratus Bechstein 1793

    Directory of Open Access Journals (Sweden)

    Lydston Rodrigues de Carvalho

    2003-07-01

    Full Text Available Strict and facultative culturable anaerobic bacteria from the digestive tract of six American black vultures (Coragyps atratus Bechstein 1793 were isolated and identified. After capture, the birds received a non-contaminated diet for one week to eliminate possible allochthonous microorganisms. Then, specimens collected from tongue, stomach and intestines were weighed, submitted to decimal dilution in an anaerobic chamber, inoculated into culture media and incubated aerobically and anaerobically at 37ºC for enumeration, isolation and identification. Isolated bacteria were submitted to tests to detect possible antagonisms between them. The total bacterial population along the digestive tract ranged from 3.46 ± 0.39 log CFU/g in the stomach to 10.75 ± 0.37 log CFU/g in the distal intestine. Some bacteria were isolated for the first time from the digestive tract of C. atratus: Actinomyces bovis, Lactobacillus cellobiosus, Micrococcus luteus, Neisseria sicca, Clostridium bifermentans, Enterobacter agglomerans, Peptostreptococcus sp., Sarcina sp., Serratia odorifera, and Shigella flexneri. Associations between microorganisms were observed during isolation on two occasions, one involving A. bovis and N. sicca, and the other involving A. bovis and a Gram-negative rod. Hetero-, iso- and autoantagonisms were observed, suggesting the ecological role of these indigenous microorganisms in terms of population auto-control and environmental barrier in the digestive tract of carrion-feeding birds.As bactérias anaeróbias estritas e facultativas cultiváveis do trato digestivo de seis urubus (Coragyps atratus Bechstein 1793 foram isoladas e identificadas. Após a captura, as aves receberam uma alimentação de baixa contaminação durante uma semana para eliminar possíveis microorganismos alóctonos. A seguir, amostras colhidas na língua, estomago e intestinos foram pesadas, submetidas a diluições decimais numa câmara anaeróbia, inoculadas em meios de

  1. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.

    Directory of Open Access Journals (Sweden)

    Jérôme Lluch

    Full Text Available Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin. However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart.The high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.

  2. Temporal Stability of the Salivary Microbiota in Oral Health

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Jensen, Allan Bardow;

    2016-01-01

    OBJECTIVES: Saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. For such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal...... variation. The purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling. DESIGN: Stimulated saliva samples were collected from 5 orally healthy individuals in 4 h intervals for 24 h, and collection was repeated 7 days later (number of samples per...... over time. CONCLUSIONS: Although there was considerable variation between subjects, microbial profiles within subjects were stable throughout a 24 hour period and after 1 week. Since there is little or no evidence of diurnal variation of the salivary microbiome, time of sampling of saliva...

  3. Dysbiosis of the gut microbiota in disease

    Directory of Open Access Journals (Sweden)

    Simon Carding

    2015-02-01

    Full Text Available There is growing evidence that dysbiosis of the gut microbiota is associated with the pathogenesis of both intestinal and extra-intestinal disorders. Intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (IBS, and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity.In many of these conditions, the mechanisms leading to disease development involves the pivotal mutualistic relationship between the colonic microbiota, their metabolic products, and the host immune system. The establishment of a ‘healthy’ relationship early in life appears to be critical to maintaining intestinal homeostasis. Whilst we do not yet have a clear understanding of what constitutes a ‘healthy’ colonic microbiota, a picture is emerging from many recent studies identifying particular bacterial species associated with a healthy microbiota. In particular, the bacterial species residing within the mucus layer of the colon, either through direct contact with host cells, or through indirect communication via bacterial metabolites, may influence whether host cellular homeostasis is maintained or whether inflammatory mechanisms are triggered. In addition to inflammation, there is some evidence that perturbations in the gut microbiota is involved with the development of colorectal cancer. In this case, dysbiosis may not be the most important factor, rather the products of interaction between diet and the microbiome. High-protein diets are thought to result in the production of carcinogenic metabolites from the colonic microbiota that may result in the induction of neoplasia in the colonic epithelium.Ever more sensitive metabolomics methodologies reveal a suite of small molecules produced in the microbiome which mimic or act as neurosignallers or neurotransmitters. Coupled with evidence that probiotic interventions may alter psychological endpoints in both humans and in

  4. Effects of levan-type fructan supplementation on growth performance, digestibility, blood profile, fecal microbiota, and immune responses after lipopolysaccharide challenge in growing pigs.

    Science.gov (United States)

    Li, J; Kim, I H

    2013-11-01

    In Exp. 1, 80 growing pigs (27.1±0.7 kg) were used in a 42-d experiment to evaluate the effect of levan-type fructan on growth performance, digestibility, blood profile, and fecal microbiota. Pigs were randomly allocated to 1 of 4 treatments, according to initial BW and gender, with 5 replicate pens per treatment and 2 barrows and 2 gilts per pen. Treatments were corn-soybean meal-based diets supplemented with 0%, 0.05%, 0.10%, or 0.20% levan-type fructan. Average daily gain and G:F increased (quadratic, P<0.05), as dietary levan-type fructan increased from 0 to 0.2%. Similarly, the apparent total tract digestibility of N and GE increased (quadratic, P<0.05), as dietary supplementation of levan-type fructan increased. Dietary levan-type fructan supplementation increased fecal Lactobacillus counts linearly (P<0.05). In Exp. 2, 20 individually housed barrows (26.2±0.6 kg) were used to evaluate immune responses after an Escherichia coli lipopolysaccharide (LPS) challenge. Pigs were fed corn-soybean meal-based diets supplemented with 0% or 0.10% levan-type fructan for 42 d. At d 42, 5 pigs from each treatment were injected with E. coli LPS (0.01% of BW) and the other 5 pigs with sterile saline solution, resulting in a 2×2 factorial arrangement of treatments. Blood was taken 0, 2, 4, 6, and 8 h after challenge. Challenge with LPS decreased blood lymphocyte percentage and had an interactive effect with levan-type fructan inclusion at 4, 6, and 8 h (P<0.01). Levan-type fructan supplementation increased (P<0.05) white blood cells at 6 and 8 h, and increased (P<0.05) lymphocyte percentage at 8 h after the challenge. Lipopolysaccharide injection increased (P<0.05) rectal temperature at 2 and 4 h, and had an interactive effect (P<0.05) with levan-type fructan supplementation at 4 h after the challenge. At 2, 4, 6, and 8 h, serum cortisol, tumor necrosis factor-α, and IL-6 concentration increased (P<0.05) by LPS challenge, and there was an interactive effect between LPS

  5. The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen.

    Directory of Open Access Journals (Sweden)

    Jonathan J Hansen

    Full Text Available BACKGROUND: Inflammatory bowel diseases (IBD may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta. Healthy, germ-free HLA-B27 transgenic (Tg rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. METHODS: Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. RESULTS: B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function "receptor activity", most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. CONCLUSIONS: B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to

  6. Comparison of the Distal Gut Microbiota from People and Animals in Africa

    OpenAIRE

    Ellis, Richard J; Bruce, Kenneth D.; Claire Jenkins; J. Russell Stothard; Lilly Ajarova; Lawrence Mugisha; Viney, Mark E

    2013-01-01

    The gut microbiota plays a key role in the maintenance of healthy gut function as well as many other aspects of health. High-throughput sequence analyses have revealed the composition of the gut microbiota, showing that there is a core signature to the human gut microbiota, as well as variation in its composition between people. The gut microbiota of animals is also being investigated. We are interested in the relationship between bacterial taxa of the human gut microbiota and those in the gu...

  7. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    Science.gov (United States)

    Roder, Cornelia; Arif, Chatchanit; Bayer, Till; Aranda, Manuel; Daniels, Camille; Shibl, Ahmed; Chavanich, Suchana; Voolstra, Christian R

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries. PMID:23924783

  8. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  9. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.

  10. Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome.

    Science.gov (United States)

    Roder, Cornelia; Arif, Chatchanit; Daniels, Camille; Weil, Ernesto; Voolstra, Christian R

    2014-02-01

    Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases. PMID:24350609

  11. Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

    KAUST Repository

    Roder, C.

    2014-01-29

    Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases. 2013 The Authors Molecular Ecology John Wiley & Sons Ltd.

  12. Gut Microbiota and Extreme Longevity.

    Science.gov (United States)

    Biagi, Elena; Franceschi, Claudio; Rampelli, Simone; Severgnini, Marco; Ostan, Rita; Turroni, Silvia; Consolandi, Clarissa; Quercia, Sara; Scurti, Maria; Monti, Daniela; Capri, Miriam; Brigidi, Patrizia; Candela, Marco

    2016-06-01

    The study of the extreme limits of human lifespan may allow a better understanding of how human beings can escape, delay, or survive the most frequent age-related causes of morbidity, a peculiarity shown by long-living individuals. Longevity is a complex trait in which genetics, environment, and stochasticity concur to determine the chance to reach 100 or more years of age [1]. Because of its impact on human metabolism and immunology, the gut microbiome has been proposed as a possible determinant of healthy aging [2, 3]. Indeed, the preservation of host-microbes homeostasis can counteract inflammaging [4], intestinal permeability [5], and decline in bone and cognitive health [6, 7]. Aiming at deepening our knowledge on the relationship between the gut microbiota and a long-living host, we provide for the first time the phylogenetic microbiota analysis of semi-supercentenarians, i.e., 105-109 years old, in comparison to adults, elderly, and centenarians, thus reconstructing the longest available human microbiota trajectory along aging. We highlighted the presence of a core microbiota of highly occurring, symbiotic bacterial taxa (mostly belonging to the dominant Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae families), with a cumulative abundance decreasing along with age. Aging is characterized by an increasing abundance of subdominant species, as well as a rearrangement in their co-occurrence network. These features are maintained in longevity and extreme longevity, but peculiarities emerged, especially in semi-supercentenarians, describing changes that, even accommodating opportunistic and allochthonous bacteria, might possibly support health maintenance during aging, such as an enrichment and/or higher prevalence of health-associated groups (e.g., Akkermansia, Bifidobacterium, and Christensenellaceae). PMID:27185560

  13. The bottlenose dolphin (Tursiops truncatus) faecal microbiota.

    Science.gov (United States)

    Soverini, Matteo; Quercia, Sara; Biancani, Barbara; Furlati, Stefano; Turroni, Silvia; Biagi, Elena; Consolandi, Clarissa; Peano, Clelia; Severgnini, Marco; Rampelli, Simone; Brigidi, Patrizia; Candela, Marco

    2016-04-01

    Cetaceans have evolved from herbivorous terrestrial artiodactyls closely related to ruminants and hippopotamuses. Delphinidae, a family included in this order, represent an extreme and successful re-adaptation of mammalian physiology to the marine habitat and piscivorous diet. The anatomical aspects of Delphinidae success are well understood, whereas some physiological aspects of their environmental fitness are less defined, such as the gut microbiota composition and its adaptation to their dietary niche. Here, we explored the faecal microbiota structure of nine adult bottlenose dolphins (Tursiops truncatus) and one breast-fed calf living in a controlled environment. According to our findings, dolphins possess a unique microbiota profile within the Mammalia class, highly resembling that of carnivorous marine fishes. The breast-fed calf showed a distinctive compositional structure of the gut microbial ecosystem, which partially overlaps with the mother's milk microbiota. Taken together, our data indicate that in dolphins the adaptation to the marine niche and piscivorous diet involved the convergence of their gut microbiota structure with that of marine fishes, overcoming the gut microbiota phylogenetic inertia previously described in terrestrial mammalians. PMID:26960390

  14. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis.

    Science.gov (United States)

    Shapira, Michael

    2016-07-01

    Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation. PMID:27039196

  15. PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss gut microbiota reveals host-specific communities of active bacteria.

    Directory of Open Access Journals (Sweden)

    Paola Navarrete

    Full Text Available This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota of rainbow trout. Full sibling fish from four unrelated families, each consisting of individuals derived from the mating of one male and one female belonging to a breeding program, were fed diets containing either vegetable proteins or vegetable oils for two months in comparison to a control diet consisting of only fish protein and fish oil. Two parallel approaches were applied on the same samples: transcriptionally active bacterial populations were examined based on RNA analysis and were compared with bacterial populations obtained from DNA analysis. Comparison of temporal temperature gradient gel electrophoresis (TTGE profiles from DNA and RNA showed important differences, indicating that active bacterial populations were better described by RNA analysis. Results showed that some bacterial groups were significantly (P<0.05 associated with specific families, indicating that microbiota composition may be influenced by the host. In addition, the effect of diet on microbiota composition was dependent on the trout family.

  16. PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria.

    Science.gov (United States)

    Navarrete, Paola; Magne, Fabien; Araneda, Cristian; Fuentes, Pamela; Barros, Luis; Opazo, Rafael; Espejo, Romilio; Romero, Jaime

    2012-01-01

    This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota of rainbow trout. Full sibling fish from four unrelated families, each consisting of individuals derived from the mating of one male and one female belonging to a breeding program, were fed diets containing either vegetable proteins or vegetable oils for two months in comparison to a control diet consisting of only fish protein and fish oil. Two parallel approaches were applied on the same samples: transcriptionally active bacterial populations were examined based on RNA analysis and were compared with bacterial populations obtained from DNA analysis. Comparison of temporal temperature gradient gel electrophoresis (TTGE) profiles from DNA and RNA showed important differences, indicating that active bacterial populations were better described by RNA analysis. Results showed that some bacterial groups were significantly (P<0.05) associated with specific families, indicating that microbiota composition may be influenced by the host. In addition, the effect of diet on microbiota composition was dependent on the trout family.

  17. Long-term alteration of intestinal microbiota in patients with ulcerative colitis by antibiotic combination therapy.

    Science.gov (United States)

    Koido, Shigeo; Ohkusa, Toshifumi; Kajiura, Takayuki; Shinozaki, Junko; Suzuki, Manabu; Saito, Keisuke; Takakura, Kazuki; Tsukinaga, Shintaro; Odahara, Shunichi; Yukawa, Toyokazu; Mitobe, Jimi; Kajihara, Mikio; Uchiyama, Kan; Arakawa, Hiroshi; Tajiri, Hisao

    2014-01-01

    Previous work has demonstrated that intestinal bacteria, such as Fusobacterium varium (F. varium), contribute to the clinical activity in ulcerative colitis (UC); thus, an antibiotic combination therapy (amoxicillin, tetracycline, and metronidazole (ATM)) against F. varium can induce and maintain UC remission. Therefore, we investigated whether ATM therapy induces a long-term alteration of intestinal microbiota in patients with UC. Patients with UC were enrolled in a multicenter, randomized, double-blind, placebo-controlled study. Biopsy samples at the beginning of the trial and again at 3 months after treatment completion were randomly obtained from 20 patients. The terminal restriction fragment length polymorphism (T-RFLP) in mucosa-associated bacterial components was examined to assess the alteration of the intestinal microbiota. Profile changes of T-RFLP in mucosa-associated bacterial components were found in 10 of 12 patients in the treatment group and in none of 8 in the placebo group. Dice similarity coefficients using the unweighted pair group method with arithmetic averages (Dice-UPGMA) confirmed that the similarity of mucosal microbiota from the descending colon was significantly decreased after the ATM therapy, and this change was maintained for at least 3 months. Moreover, at 3 months after treatment completion, the F. varium/β-actin ratio, examined by real-time PCR using nested PCR products from biopsy samples, was reduced less than 40% in 8 of 12 treated patients, which was higher, but not significantly, than in 4 of 8 patients in the placebo group. Together, these results suggest that ATM therapy induces long-term alterations in the intestinal microbiota of patients with UC, which may be associated, at least in part, with clinical effects of the therapy. PMID:24489770

  18. Long-term alteration of intestinal microbiota in patients with ulcerative colitis by antibiotic combination therapy.

    Directory of Open Access Journals (Sweden)

    Shigeo Koido

    Full Text Available Previous work has demonstrated that intestinal bacteria, such as Fusobacterium varium (F. varium, contribute to the clinical activity in ulcerative colitis (UC; thus, an antibiotic combination therapy (amoxicillin, tetracycline, and metronidazole (ATM against F. varium can induce and maintain UC remission. Therefore, we investigated whether ATM therapy induces a long-term alteration of intestinal microbiota in patients with UC. Patients with UC were enrolled in a multicenter, randomized, double-blind, placebo-controlled study. Biopsy samples at the beginning of the trial and again at 3 months after treatment completion were randomly obtained from 20 patients. The terminal restriction fragment length polymorphism (T-RFLP in mucosa-associated bacterial components was examined to assess the alteration of the intestinal microbiota. Profile changes of T-RFLP in mucosa-associated bacterial components were found in 10 of 12 patients in the treatment group and in none of 8 in the placebo group. Dice similarity coefficients using the unweighted pair group method with arithmetic averages (Dice-UPGMA confirmed that the similarity of mucosal microbiota from the descending colon was significantly decreased after the ATM therapy, and this change was maintained for at least 3 months. Moreover, at 3 months after treatment completion, the F. varium/β-actin ratio, examined by real-time PCR using nested PCR products from biopsy samples, was reduced less than 40% in 8 of 12 treated patients, which was higher, but not significantly, than in 4 of 8 patients in the placebo group. Together, these results suggest that ATM therapy induces long-term alterations in the intestinal microbiota of patients with UC, which may be associated, at least in part, with clinical effects of the therapy.

  19. Metabolomics analysis identifies intestinal microbiota-derived biomarkers of colonization resistance in clindamycin-treated mice.

    Directory of Open Access Journals (Sweden)

    Robin L P Jump

    Full Text Available BACKGROUND: The intestinal microbiota protect the host against enteric pathogens through a defense mechanism termed colonization resistance. Antibiotics excreted into the intestinal tract may disrupt colonization resistance and alter normal metabolic functions of the microbiota. We used a mouse model to test the hypothesis that alterations in levels of bacterial metabolites in fecal specimens could provide useful biomarkers indicating disrupted or intact colonization resistance after antibiotic treatment. METHODS: To assess in vivo colonization resistance, mice were challenged with oral vancomycin-resistant Enterococcus or Clostridium difficile spores at varying time points after treatment with the lincosamide antibiotic clindamycin. For concurrent groups of antibiotic-treated mice, stool samples were analyzed using quantitative real-time polymerase chain reaction to assess changes in the microbiota and using non-targeted metabolic profiling. To assess whether the findings were applicable to another antibiotic class that suppresses intestinal anaerobes, similar experiments were conducted with piperacillin/tazobactam. RESULTS: Colonization resistance began to recover within 5 days and was intact by 12 days after clindamycin treatment, coinciding with the recovery bacteria from the families Lachnospiraceae and Ruminococcaceae, both part of the phylum Firmicutes. Clindamycin treatment caused marked changes in metabolites present in fecal specimens. Of 484 compounds analyzed, 146 (30% exhibited a significant increase or decrease in concentration during clindamycin treatment followed by recovery to baseline that coincided with restoration of in vivo colonization resistance. Identified as potential biomarkers of colonization resistance, these compounds included intermediates in carbohydrate or protein metabolism that increased (pentitols, gamma-glutamyl amino acids and inositol metabolites or decreased (pentoses, dipeptides with clindamycin treatment

  20. Invertebrate footprints on detritus processing, bacterial community structure, and spatiotemporal redox profiles

    OpenAIRE

    Hunting, E.R.; Whatley, M. H.; Geest, van der, A.H.M.; Mulder, C; Kraak, M.H.S.; Breure, A M; Admiraal, W.

    2012-01-01

    Detritus processing is driven by a complex interplay between macroinvertebrate and microbial activities. Bioturbation/feeding activities of invertebrates in sediments are known to influence decomposition rates. However, direct effects of invertebrates on bacterial communities and detritus processing remain ill-defined, mainly because identifying interactions between invertebrates and sediments is methodologically challenging. We incubated 5 macroinvertebrate species with various bioturbation/...

  1. Dietary carbohydrate source influences molecular fingerprints of the rat faecal microbiota

    Directory of Open Access Journals (Sweden)

    Dragsted Lars O

    2006-11-01

    Full Text Available Abstract Background A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group, sucrose, potato starch, inulin (a long- chained fructan or oligofructose (a short-chained fructan. Fructans are, opposite sucrose and starches, not digestible by mammalian gut enzymes, but are known to be fermentable by specific bacteria in the large intestine. Results Animals fed with diets containing potato starch, or either of the fructans had a significantly (p Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE of PCR amplified bacterial 16S rRNA genes as well as of Reverse Transcriptase-PCR amplified bacterial 16S rRNA resulted in different phylogenetic profiles for each of the five animal groups as revealed by Principal Component Analysis (PCA of band patterns. Conclusion Even though sucrose and cornstarch are both easily digestible and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though they are chemically similar, different intestinal bacteria ferment them. Comparison of DNA-based and RNA-based profiles suggested that two species within the phylum Bacteroidetes were not abundant in numbers but had a particularly high ribosome content in the animals fed with inulin.

  2. Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures.

    Science.gov (United States)

    Geng, Haifeng; Sale, Kenneth L; Tran-Gyamfi, Mary Bao; Lane, Todd W; Yu, Eizadora T

    2016-07-01

    Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems. PMID:26956183

  3. Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet

    Science.gov (United States)

    Heinritz, Sonja N.; Weiss, Eva; Eklund, Meike; Aumiller, Tobias; Louis, Sandrine; Rings, Andreas; Messner, Sabine; Camarinha-Silva, Amélia; Seifert, Jana; Bischoff, Stephan C.; Mosenthin, Rainer

    2016-01-01

    The intestinal microbiota and its metabolites appear to be an important factor for gastrointestinal function and health. However, research is still needed to further elaborate potential relationships between nutrition, gut microbiota and host’s health by means of a suitable animal model. The present study examined the effect of two different diets on microbial composition and activity by using the pig as a model for humans. Eight pigs were equally allotted to two treatments, either fed a low-fat/high-fiber (LF), or a high-fat/low-fiber (HF) diet for 7 weeks. Feces were sampled at day 7 of every experimental week. Diet effects on fecal microbiota were assessed using quantitative real-time PCR, DNA fingerprinting and metaproteomics. Furthermore, fecal short-chain fatty acid (SCFA) profiles and ammonia concentrations were determined. Gene copy numbers of lactobacilli, bifidobacteria (P0.05). Results provide evidence that beginning from the start of the experiment, the LF diet stimulated beneficial bacteria and SCFA production, especially butyrate (P<0.05), while the HF diet fostered those bacterial groups which have been associated with a negative impact on health conditions. These findings correspond to results in humans and might strengthen the hypothesis that the response of the porcine gut microbiota to a specific dietary modulation is in support of using the pig as suitable animal model for humans to assess diet-gut-microbiota interactions. Data are available via ProteomeXchange with identifier PXD003447. PMID:27100182

  4. Epidemiological, clinical and prognostic profile of childhood acute bacterial meningitis in a resource poor setting

    Directory of Open Access Journals (Sweden)

    Bankole Peter Kuti

    2015-01-01

    Full Text Available Background: Childhood bacterial meningitis is a neurologic emergency that continues to kill and maims children particularly in developing countries with poor immunization coverage. Objective: This study set out to assess the hospital incidence, pattern of presentation, etiologic agents, outcome and determinants of mortality among the children admitted with bacterial meningitis at the Wesley Guild Hospital (WGH, Ilesa. Patients and Methods: We carried out a retrospective review of admitted cases of bacterial meningitis in children aged one month to 15 years at the WGH, Ilesa over a three year period by looking at the hospital records. Factors in the history and examinations were compared among survivors and those that died to determine factors significantly associated with mortality in these children. Results: Eighty-one (5.5% of the 1470 childhood admissions during the study period had bacterial meningitis. Male preponderance was observed and two-thirds of the children were infants. More cases were admitted during the wet rainy season than during the dry harmattan season. Haemophilus influenzae type B and Streptococcus pneumoniae were the leading etiologic agents and ciprofloxacin and ceftriaxone adequately cover for these organisms. Twenty-two (27.2% of the 81 children died, while 34 (42.0% survived with neurologic deficits. Children with multiple seizures, coma, neck retraction, hyponatremia, hypoglycorrhachia, turbid CSF as well as Gram positive meningitis at presentation were found to more likely to die (P < 0.05. None of these factors however independently predict mortality. Conclusion: Childhood bacterial meningitis often results in death and neurologic deficit among infants and young children admitted at the WGH, Ilesa. Children diagnosed with meningitis who in addition had multiple seizures, neck retraction and coma at presentation are at increased risk of dying.

  5. Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks.

    Directory of Open Access Journals (Sweden)

    Alexander Kurilshikov

    Full Text Available Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species, Rickettsia (I. persulcatus and D. reticulatus and Francisella (D. reticulatus. B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002. Between-sex variation was confirmed by PERMANOVA testing in I

  6. Assessment of changes in community level physiological profile and molecular diversity of bacterial communities in different stages of jute retting.

    Science.gov (United States)

    Das, Biswapriya; Chakrabarti, Kalyan; Ghosh, Sagarmoy; Chakraborty, Ashis; Saha, Manabendra Nath

    2013-12-01

    Retting of jute is essentially microbiological and biochemical in nature. Community Level Physiological Profiles (CLPP) as well as genomic diversity of bacterial communities were assessed in water samples collected during pre-retting, after 1st and 2nd charges of retting. The water samples were collected from two widely cultivated jute growing locations, Sonatikari (22 degrees 41'27"N; 88 degrees 35'44"E) and Baduria (22 degrees 44'24"N; 88 degrees 47'24"E), West Bengal, India. The CLPP, expressed as net area under substrate utilization curve, was studied by carbon source utilization patterns in BIOLOG Ecoplates. Molecular diversity was studied by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) of total DNA from water samples. Both between locations and stages of retting, substrate utilizations pattern were carbohydrates > carboxylic acids > polymers > amino acids > amines/amides > phenolic compounds. Differential substrate utilization pattern as well as variation in banding pattern in DGGE profiles was observed between the two locations and at different stages of retting. The variations in CLPP in different stages of retting were due to the change in bacterial communities. PMID:24506039

  7. Effects of different methods of DNA extraction for activated sludge on the subsequent analysis of bacterial community profiles.

    Science.gov (United States)

    Sun, Lianpeng; Ouyang, Xiong; Tang, Yueheng; Yang, Ying; Luo, Ying

    2012-02-01

    The effect of different DNA extraction protocols on activated sludge DNA yield and bacterial community composition was evaluated by temperature gradient gel electrophoresis (TGGE). Nine different procedures to extract DNA were compared-sonication (30s), sonication (40s), sonication (50s), freezing-thawing, bead milling, sodium dodecyl sulfate (SDS)-lysozyme, SDS-proteinase K, SDS-lysozyme-proteinase, and a commercial extraction kit. It was found that the TGGE profiles and the DNA band numbers made significant differences via various extraction methods. The yield and purity of DNA extracted by sonication and other physical methods were not satisfactory, while the DNA purity extracted by SDS and other chemical-biological methods were better. Crude DNA extracts isolated by sonication and other physical methods passed the polymerase chain reaction, despite the absence of purification and acquired affluent DNA bands in TGGE. The affluence of bands in TGGE was not consistent with the yield and purification of DNA, but was correlative with extraction protocols. To analyze the activated sludge bacterial community by TGGE fingerprint, it is necessary to make a synthesis of the TGGE fingerprint profiles of chemical and physical DNA extraction methods to overcome the representative bias.

  8. Breast milk, microbiota, and intestinal immune homeostasis.

    Science.gov (United States)

    Walker, W Allan; Iyengar, Rajashri Shuba

    2015-01-01

    Newborns adjust to the extrauterine environment by developing intestinal immune homeostasis. Appropriate initial bacterial colonization is necessary for adequate intestinal immune development. An environmental determinant of adequate colonization is breast milk. Although the full-term infant is developmentally capable of mounting an immune response, the effector immune component requires bacterial stimulation. Breast milk stimulates the proliferation of a well-balanced and diverse microbiota, which initially influences a switch from an intrauterine TH2 predominant to a TH1/TH2 balanced response and with activation of T-regulatory cells by breast milk-stimulated specific organisms (Bifidobacteria, Lactobacillus, and Bacteroides). As an example of its effect, oligosaccharides in breast milk are fermented by colonic bacteria producing an acid milieu for bacterial proliferation. In addition, short-chain fatty acids in breast milk activate receptors on T-reg cells and bacterial genes, which preferentially mediate intestinal tight junction expression and anti-inflammation. Other components of breast milk (defensins, lactoferrin, etc.) inhibit pathogens and further contribute to microbiota composition. The breast milk influence on initial intestinal microbiota also prevents expression of immune-mediated diseases (asthma, inflammatory bowel disease, type 1 diabetes) later in life through a balanced initial immune response, underscoring the necessity of breastfeeding as the first source of nutrition. PMID:25310762

  9. Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH

    Science.gov (United States)

    Human vaginal microbiota affect reproductive performance and perinatal health. Although a number of common reproductive disorders in livestock involve bacterial infection, very little is known about their normal vaginal microbiota. Therefore, we sought to determine the species composition of sheep a...

  10. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies

    OpenAIRE

    Distrutti, Eleonora; Monaldi, Lorenzo; Ricci, Patrizia; Fiorucci, Stefano

    2016-01-01

    In the last decade the impressive expansion of our knowledge of the vast microbial community that resides in the human intestine, the gut microbiota, has provided support to the concept that a disturbed intestinal ecology might promote development and maintenance of symptoms in irritable bowel syndrome (IBS). As a correlate, manipulation of gut microbiota represents a new strategy for the treatment of this multifactorial disease. A number of attempts have been made to modulate the gut bacteri...

  11. Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae Using 16S rRNA Gene Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Michel Diouf

    Full Text Available Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers.

  12. Bacterial profiling of White Plague Disease in a comparative coral species framework

    OpenAIRE

    Roder, Cornelia; Arif, Chatchanit; Bayer, Till; Aranda, Manuel; Daniels, Camille; Shibl, Ahmed; Chavanich, Suchana; VOOLSTRA, CHRISTIAN R.

    2013-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studie...

  13. Physico-chemical Profile and Microbial Diversity During Bioconversion of Sugarcane Press Mud Using Bacterial Suspension

    Directory of Open Access Journals (Sweden)

    Tushar Chandra SARKER

    2013-08-01

    Full Text Available This study was aimed at investigating the physico-chemical and microbial diversity for rapid composting of sugarcane press mud (PM leading to organic manure. Five bacterial strains (Cellulomonas sp., Klebsiella sp., Proteus sp., Enterobacter sp., Salmonella sp. were tested under in vivo conditions for bioconversion of PM using pile method. Results revealed that combined inoculation of bacterial consortia was found to be the best decomposer of PM resulting reduction of organic carbon content (26.75%, C:N ratio (12.44%. In parallel, it increased the nitrogen (2.34%, phosphorous (1.15% and potassium (1.37% content along with the population of microorganisms i.e. bacteria, fungi and actinomycetes. However, the population of tested bacteria was gradually depleted after completion of PM decomposition together with pathogenic bacteria and fungi due to full conversion of carbon component into other minerals, i.e. N, P, K etc. Taken together, these findings certainly pinpoints the effective role of bacterial suspension for composting sugarcane press mud which the eventually be used as organic manure.

  14. Changes in cecal microbiota and mucosal gene expression revealed new aspects of epizootic rabbit enteropathy.

    Directory of Open Access Journals (Sweden)

    Christine Bäuerl

    Full Text Available Epizootic Rabbit Enteropathy (ERE is a severe disease of unknown aetiology that mainly affects post-weaning animals. Its incidence can be prevented by antibiotic treatment suggesting that bacterial elements are crucial for the development of the disease. Microbial dynamics and host responses during the disease were studied. Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics, followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR. In healthy animals, cecal microbiota with or without antibiotic pretreatment was very similar and dominated by Alistipes and Ruminococcus. Proportions of both genera decreased in ERE rabbits whereas Bacteroides, Akkermansia and Rikenella increased, as well as Clostridium, γ-Proteobacteria and other opportunistic and pathogenic species. The ERE group displayed remarkable dysbiosis and reduced taxonomic diversity. Transcription rate of mucins and inflammatory cytokines was very high in ERE rabbits, except IL-2, and its analysis revealed the existence of two clearly different gene expression patterns corresponding to Inflammatory and (mucin Secretory Profiles. Furthermore, these profiles were associated to different bacterial species, suggesting that they may correspond to different stages of the disease. Other data obtained in this work reinforced the notion that ERE morbidity and mortality is possibly caused by an overgrowth of different pathogens in the gut of animals whose immune defence mechanisms seem not to be adequately responding.

  15. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

    Science.gov (United States)

    Wilms, Reinhard; Sass, Henrik; Köpke, Beate; Köster, Jürgen; Cypionka, Heribert; Engelen, Bert

    2006-04-01

    The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

  16. Rectal swabs for analysis of the intestinal microbiota.

    Directory of Open Access Journals (Sweden)

    Andries E Budding

    Full Text Available The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

  17. Data Mining of Lung Microbiota in Cystic Fibrosis Patients

    Science.gov (United States)

    Xiao, Yan; Wang, Jianwei; Qin, Xuemei

    2016-01-01

    The major therapeutic strategy used to treat exacerbated cystic fibrosis (CF) is antibiotic treatment. As this approach easily generates antibiotic-resistant strains of opportunistic bacteria, optimized antibiotic therapies are required to effectively control chronic and recurrent bacterial infections in CF patients. A promising future for the proper use of antibiotics is the management of lung microbiota. However, the impact of antibiotic treatments on CF microbiota and vice versa is not fully understood. This study analyzed 718 sputum samples from 18 previous studies to identify differences between CF and uninfected lung microbiota and to evaluate the effects of antibiotic treatments on exacerbated CF microbiota. A reference-based OTU (operational taxonomic unit) picking method was used to combine analyses of data generated using different protocols and platforms. Findings show that CF microbiota had greater richness and lower diversity in the community structure than uninfected control (NIC) microbiota. Specifically, CF microbiota showed higher levels of opportunistic bacteria and dramatically lower levels of commensal bacteria. Antibiotic treatment affected exacerbated CF microbiota notably but only transiently during the treatment period. Limited decrease of the dominant opportunistic bacteria and a dramatic decrease of commensal bacteria were observed during the antibiotic treatment for CF exacerbation. Simultaneously, low abundance opportunistic bacteria were thriving after the antibiotic treatment. The inefficiency of the current antibiotic treatment against major opportunistic bacteria and the detrimental effects on commensal bacteria indicate that the current empiric antibiotic treatment on CF exacerbation should be reevaluated and optimized. PMID:27741283

  18. Intestinal microbiota in pathophysiology and management of irritable bowel syndrome.

    Science.gov (United States)

    Lee, Kang Nyeong; Lee, Oh Young

    2014-07-21

    Irritable bowel syndrome (IBS) is a functional bowel disorder without any structural or metabolic abnormalities that sufficiently explain the symptoms, which include abdominal pain and discomfort, and bowel habit changes such as diarrhea and constipation. Its pathogenesis is multifactorial: visceral hypersensitivity, dysmotility, psychosocial factors, genetic or environmental factors, dysregulation of the brain-gut axis, and altered intestinal microbiota have all been proposed as possible causes. The human intestinal microbiota are composed of more than 1000 different bacterial species and 10(14) cells, and are essential for the development, function, and homeostasis of the intestine, and for individual health. The putative mechanisms that explain the role of microbiota in the development of IBS include altered composition or metabolic activity of the microbiota, mucosal immune activation and inflammation, increased intestinal permeability and impaired mucosal barrier function, sensory-motor disturbances provoked by the microbiota, and a disturbed gut-microbiota-brain axis. Therefore, modulation of the intestinal microbiota through dietary changes, and use of antibiotics, probiotics, and anti-inflammatory agents has been suggested as strategies for managing IBS symptoms. This review summarizes and discusses the accumulating evidence that intestinal microbiota play a role in the pathophysiology and management of IBS. PMID:25083061

  19. Systemic effects of gut microbiota and its relationship with disease and modulation

    OpenAIRE

    Ho, Jolie TK; Chan, Godfrey CF; Li, James CB

    2015-01-01

    The gut microbiota makes up the majority of the human bacterial population, and although the gut microbiota resides in the intestines, it is able to exert systemic effects. Therefore, many diseases and conditions could be impacted by the gut microbiota when its composition is imbalanced, otherwise known as dysbiosis. However, apart from understanding the illnesses, we must also try to understand the intestinal flora itself to move forward and develop potential treatments.

  20. Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection

    OpenAIRE

    Koh, Hyeon-Woo; Kim, Myun Soo; Lee, Jong-Soo; Kim, Hongik; Park, Soo-Je

    2015-01-01

    The gastrointestinal tract of mammals is a complex ecosystem with distinct environments and comprises hundreds of different types of bacterial cells. The gut microbiota may play a critical role in the gut health of the host. We herein attempted to identify a microbiota shift that may be affected by porcine epidemic diarrhea (PED). We observed significant differences in microbiota between the control and PED virus (PEDV)-infected groups at both the phylum and genus level. Most commensal bacter...

  1. Quantitative profiling of Drosophila melanogaster Dscam1 isoforms reveals no changes in splicing after bacterial exposure.

    Directory of Open Access Journals (Sweden)

    Sophie A O Armitage

    Full Text Available The hypervariable Dscam1 (Down syndrome cell adhesion molecule 1 gene can produce thousands of different ectodomain isoforms via mutually exclusive alternative splicing. Dscam1 appears to be involved in the immune response of some insects and crustaceans. It has been proposed that the diverse isoforms may be involved in the recognition of, or the defence against, diverse parasite epitopes, although evidence to support this is sparse. A prediction that can be generated from this hypothesis is that the gene expression of specific exons and/or isoforms is influenced by exposure to an immune elicitor. To test this hypothesis, we for the first time, use a long read RNA sequencing method to directly investigate the Dscam1 splicing pattern after exposing adult Drosophila melanogaster and a S2 cell line to live Escherichia coli. After bacterial exposure both models showed increased expression of immune-related genes, indicating that the immune system had been activated. However there were no changes in total Dscam1 mRNA expression. RNA sequencing further showed that there were no significant changes in individual exon expression and no changes in isoform splicing patterns in response to bacterial exposure. Therefore our studies do not support a change of D. melanogaster Dscam1 isoform diversity in response to live E. coli. Nevertheless, in future this approach could be used to identify potentially immune-related Dscam1 splicing regulation in other host species or in response to other pathogens.

  2. Profile of oritavancin and its potential in the treatment of acute bacterial skin structure infections

    Science.gov (United States)

    Mitra, Subhashis; Saeed, Usman; Havlichek, Daniel H; Stein, Gary E

    2015-01-01

    Oritavancin, a semisynthetic derivative of the glycopeptide antibiotic chloroeremomycin, received the US Food and Drug Administration approval for the treatment of acute bacterial skin and skin structure infections caused by susceptible Gram-positive bacteria in adults in August 2014. This novel second-generation semisynthetic lipoglycopeptide antibiotic has activity against a broad spectrum of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate S. aureus (VISA), and vancomycin-resistant Enterococcus. Oritavancin inhibits bacterial cell wall synthesis and is rapidly bactericidal against many Gram-positive pathogens. The long half-life of this drug enables a single-dose administration. Oritavancin is not metabolized in the body, and the unchanged drug is slowly excreted by the kidneys. In two large Phase III randomized, double-blind, clinical trials, oritavancin was found to be non-inferior to vancomycin in achieving the primary composite end point in the treatment of acute Gram-positive skin and skin structure infections. Adverse effects noted were mostly mild with nausea, headache, and vomiting being the most common reported side effects. Oritavancin has emerged as another useful antimicrobial agent for treatment of acute Gram-positive skin and skin structure infections, including those caused by MRSA and VISA. PMID:26185459

  3. Profile of oritavancin and its potential in the treatment of acute bacterial skin structure infections

    Directory of Open Access Journals (Sweden)

    Mitra S

    2015-07-01

    Full Text Available Subhashis Mitra, Usman Saeed, Daniel H Havlichek, Gary E Stein Department of Infectious Diseases, Michigan State University, East Lansing, MI, USA Abstract: Oritavancin, a semisynthetic derivative of the glycopeptide antibiotic chloroeremomycin, received the US Food and Drug Administration approval for the treatment of acute bacterial skin and skin structure infections caused by susceptible Gram-positive bacteria in adults in August 2014. This novel second-generation semisynthetic lipoglycopeptide antibiotic has activity against a broad spectrum of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA, vancomycin-intermediate S. aureus (VISA, and vancomycin-resistant Enterococcus. Oritavancin inhibits bacterial cell wall synthesis and is rapidly bactericidal against many Gram-positive pathogens. The long half-life of this drug enables a single-dose administration. Oritavancin is not metabolized in the body, and the unchanged drug is slowly excreted by the kidneys. In two large Phase III randomized, double-blind, clinical trials, oritavancin was found to be non-inferior to vancomycin in achieving the primary composite end point in the treatment of acute Gram-positive skin and skin structure infections. Adverse effects noted were mostly mild with nausea, headache, and vomiting being the most common reported side effects. Oritavancin has emerged as another useful antimicrobial agent for treatment of acute Gram-positive skin and skin structure infections, including those caused by MRSA and VISA. Keywords: antibiotic, Gram-positive bacteria, MRSA, VRSA, vancomycin, MIC

  4. Defining microbiota for developing new probiotics

    OpenAIRE

    Collado, Maria Carmen; Bäuerl, Christine; Pérez-Martínez, Gaspar

    2012-01-01

    The human body harbors complex communities of microbes that play a prominent role in human health. Detailed characterization of the microbiota in the target population forms the basis of probiotic use. Probiotics are defined as live bacterial preparations with clinically documented health effects in humans and independently of their genus and species, probiotic strains are unique and their beneficial properties on human health have to be assessed in a case-by-case manner. Understanding the me...

  5. Host Genetic and Environmental Effects on Mouse Cecum Microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, James H [ORNL; Foster, Carmen M [ORNL; Vishnivetskaya, Tatiana A [ORNL; Campbell, Alisha G [ORNL; Yang, Zamin Koo [ORNL; Wymore, Ann [ORNL; Palumbo, Anthony Vito [ORNL; Podar, Mircea [ORNL

    2012-01-01

    The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

  6. Microbiota-induced obesity requires farnesoid X receptor

    DEFF Research Database (Denmark)

    Parséus, Ava; Sommer, Nina; Sommer, Felix;

    2016-01-01

    OBJECTIVE: The gut microbiota has been implicated as an environmental factor that modulates obesity, and recent evidence suggests that microbiota-mediated changes in bile acid profiles and signalling through the bile acid nuclear receptor farnesoid X receptor (FXR) contribute to impaired host...... metabolism. Here we investigated if the gut microbiota modulates obesity and associated phenotypes through FXR. DESIGN: We fed germ-free (GF) and conventionally raised (CONV-R) wild-type and Fxr-/- mice a high-fat diet (HFD) for 10 weeks. We monitored weight gain and glucose metabolism and analysed the gut...... steatosis and expression of genes involved in lipid uptake. By transferring the caecal microbiota from HFD-fed Fxr-/- and wild-type mice into GF mice, we showed that the obesity phenotype was transferable. CONCLUSIONS: Our results indicate that the gut microbiota promotes diet-induced obesity and associated...

  7. The physico-chemical properties of dietary fibre determine metabolic responses, short-chain Fatty Acid profiles and gut microbiota composition in rats fed low- and high-fat diets.

    Directory of Open Access Journals (Sweden)

    Frida Fåk

    Full Text Available The aim of this study was to investigate how physico-chemical properties of two dietary fibres, guar gum and pectin, affected weight gain, adiposity, lipid metabolism, short-chain fatty acid (SCFA profiles and the gut microbiota in male Wistar rats fed either low- or high-fat diets for three weeks. Both pectin and guar gum reduced weight gain, adiposity, liver fat and blood glucose levels in rats fed a high-fat diet. Methoxylation degree of pectin (low, LM and high (HM and viscosity of guar gum (low, medium or high resulted in different effects in the rats, where total blood and caecal amounts of SCFA were increased with guar gum (all viscosities and with high methoxylated (HM pectin. However, only guar gum with medium and high viscosity increased the levels of butyric acid in caecum and blood. Both pectin and guar gum reduced cholesterol, liver steatosis and blood glucose levels, but to varying extent depending on the degree of methoxylation and viscosity of the fibres. The medium viscosity guar gum was the most effective preparation for prevention of diet-induced hyperlipidaemia and liver steatosis. Caecal abundance of Akkermansia was increased with high-fat feeding and with HM pectin and guar gum of all viscosities tested. Moreover, guar gum had distinct bifidogenic effects independent of viscosity, increasing the caecal abundance of Bifidobacterium ten-fold. In conclusion, by tailoring the viscosity and possibly also the degree of methoxylation of dietary fibre, metabolic effects may be optimized, through a targeted modulation of the gut microbiota and its metabolites.

  8. Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

    Science.gov (United States)

    Zackular, Joseph P.; Baxter, Nielson T.

    2015-01-01

    ABSTRACT There is growing evidence that individuals with colonic adenomas and carcinomas harbor a distinct microbiota. Alterations to the gut microbiota may allow the outgrowth of bacterial populations that induce genomic mutations or exacerbate tumor-promoting inflammation. In addition, it is likely that the loss of key bacterial populations may result in the loss of protective functions that are normally provided by the microbiota. We explored the role of the gut microbiota in colon tumorigenesis by using an inflammation-based murine model. We observed that perturbing the microbiota with different combinations of antibiotics reduced the number of tumors at the end of the model. Using the random forest machine learning algorithm, we successfully modeled the number of tumors that developed over the course of the model on the basis of the initial composition of the microbiota. The timing of antibiotic treatment was an important determinant of tumor outcome, as colon tumorigenesis was arrested by the use of antibiotics during the early inflammation period of the murine model. Together, these results indicate that it is possible to predict colon tumorigenesis on the basis of the composition of the microbiota and that altering the gut microbiota can alter the course of tumorigenesis. IMPORTANCE Mounting evidence indicates that alterations to the gut microbiota, the complex community of bacteria that inhabits the gastrointestinal tract, are strongly associated with the development of colorectal cancer. We used antibiotic perturbations to a murine model of inflammation-driven colon cancer to generate eight starting communities that resulted in various severities of tumorigenesis. Furthermore, we were able to quantitatively predict the final number of tumors on the basis of the initial composition of the gut microbiota. These results further bolster the evidence that the gut microbiota is involved in mediating the development of colorectal cancer. As a final proof of

  9. Aerobic bacterial profile and antibiotic resistance in patients with diabetic foot infections

    Directory of Open Access Journals (Sweden)

    Michele Cezimbra Perim

    2015-10-01

    Full Text Available ABSTRACTINTRODUCTION: This study aimed to determine the frequencies of bacterial isolates cultured from diabetic foot infections and assess their resistance and susceptibility to commonly used antibiotics.METHODS: This prospective study included 41 patients with diabetic foot lesions. Bacteria were isolated from foot lesions, and their antibiotic susceptibility pattern was determined using the Kirby-Bauer disk diffusion method and/or broth method [minimum inhibitory concentration (MIC].RESULTS: The most common location of ulceration was the toe (54%, followed by the plantar surface (27% and dorsal portion (19%. A total of 89 bacterial isolates were obtained from 30 patients. The infections were predominantly due to Gram-positive bacteria and polymicrobial bacteremia. The most commonly isolated Gram-positive bacteria were Staphylococcus aureus, followed by Staphylococcus saprophyticus, Staphylococcus epidermidis, Streptococcus agalactiae, and Streptococcus pneumoniae. The most commonly isolated Gram-negative bacteria were Proteus spp. and Enterobacterspp., followed by Escherichia coli, Pseudomonasspp., and Citrobacterspp. Nine cases of methicillin-resistant Staphylococcus aureus (MRSA had cefoxitin resistance, and among these MRSA isolates, 3 were resistant to vancomycin with the MIC technique. The antibiotic imipenem was the most effective against both Gram-positive and Gram-negative bacteria, and gentamicin was effective against Gram-negative bacteria.CONCLUSIONS: The present study confirmed the high prevalence of multidrug-resistant pathogens in diabetic foot ulcers. It is necessary to evaluate the different microorganisms infecting the wound and to know the antibiotic susceptibility patterns of the isolates from the infected wound. This knowledge is crucial for planning treatment with the appropriate antibiotics, reducing resistance patterns, and minimizing healthcare costs.

  10. Variability of the Sheep Lung Microbiota

    Science.gov (United States)

    Wright, Steven; Pollock, Jolinda; Tennant, Peter; Collie, David; McLachlan, Gerry

    2016-01-01

    ABSTRACT Sequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n = 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota. IMPORTANCE Until recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human

  11. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

    DEFF Research Database (Denmark)

    Adamberg, Kaarel; Tomson, Katrin; Talve, Tiina;

    2015-01-01

    The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry...

  12. Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili

    NARCIS (Netherlands)

    Tytgat, Hanne; Teijlingen, van N.H.; Sullan, R.M.; Douillard, F.P.; Rasinkangas, P.; Messing, M.; Reunanen, J.; Satokari, R.; Vanderleyden, J.; Dufrêne, Y.F.; Geijtenbeek, T.B.H.; Vos, de W.M.; Lebeer, S.

    2016-01-01

    Mapping of the microbial molecules underlying microbiota-host interactions is key to understand how microbiota preserve mucosal homeostasis. A pivotal family of such bacterial molecules are pili. Pili are proteinaceous cell wall appendages with a well-documented role in adhesion, whilst their role i

  13. The Gut Microbiota and their Metabolites : Potential Implications for the Host Epigenome

    NARCIS (Netherlands)

    Mischke, Mona; Plösch, Torsten

    2016-01-01

    The gut microbiota represents a metabolically active biomass of up to 2 kg in adult humans. Microbiota-derived molecules significantly contribute to the host metabolism. Large amounts of bacterial metabolites are taken up by the host and are subsequently utilized by the human body. For instance, sho

  14. Microbiota and the gut-brain axis.

    Science.gov (United States)

    Bienenstock, John; Kunze, Wolfgang; Forsythe, Paul

    2015-08-01

    Changes in gut microbiota can modulate the peripheral and central nervous systems, resulting in altered brain functioning, and suggesting the existence of a microbiota gut-brain axis. Diet can also change the profile of gut microbiota and, thereby, behavior. Effects of bacteria on the nervous system cannot be disassociated from effects on the immune system since the two are in constant bidirectional communication. While the composition of the gut microbiota varies greatly among individuals, alterations to the balance and content of common gut microbes may affect the production of molecules such as neurotransmitters, e.g., gamma amino butyric acid, and the products of fermentation, e.g., the short chain fatty acids butyrate, propionate, and acetate. Short chain fatty acids, which are pleomorphic, especially butyrate, positively influence host metabolism by promoting glucose and energy homeostasis, regulating immune responses and epithelial cell growth, and promoting the functioning of the central and peripheral nervous systems. In the future, the composition, diversity, and function of specific probiotics, coupled with similar, more detailed knowledge about gut microbiota, will potentially help in developing more effective diet- and drug-based therapies. PMID:26175487

  15. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    Science.gov (United States)

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.

  16. Bacterial composition in whole saliva from patients with severe hyposalivation

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Fiehn, Nils-Erik;

    2016-01-01

    OBJECTIVE: The purpose of this study was to compare the microbiota of stimulated whole saliva samples from patients with severe hyposalivation to samples from individuals with normal whole saliva flow rates. It was hypothesized that the two groups differ with regard to salivary bacterial profiles...... of stimulated whole saliva samples was characterized by HOMINGS. RESULTS: The two groups had comparable caries experience measured by decayed-missed-filled-surfaces/-teeth and decayed-missed-filled-root surfaces as well as active caries lesions. In addition, no single probe-target was present with a significant...

  17. Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection.

    Directory of Open Access Journals (Sweden)

    Yang Song

    Full Text Available Clostridium difficile causes antibiotic-associated diarrhea and pseudomembraneous colitis and is responsible for a large and increasing fraction of hospital-acquired infections. Fecal microbiota transplantation (FMT is an alternate treatment option for recurrent C. difficile infection (RCDI refractory to antibiotic therapy. It has recently been discussed favorably in the clinical and scientific communities and is receiving increasing public attention. However, short- and long-term health consequences of FMT remain a concern, as the effects of the transplanted microbiota on the patient remain unknown. To shed light on microbial events associated with RCDI and treatment by FMT, we performed fecal microbiota analysis by 16S rRNA gene amplicon pyrosequencing of 14 pairs of healthy donors and RCDI patients treated successfully by FMT. Post-FMT patient and healthy donor samples collected up to one year after FMT were studied longitudinally, including one post-FMT patient with antibiotic-associated relapse three months after FMT. This analysis allowed us not only to confirm prior reports that RCDI is associated with reduced diversity and compositional changes in the fecal microbiota, but also to characterize previously undocumented post-FMT microbiota dynamics. Members of the Streptococcaceae, Enterococcaceae, or Enterobacteriaceae were significantly increased and putative butyrate producers, such as Lachnospiraceae and Ruminococcaceae were significantly reduced in samples from RCDI patients before FMT as compared to post-FMT patient and healthy donor samples. RCDI patient samples showed more case-specific variations than post-FMT patient and healthy donor samples. However, none of the bacterial groups were invariably associated with RCDI or successful treatment by FMT. Overall microbiota compositions in post-FMT patients, specifically abundances of the above-mentioned Firmicutes, continued to change for at least 16 weeks after FMT, suggesting that

  18. Galacto-oligosaccharides attenuate renal injury with microbiota modification.

    Science.gov (United States)

    Furuse, Satoshi U; Ohse, Takamoto; Jo-Watanabe, Airi; Shigehisa, Akira; Kawakami, Koji; Matsuki, Takahiro; Chonan, Osamu; Nangaku, Masaomi

    2014-07-01

    Tubulointerstitial injury is central to the progression of end-stage renal disease. Recent studies have revealed that one of the most investigated uremic toxins, indoxyl sulfate (IS), caused tubulointerstitial injury through oxidative stress and endoplasmic reticulum (ER) stress. Because indole, the precursor of IS, is synthesized from dietary tryptophan by the gut microbiota, we hypothesized that the intervention targeting the gut microbiota in kidney disease with galacto-oligosaccharides (GOS) would attenuate renal injury. After 2 weeks of GOS administration for 5/6 nephrectomized (Nx) or sham-operated (Sham) rats, cecal indole and serum IS were measured, renal injury was evaluated, and the effects of GOS on the gut microbiota were examined using pyrosequencing methods. Cecal indole and serum IS were significantly decreased and renal injury was improved with decreased infiltrating macrophages in GOS-treated Nx rats. The expression levels of ER stress markers and apoptosis were significantly increased in the Nx rats and decreased with GOS. The microbiota analysis indicated that GOS significantly increased three bacterial families and decreased five families in the Nx rats. In addition, the analysis also revealed that the bacterial family Clostridiaceae was significantly increased in the Nx rats compared with the Sham rats and decreased with GOS. Taken altogether, our data show that GOS decreased cecal indole and serum IS, attenuated renal injury, and modified the gut microbiota in the Nx rats, and that the gut microbiota were altered in kidney disease. GOS could be a novel therapeutic agent to protect against renal injury.

  19. Bacterial Profile of Blood Stream Infection and Antibiotic Resistance Pattern of Isolates.

    Directory of Open Access Journals (Sweden)

    Usha Arora, Pushpa Devi

    2007-10-01

    Full Text Available Blood samples from 2542 clinically diagnosed cases of septicemia were processed. Out of these 946(76.55% were from Pediatric Department and rest from other Departments. Growth was obtained in509(20.02% cases . Candida spp were isolated from 23 (4.57 cases Out of 486 bacterial isolates 52.67% were gram positive bacteria whereas 47.33% were gram negative bacilli . Staph aureus 133 (27.37%wasthe predominant organisms followed by CONS 98 (20.1%. Amongst gram negative organismsEnterobacter 69 (14.19 % was the most predominant followed by Esch coli 45 (9.27 % Pseudomonas 37(7.62 % and Acinetobacter spp 34 (6.69 %. Amongst gram positive organisms maximum resistancewas seen with ampicillin (74.61% and erythromycin (69.67 %. Most of the gram negative bacilli wereMDR (71%. Maximum resistance was observed with ampicillin (86.1% cephalexin (68.07% andpiperacillin (57.71%. Most successful drugs were amikacin,gentamicin and cefotaxime. 34.35% of theisolates were ESBL producers.

  20. Predictive modeling of gingivitis severity and susceptibility via oral microbiota.

    Science.gov (United States)

    Huang, Shi; Li, Rui; Zeng, Xiaowei; He, Tao; Zhao, Helen; Chang, Alice; Bo, Cunpei; Chen, Jie; Yang, Fang; Knight, Rob; Liu, Jiquan; Davis, Catherine; Xu, Jian

    2014-09-01

    Predictive modeling of human disease based on the microbiota holds great potential yet remains challenging. Here, 50 adults underwent controlled transitions from naturally occurring gingivitis, to healthy gingivae (baseline), and to experimental gingivitis (EG). In diseased plaque microbiota, 27 bacterial genera changed in relative abundance and functional genes including 33 flagellar biosynthesis-related groups were enriched. Plaque microbiota structure exhibited a continuous gradient along the first principal component, reflecting transition from healthy to diseased states, which correlated with Mazza Gingival Index. We identified two host types with distinct gingivitis sensitivity. Our proposed microbial indices of gingivitis classified host types with 74% reliability, and, when tested on another 41-member cohort, distinguished healthy from diseased individuals with 95% accuracy. Furthermore, the state of the microbiota in naturally occurring gingivitis predicted the microbiota state and severity of subsequent EG (but not the state of the microbiota during the healthy baseline period). Because the effect of disease is greater than interpersonal variation in plaque, in contrast to the gut, plaque microbiota may provide advantages in predictive modeling of oral diseases.

  1. Microbiota-Independent Ameliorative Effects of Antibiotics on Spontaneous Th2-Associated Pathology of the Small Intestine.

    Science.gov (United States)

    Han, Daehee; Walsh, Matthew C; Kim, Kwang Soon; Hong, Sung-Wook; Lee, Junyoung; Yi, Jaeu; Rivas, Gloriany; Surh, Charles D; Choi, Yongwon

    2015-01-01

    We have previously generated a mouse model of spontaneous Th2-associated disease of the small intestine called TRAF6ΔDC, in which dendritic cell (DC)-intrinsic expression of the signaling mediator TRAF6 is ablated. Interestingly, broad-spectrum antibiotic treatment ameliorates TRAF6ΔDC disease, implying a role for commensal microbiota in disease development. However, the relationship between the drug effects and commensal microbiota status remains to be formally demonstrated. To directly assess this relationship, we have now generated TRAF6ΔDC bone marrow chimera mice under germ-free (GF) conditions lacking commensal microbiota, and found, unexpectedly, that Th2-associated disease is actually exacerbated in GF TRAF6ΔDC mice compared to specific pathogen-free (SPF) TRAF6ΔDC mice. At the same time, broad-spectrum antibiotic treatment of GF TRAF6ΔDC mice has an ameliorative effect similar to that observed in antibiotics-treated SPF TRAF6ΔDC mice, implying a commensal microbiota-independent effect of broad-spectrum antibiotic treatment. We further found that treatment of GF TRAF6ΔDC mice with broad-spectrum antibiotics increases Foxp3+ Treg populations in lymphoid organs and the small intestine, pointing to a possible mechanism by which treatment may directly exert an immunomodulatory effect. To investigate links between the exacerbated phenotype of the small intestines of GF TRAF6ΔDC mice and local microbiota, we performed microbiotic profiling of the luminal contents specifically within the small intestines of diseased TRAF6ΔDC mice, and, when compared to co-housed control mice, found significantly increased total bacterial content characterized by specific increases in Firmicutes Lactobacillus species. These data suggest a protective effect of Firmicutes Lactobacillus against the spontaneous Th2-related inflammation of the small intestine of the TRAF6ΔDC model, and may represent a potential mechanism for related disease phenotypes.

  2. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  3. Characterization of Bacterial Strains Isolated Through Microbial Profiling of Urine Samples

    Directory of Open Access Journals (Sweden)

    Poulomi Nandy

    2007-01-01

    Full Text Available The present study was conducted to determine the microbial profile in urine samples. Differential and selective chromogenic culture media were used for the rapid detection, identification and enumeration of urinary tract pathogens namely, E. coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, Enterococcus faecalis, Proteus mirabilis. Urine samples of normal healthy individuals as well as patients with Urinary Tract Infection (UTI were screened on hicrome agar plates. The cultivable bacteria present in urine were isolated based on chromogenic detection. Antibiotic sensitivity assay, morphological characterization and biochemical tests, namely protease, oxidase, catalase, lipase, DNase and lecithinase assay were performed with the 15 isolates obtained from urine samples. The molecular analyses of the isolates were done through partial sequencing of the 16SrDNA gene; six of them were found to be novel and submitted in GenBank under the accession numbers EF644491-96. Phylogenetic tree of the isolates were constructed by neighbour joining method.

  4. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Bardow, Allan;

    2016-01-01

    BACKGROUND AND OBJECTIVE: The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial...... composition may not reflect the more natural, unstimulated state. The purpose of this study was to validate whether stimulated saliva is an adequate surrogate for unstimulated saliva in determining salivary microbiomes. DESIGN: Unstimulated (n=20) and stimulated (n=20) saliva samples were collected from 20...... for multiple comparison, cluster analysis, principal component analysis, and correspondence analysis. RESULTS: From a total of 40 saliva samples, 496 probe targets were identified with a mean number of targets per sample of 203 (range: 146-303), and a mean number of probe targets of 206 and 200 in unstimulated...

  5. Investigation of parasitic and bacterial diseases in pigs with analysis of hematological and serum biochemical profile.

    Science.gov (United States)

    Kalai, K; Nehete, R S; Ganguly, S; Ganguli, M; Dhanalakshmi, S; Mukhopadhayay, S K

    2012-04-01

    The present study was undertaken to evaluate various disease conditions prevalent in slaughtered pigs and zoonotic importance. The study was conducted on two hundred non-descript pigs slaughtered at an organized slaughter house, Mumbai. The animals included in the study were randomly selected. Post mortem examination of the animals was performed to note various disease conditions and tissues were collected for histopathology. Direct examination of stool was found negative for parasites. Gross and microscopical examination revealed presence of Ascarops strongylina, Sarcocyst, Hydatid cyst, Cysticercus cellulosae, Ascaris suum and Cysticercus tenuicollis, along with bacteria like Salmonella, Pseudomonas, Shigella, Streptococci, Proteus and Pasteurella spp. were isolated. Indirect ELISA was performed for detection of antibody titer in the pig serum against classical swine fever. Studies on hematological and serum biochemical profile revealed decreased total protein concentration and globulin level with leukocytosis and neutrophilia and in parasitic infections eosinophilia was evident. PMID:23542948

  6. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults

    DEFF Research Database (Denmark)

    Larsen, Nadja; Vogensen, Finn Kvist; van der Berg, Franciscus Winfried J;

    2010-01-01

    Background Recent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control...... = 0.04). Conclusions The results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies...... to control metabolic diseases by modifying the gut microbiota....

  7. Functional Expression of Dental Plaque Microbiota

    Directory of Open Access Journals (Sweden)

    Scott Norman Peterson

    2014-08-01

    Full Text Available Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota’s transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.

  8. Culture-independent bacterial community profiling of carbon dioxide treated raw milk.

    Science.gov (United States)

    Lo, Raquel; Turner, Mark S; Weeks, Mike; Bansal, Nidhi

    2016-09-16

    Due to technical simplicity and strong inhibition against the growth of psychrotrophic bacteria in milk, CO2 treatment has emerged as an attractive processing aid to increase the storage time of raw milk before downstream processing. However, it is yet to be adopted by the industry. In order to further explore the suitability of CO2 treatment for raw milk processing, the bacterial populations of carbonated raw milk collected locally from five different sources in Australia were analysed with next-generation sequencing. Growth inhibition by CO2 was confirmed, with spoilage delayed by at least 7days compared with non-carbonated controls. All non-carbonated controls were spoiled by Gammaproteobacteria, namely Pseudomonas fluorescens group bacteria, Serratia and Erwinia. Two out of the five carbonated samples shared the same spoilage bacteria as their corresponding controls. The rest of the three carbonated samples were spoiled by the lactic acid bacterium (LAB) Leuconostoc. This is consistent with higher tolerance of LAB towards CO2 and selection of LAB in meat products stored in CO2-enriched modified atmosphere packaging. No harmful bacteria were found to be selected by CO2. LAB are generally regarded as safe (GRAS), thus the selection for Leuconostoc by CO2 in some of the samples poses no safety concern. In addition, we have confirmed previous findings that 454 pyrosequencing and Illumina sequencing of 16S rRNA gene amplicons from the same sample yield highly similar results. This supports comparison of results obtained with the two different sequencing platforms, which may be necessary considering the imminent discontinuation of 454 pyrosequencing. PMID:27344229

  9. Human gut microbiota: repertoire and variations.

    Science.gov (United States)

    Lagier, Jean-Christophe; Million, Matthieu; Hugon, Perrine; Armougom, Fabrice; Raoult, Didier

    2012-01-01

    The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species, the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea, and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics, or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.

  10. Childhood obesity: a role for gut microbiota?

    Science.gov (United States)

    Sanchez, Marina; Panahi, Shirin; Tremblay, Angelo

    2014-12-23

    Obesity is a serious public health issue affecting both children and adults. Prevention and management of obesity is proposed to begin in childhood when environmental factors exert a long-term effect on the risk for obesity in adulthood. Thus, identifying modifiable factors may help to reduce this risk. Recent evidence suggests that gut microbiota is involved in the control of body weight, energy homeostasis and inflammation and thus, plays a role in the pathophysiology of obesity. Prebiotics and probiotics are of interest because they have been shown to alter the composition of gut microbiota and to affect food intake and appetite, body weight and composition and metabolic functions through gastrointestinal pathways and modulation of the gut bacterial community. As shown in this review, prebiotics and probiotics have physiologic functions that contribute to changes in the composition of gut microbiota, maintenance of a healthy body weight and control of factors associated with childhood obesity through their effects on mechanisms controlling food intake, fat storage and alterations in gut microbiota.

  11. Human gut microbiota: repertoire and variations

    Directory of Open Access Journals (Sweden)

    Jean-Christophe eLagier

    2012-11-01

    Full Text Available The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.

  12. Childhood Obesity: A Role for Gut Microbiota?

    Directory of Open Access Journals (Sweden)

    Marina Sanchez

    2014-12-01

    Full Text Available Obesity is a serious public health issue affecting both children and adults. Prevention and management of obesity is proposed to begin in childhood when environmental factors exert a long-term effect on the risk for obesity in adulthood. Thus, identifying modifiable factors may help to reduce this risk. Recent evidence suggests that gut microbiota is involved in the control of body weight, energy homeostasis and inflammation and thus, plays a role in the pathophysiology of obesity. Prebiotics and probiotics are of interest because they have been shown to alter the composition of gut microbiota and to affect food intake and appetite, body weight and composition and metabolic functions through gastrointestinal pathways and modulation of the gut bacterial community. As shown in this review, prebiotics and probiotics have physiologic functions that contribute to changes in the composition of gut microbiota, maintenance of a healthy body weight and control of factors associated with childhood obesity through their effects on mechanisms controlling food intake, fat storage and alterations in gut microbiota.

  13. Effects of probiotics strain MA18/5M and subsp. strain SB-CNCM I-1079 on fecal and intestinal microbiota of nursing and weanling piglets.

    Science.gov (United States)

    Brousseau, J-P; Talbot, G; Beaudoin, F; Lauzon, K; Roy, D; Lessard, M

    2015-11-01

    In this study, the influence of (PA) and subsp. (SCB) on fecal and intestinal microbiota of piglets during lactation and after weaning was monitored. Forty sows and their litters were used and allocated to the following dietary treatments: 1) PA, 2) SCB, 3) a mixture of the 2 probiotics (PA+SCB), 4) antibiotics (ATB), and 5) control (CTRL). Four weeks before parturition, probiotic-treated sows started receiving a daily probiotic dose of at least 2.5 × 10 cfu mixed in 500 g of feed until the end of lactation. The other groups were fed a diet without probiotics and ATB. Two days after birth, piglets received, daily, 1 × 10 cfu of the same probiotics as their mother. At weaning (d 21), these piglets were fed a basal diet enriched with the same probiotics whereas piglets from untreated litters were fed the basal diet with or without ATB. Two piglets per litter were randomly chosen to evaluate the influence of treatments on fecal microbial composition (d 10 and 28) and on ileum and colon microbiota at d 37. The microbiota was characterized by culture on selective media and by 16S rRNA gene diversity assessment using the terminal RFLP technique and clone library analysis to evaluate diversity index and phylum affiliation. Terminal RFLP profiles were also analyzed to determine differences in microbial composition between animals receiving different treatments and to identify diet-specific terminal restriction fragments (TRF) using pairwise multiresponse permutation procedures (MRPP) and indicator species analysis. Before weaning, administration of probiotics to sows and piglets had minor effect on fecal microbiota of piglets. Most modulatory effects of probiotics on ileum and colon microbiota were observed on d 37. Results revealed that PA or ATB treatments reduced ileal microbiota diversity compared with the CTRL ( < 0.05) and promoted the establishment of Firmicutes whereas SCB consumption positively influenced the establishment of the Porphyromonadaceae and

  14. Microbiota influences morphology and reproduction of the brown alga Ectocarpus sp.

    Directory of Open Access Journals (Sweden)

    Javier Esteban Tapia

    2016-02-01

    Full Text Available Associated microbiota play crucial roles in health and disease of higher organisms. For macroalgae, some associated bacteria exert beneficial effects on nutrition, morphogenesis and growth. However, current knowledge on macroalgae-microbiota interactions is mostly based on studies on green and red seaweeds. In this study, we report that when cultured under axenic conditions, the filamentous brown algal model Ectocarpus sp. loses its branched morphology and grows with a small ball-like appearance. Nine strains of periphytic bacteria isolated from Ectocarpus sp. unialgal cultures were identified by 16S rRNA sequencing, and assessed for their effect on morphology, reproduction and the metabolites secreted by axenic Ectocarpus sp. Six of these isolates restored morphology and reproduction features of axenic Ectocarpus sp. Bacteria-algae co-culture supernatants, but not the supernatant of the corresponding bacterium growing alone, also recovered morphology and reproduction of the alga. Furthermore, colonization of axenic Ectocarpus sp. with a single bacterial isolate impacted significantly the metabolites released by the alga. These results show that the branched typical morphology and the individuals produced by Ectocarpus sp. are strongly dependent on the presence of bacteria, while the bacterial effect on the algal exometabolome profile reflects the impact of bacteria on the whole physiology of this alga.

  15. Molecular characterization of the stomach microbiota in patients with gastric cancer and controls

    Energy Technology Data Exchange (ETDEWEB)

    Dicksved, J.; Lindberg, M.; Rosenquist, M.; Enroth, H.; Jansson, J.K.; Engstrand, L.

    2009-01-15

    Persistent infection of the gastric mucosa by Helicobacter pylori, can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk in developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer, however their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with five dyspeptic controls using the molecular profiling approach, terminal-restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the gastric cancer microbiota was instead dominated by different species of the genera Streptococcus, Lactobacillus, Veillonella and Prevotella. The respective role of these species in development of gastric cancer remains to be determined.

  16. Defining microbiota for developing new probiotics.

    Science.gov (United States)

    Collado, Maria Carmen; Bäuerl, Christine; Pérez-Martínez, Gaspar

    2012-01-01

    The human body harbors complex communities of microbes that play a prominent role in human health. Detailed characterization of the microbiota in the target population forms the basis of probiotic use. Probiotics are defined as live bacterial preparations with clinically documented health effects in humans, and independent of their genus and species, probiotic strains are unique and their beneficial properties on human health have to be assessed in a case-by-case manner. Understanding the mechanisms by which probiotics influence microbiota would facilitate the use of probiotics for both dietary management and reduction in risk of specific diseases. The development of high throughput sequencing methods has allowed metagenomic approaches to study the human microbiome. These efforts are starting to generate an inventory of bacterial taxons and functional features bound to particular health or disease status that allow inferring aspects of the microbiome's function. In the future, this information will allow the rational design of dietary interventions aimed to improve consumer's health via modulation of the microbiota.

  17. Defining microbiota for developing new probiotics

    Science.gov (United States)

    Collado, Maria Carmen; Bäuerl, Christine; Pérez-Martínez, Gaspar

    2012-01-01

    The human body harbors complex communities of microbes that play a prominent role in human health. Detailed characterization of the microbiota in the target population forms the basis of probiotic use. Probiotics are defined as live bacterial preparations with clinically documented health effects in humans, and independent of their genus and species, probiotic strains are unique and their beneficial properties on human health have to be assessed in a case-by-case manner. Understanding the mechanisms by which probiotics influence microbiota would facilitate the use of probiotics for both dietary management and reduction in risk of specific diseases. The development of high throughput sequencing methods has allowed metagenomic approaches to study the human microbiome. These efforts are starting to generate an inventory of bacterial taxons and functional features bound to particular health or disease status that allow inferring aspects of the microbiome's function. In the future, this information will allow the rational design of dietary interventions aimed to improve consumer's health via modulation of the microbiota. PMID:23990820

  18. Defining microbiota for developing new probiotics

    Directory of Open Access Journals (Sweden)

    Maria Carmen Collado

    2012-06-01

    Full Text Available The human body harbors complex communities of microbes that play a prominent role in human health. Detailed characterization of the microbiota in the target population forms the basis of probiotic use. Probiotics are defined as live bacterial preparations with clinically documented health effects in humans, and independent of their genus and species, probiotic strains are unique and their beneficial properties on human health have to be assessed in a case-by-case manner. Understanding the mechanisms by which probiotics influence microbiota would facilitate the use of probiotics for both dietary management and reduction in risk of specific diseases. The development of high throughput sequencing methods has allowed metagenomic approaches to study the human microbiome. These efforts are starting to generate an inventory of bacterial taxons and functional features bound to particular health or disease status that allow inferring aspects of the microbiome's function. In the future, this information will allow the rational design of dietary interventions aimed to improve consumer's health via modulation of the microbiota.

  19. A key genetic factor for fucosyllactose utilization affects infant gut microbiota development

    Science.gov (United States)

    Matsuki, Takahiro; Yahagi, Kana; Mori, Hiroshi; Matsumoto, Hoshitaka; Hara, Taeko; Tajima, Saya; Ogawa, Eishin; Kodama, Hiroko; Yamamoto, Kazuya; Yamada, Takuji; Matsumoto, Satoshi; Kurokawa, Ken

    2016-01-01

    Recent studies have demonstrated that gut microbiota development influences infants' health and subsequent host physiology. However, the factors shaping the development of the microbiota remain poorly understood, and the mechanisms through which these factors affect gut metabolite profiles have not been extensively investigated. Here we analyse gut microbiota development of 27 infants during the first month of life. We find three distinct clusters that transition towards Bifidobacteriaceae-dominant microbiota. We observe considerable differences in human milk oligosaccharide utilization among infant bifidobacteria. Colonization of fucosyllactose (FL)-utilizing bifidobacteria is associated with altered metabolite profiles and microbiota compositions, which have been previously shown to affect infant health. Genome analysis of infants' bifidobacteria reveals an ABC transporter as a key genetic factor for FL utilization. Thus, the ability of bifidobacteria to utilize FL and the presence of FL in breast milk may affect the development of the gut microbiota in infants, and might ultimately have therapeutic implications. PMID:27340092

  20. Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review.

    Science.gov (United States)

    Choi, Ki Young; Lee, Tae Kwon; Sul, Woo Jun

    2015-09-01

    Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future. PMID:26323514

  1. Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review.

    Science.gov (United States)

    Choi, Ki Young; Lee, Tae Kwon; Sul, Woo Jun

    2015-09-01

    Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

  2. The microbiota and microbiome in aging: potential implications in health and age-related diseases.

    Science.gov (United States)

    Zapata, Heidi J; Quagliarello, Vincent J

    2015-04-01

    Advances in bacterial deoxyribonucleic acid sequencing allow for characterization of the human commensal bacterial community (microbiota) and its corresponding genome (microbiome). Surveys of healthy adults reveal that a signature composite of bacteria characterizes each unique body habitat (e.g., gut, skin, oral cavity, vagina). A myriad of clinical changes, including a basal proinflammatory state (inflamm-aging), that directly interface with the microbiota of older adults and enhance susceptibility to disease accompany aging. Studies in older adults demonstrate that the gut microbiota correlates with diet, location of residence (e.g., community dwelling, long-term care settings), and basal level of inflammation. Links exist between the microbiota and a variety of clinical problems plaguing older adults, including physical frailty, Clostridium difficile colitis, vulvovaginal atrophy, colorectal carcinoma, and atherosclerotic disease. Manipulation of the microbiota and microbiome of older adults holds promise as an innovative strategy to influence the development of comorbidities associated with aging.

  3. Molecular analysis of the gut microbiota of identical twins with Crohn's disease

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Janet; Dicksved, Johan; Halfvarson, Jonas; Rosenquist, Magnus; Jarnerot, Gunnar; Tysk, Curt; Apajalahti, Juha; Engstrand, Lars; Jansson, Janet K.

    2008-03-14

    Increasing evidence suggests that a combination of host genetics and the composition of the gut microbiota are important for development of Crohn's disease (CD). Our aim was to study identical twins with CD to determine microbial factors independently of host genetics. Fecal samples were studied from 10 monozygotic twin pairs with CD (discordant n=6, concordant n=4) and 8 healthy twin pairs. DNA was extracted, 16S rRNA genes were PCR amplified and T-RFLP fingerprints generated using general bacterial and Bacteroides group specific primers. The microbial communities were also profiled based on their % G+C contents. Bacteroides 16S rRNA genes were cloned and sequenced from a subset of the samples. The bacterial diversity in each sample and similarity indices between samples were estimated based on the T-RFLP data using a combination of statistical approaches. Healthy individuals had a significantly higher bacterial diversity compared to individuals with CD. The fecal microbial communities were more similar between healthy twins than between twins with CD, especially when these were discordant for the disease. The microbial community profiles of individuals with ileal CD were significantly different from healthy individuals and those with colonic CD. Also, CD individuals had a lower relative abundance of B. uniformis and higher relative abundances of B. ovatus and B. vulgatus. Our results suggest that genetics and/or environmental exposure during childhood in part determine the gut microbial composition. However, CD is associated with dramatic changes in the gut microbiota and this was particularly evident for individuals with ileal CD.

  4. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens.

    Science.gov (United States)

    Pamer, Eric G

    2016-04-29

    The intestinal microbiota, which is composed of diverse populations of commensal bacterial species, provides resistance against colonization and invasion by pathogens. Antibiotic treatment can damage the intestinal microbiota and, paradoxically, increase susceptibility to infections. Reestablishing microbiota-mediated colonization resistance after antibiotic treatment could markedly reduce infections, particularly those caused by antibiotic-resistant bacteria. Ongoing studies are identifying commensal bacterial species that can be developed into next-generation probiotics to reestablish or enhance colonization resistance. These live medicines are at various stages of discovery, testing, and production and are being subjected to existing regulatory gauntlets for eventual introduction into clinical practice. The development of next-generation probiotics to reestablish colonization resistance and eliminate potential pathogens from the gut is warranted and will reduce health care-associated infections caused by highly antibiotic-resistant bacteria. PMID:27126035

  5. Dynamics of bacterial metabolic profile and community structure during the mineralization of organic carbon in intensive swine farm wastewater

    Directory of Open Access Journals (Sweden)

    Xiaoyan Ma

    2015-06-01

    Full Text Available Land application of intensive swine farm wastewater has raised serious environmental concerns due to the accumulation and microbially mediated transformation of large amounts of swine wastewater organic C (SWOC. Therefore, the study of SWOC mineralization and dynamics of wastewater microorganisms is essential to understand the environmental impacts of swine wastewater application. We measured the C mineralization of incubated swine wastewaters with high (wastewater H and low (wastewater L organic C concentrations. The dynamics of bacteria metabolic profile and community structure were also investigated. The results showed that SWOC mineralization was properly fitted by the two-simultaneous reactions model. The initial potential rate of labile C mineralization of wastewater H was 46% higher than that of wastewater L, whereas the initial potential rates of recalcitrant C mineralization of wastewaters H and L were both around 23 mg L-1 d-1. The bacterial functional and structural diversities significantly decreased for both the wastewaters during SWOC mineralization, and were all negatively correlated to specific UV absorbance (SUVA254; P < 0.01. The bacteria in the raw wastewaters exhibited functional similarity, and both metabolic profile and community structure changed with the mineralization of SWOC, mainly under the influence of SUVA254 (P < 0.001. These results suggested that SWOC mineralization was characterized by rapid mineralization of labile C and subsequent slow decomposition of recalcitrant C pool, and the quality of SWOC varied between the wastewaters with different amounts of organic C. The decreased bio-availability of dissolved organic matter affected the dynamics of wastewater bacteria during SWOC mineralization.

  6. Anti-inflammatory effect and prostate gene expression profiling of steryl ferulate on experimental rats with non-bacterial prostatitis.

    Science.gov (United States)

    Hu, Yinzhou; Xiong, Lina; Huang, Weisu; Cai, Huafang; Luo, Yanxi; Zhang, Ying; Lu, Baiyi

    2014-06-01

    Steryl ferulate (SF) is a bioactive mixture extracted from rice bran and shows higher inhibitory activity against inflammation than the corresponding free sterols. In this study, the aim was to investigate the anti-inflammatory effect and prostate gene expression profiling of SF using a Xiaozhiling-induced non-bacterial prostatitis (NBP) rat model. The anti-inflammatory effect was evaluated by prostate weight, prostate index, acid phosphatase, density of lecithin corpuscles (DLC), white blood cell count (WBC), and prostatic histologic section. Prostate gene expression profiling was assessed by a cDNA microarray and validated by quantitative real-time PCR of five selected genes. Pathway analysis and Gene ontology (GO) analysis were applied to determine the roles of these differentially expressed genes involved in these biological pathways or GO terms. SF treatment could significantly inhibit prostate weight, prostate index, total acid phosphatase, prostatic acid phosphatase and WBC, suppress the severity of histological lesion and increase the DLC. Compared with the control group, the SF treatment group contained 238 up-regulated genes and 111 down-regulated genes. GO analysis demonstrated that the most significant expression genes were closely related to the terms of fibrinolysis, inflammatory response, high-density lipoprotein particle, protein-lipid complex, enzyme inhibitor activity, peptidase inhibitor activity and others. Canonical pathway analysis indicated five pathways were significantly regulated, which were associated with inflammation and tumorgenesis. In conclusion, SF may be used as a health supplement to prevent NBP, in that it could inhibit prostate inflammation in NBP patients by affecting the expression of genes in the related GO terms and pathways. PMID:24686498

  7. Antibiotic sensitivity profile of bacterial pathogens in postoperative wound infections at a tertiary care hospital in Gujarat, India

    Directory of Open Access Journals (Sweden)

    Nutanbala N Goswami

    2011-01-01

    Full Text Available Objective: To find out the most common bacterial pathogens responsible for post-operative wound infection and their antibiotic sensitivity profile. Materials and Methods: This prospective, observational study was carried out in patients of postoperative wound infection. Samples from wound discharge were collected using a sterile swab and studied for identification of isolates by Gram stains and culture growth followed by in vitro antibiotic susceptibility testing performed by disc diffusion method on Mueller Hinton agar. Results: Out of 183 organisms, 126 (68.85% isolated organisms were gram negative. Staphylococcus aureus, 48 (26.23%, was the predominant organism. S. aureus was sensitive to rifampicin (89.58%, levofloxacin (60.42%, and vancomycin (54.17%. Pseudomonas aeruginosa was sensitive to ciprofloxacin (83.78%, gatifloxacin (51.35%, and meropenem (51.35%. Escherichia coli was sensitive to levofloxacin (72.41% and ciprofloxacin (62.07%. Klebsiella pneumoniae was sensitive to ciprofloxacin (63.16%, levofloxacin (63.16%, gatifloxacin (63.16%, and linezolid (56.52%. Proteus mirabilis was sensitive to ciprofloxacin (75% and linezolid (62.50. Proteus vulgaris was sensitive to ampicillin+sulbactam (57.14% followed by levofloxacin (50%. Conclusions: There is an alarming increase of infections caused by antibiotic-resistant bacteria, particularly in the emergence of VRSA/VISA, meropenem, and third generation cephalosporin resistant Pseudomonas aeruginosa. Linezolid showing sensitivity against Gram negative bacteria.

  8. Diabetes, periodontitis, and the subgingival microbiota

    Directory of Open Access Journals (Sweden)

    Edward J. Ohlrich

    2010-12-01

    Full Text Available Both type 1 and type 2 diabetes have been associated with increased severity of periodontal disease for many years. More recently, the impact of periodontal disease on glycaemic control has been investigated. The role of the oral microbiota in this two-way relationship is at this stage unknown. Further studies, of a longitudinal nature and investigating a wider array of bacterial species, are required in order to conclusively determine if there is a difference in the oral microbiota of diabetics and non-diabetics and whether this difference accounts, on the one hand, for the increased severity of periodontal disease and on the other for the poorer glycaemic control seen in diabetics.

  9. The Role of the Gut Microbiota in Childhood Obesity

    DEFF Research Database (Denmark)

    Pihl, Andreas Friis; Fonvig, Cilius Esmann; Stjernholm, Theresa;

    2016-01-01

    associated with obesity. METHODS: We conducted a systematic search for literature available before October 2015 in the PubMed and Scopus databases, focusing on the interplay between the gut microbiota, childhood obesity, and metabolism. RESULTS: The review discusses the potential role of the bacterial...

  10. Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites.

    Science.gov (United States)

    Rakoff-Nahoum, Seth

    2016-04-13

    Microbial colonization after birth profoundly affects development of the host. In a recent paper, Gomez de Agüero et al. (2016) reveal a new aspect of ontogeny influenced by the microbiota: the impact of gestational gut bacterial metabolites on early immune maturation of the neonatal intestine. PMID:27078061

  11. An uncooked vegan diet shifts the profile of human fecal microflora: computerized analysis of direct stool sample gas-liquid chromatography profiles of bacterial cellular fatty acids.

    OpenAIRE

    Peltonen, R; Ling, W H; Hänninen, O.; Eerola, E

    1992-01-01

    The effect of an uncooked extreme vegan diet on fecal microflora was studied by direct stool sample gas-liquid chromatography (GLC) of bacterial cellular fatty acids and by quantitative bacterial culture by using classical microbiological techniques of isolation, identification, and enumeration of different bacterial species. Eighteen volunteers were divided randomly into two groups. The test group received an uncooked vegan diet for 1 month and a conventional diet of mixed Western type for t...

  12. Gut microbiota: its role in hepatic encephalopathy.

    Science.gov (United States)

    Rai, Rahul; Saraswat, Vivek A; Dhiman, Radha K

    2015-03-01

    Ammonia, a key factor in the pathogenesis of hepatic encephalopathy (HE), is predominantly derived from urea breakdown by urease producing large intestinal bacteria and from small intestine and kidneys, where the enzyme glutaminases releases ammonia from circulating glutamine. Non-culture techniques like pyrosequencing of bacterial 16S ribosomal ribonucleic acid are used to characterize fecal microbiota. Fecal microbiota in patients with cirrhosis have been shown to alter with increasing Child-Turcotte-Pugh (CTP) and Model for End stage Liver Disease (MELD) scores, and with development of covert or overt HE. Cirrhosis dysbiosis ratio (CDR), the ratio of autochthonous/good bacteria (e.g. Lachnospiraceae, Ruminococcaceae and Clostridiales) to non-autochthonous/pathogenic bacteria (e.g. Enterobacteriaceae and Streptococcaceae), is significantly higher in controls and patients with compensated cirrhosis than patients with decompensated cirrhosis. Although their stool microbiota do not differ, sigmoid colonic mucosal microbiota in liver cirrhosis patients with and without HE, are different. Linkage of pathogenic colonic mucosal bacteria with poor cognition and inflammation suggests that important processes at the mucosal interface, such as bacterial translocation and immune dysfunction, are involved in the pathogenesis of HE. Fecal microbiome composition does not change significantly when HE is treated with lactulose or when HE recurs after lactulose withdrawal. Despite improving cognition and endotoxemia as well as shifting positive correlation of pathogenic bacteria with metabolites, linked to ammonia, aromatic amino acids and oxidative stress, to a negative correlation, rifaximin changes gut microbiome composition only modestly. These observations suggest that the beneficial effects of lactulose and rifaximin could be associated with a change in microbial metabolic function as well as an improvement in dysbiosis. PMID:26041954

  13. Human gut microbiota: does diet matter?

    Science.gov (United States)

    Maukonen, Johanna; Saarela, Maria

    2015-02-01

    The human oro-gastrointestinal (GI) tract is a complex system, consisting of oral cavity, pharynx, oesophagus, stomach, small intestine, large intestine, rectum and anus, which all together with the accessory digestive organs constitute the digestive system. The function of the digestive system is to break down dietary constituents into small molecules and then absorb these for subsequent distribution throughout the body. Besides digestion and carbohydrate metabolism, the indigenous microbiota has an important influence on host physiological, nutritional and immunological processes, and commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. The main external factors that can affect the composition of the microbial community in generally healthy adults include major dietary changes and antibiotic therapy. Changes in some selected bacterial groups have been observed due to controlled changes to the normal diet e.g. high-protein diet, high-fat diet, prebiotics, probiotics and polyphenols. More specifically, changes in the type and quantity of non-digestible carbohydrates in the human diet influence both the metabolic products formed in the lower regions of the GI tract and the bacterial populations detected in faeces. The interactions between dietary factors, gut microbiota and host metabolism are increasingly demonstrated to be important for maintaining homeostasis and health. Therefore the aim of this review is to summarise the effect of diet, and especially dietary interventions, on the human gut microbiota. Furthermore, the most important confounding factors (methodologies used and intrinsic human factors) in relation to gut microbiota analyses are elucidated. PMID:25156389

  14. Gut Microbiota: The Brain Peacekeeper

    OpenAIRE

    Mu, Chunlong; Yang, Yuxiang; Zhu, Weiyun

    2016-01-01

    Gut microbiota regulates intestinal and extraintestinal homeostasis. Accumulating evidence suggests that the gut microbiota may also regulate brain function and behavior. Results from animal models indicate that disturbances in the composition and functionality of some microbiota members are associated with neurophysiological disorders, strengthening the idea of a microbiota–gut–brain axis and the role of microbiota as a “peacekeeper” in the brain health. Here, we review recent discoveries on...

  15. Impact of the blood meal on humoral immunity and microbiota in the gut of female Culicoides sonorensis.

    Science.gov (United States)

    Nayduch, Dana; Erram, Dinesh; Lee, Matthew B; Zurek, Ludek; Saski, Christopher A

    2015-01-01

    Although Culicoides sonorensis is an important vector of orbiviruses causing significant disease in domestic and wild ruminants in the USA, little is known about factors contributing to midge vector competence. In other vectors such as mosquitoes, interactions among the humoral immune response, microbiota, and ingested pathogens within the vector gut directly impact pathogen survival and therefore vectoring potential. We recently described components of the humoral immune response in the reference transcriptome for adult female C. sonorensis and analysed their temporal expression profiles across several dietary states (unfed, blood, or sugar fed). Blood feeding altered the transcription of several humoral immune components of the Immune deficiency (Imd), dual‑oxidase (DUOX), and Janus Kinase and Signal Transducer and Activator of Transcription (JAK/STAT) pathways. Genes for immune effectors, such as antimicrobial peptides, were in particular highly induced. Since blood feeding also stimulated proliferation and diversification of bacterial populations colonising the gut of female midges, we infer that changes in immune gene expression were a result of fluctuations in gut microbiota. Thus, diet can indirectly (via microbiota) impact gut immune status and therefore should be carefully considered in subsequent studies assessing vector competence in biting midges. PMID:26741251

  16. The Gut Microbiota and Irritable Bowel Syndrome: Friend or Foe?

    Directory of Open Access Journals (Sweden)

    Uday C. Ghoshal

    2012-01-01

    Full Text Available Progress in the understanding of the pathophysiology of irritable bowel syndrome (IBS, once thought to be a purely psychosomatic disease, has advanced considerably and low-grade inflammation and changes in the gut microbiota now feature as potentially important. The human gut harbours a huge microbial ecosystem, which is equipped to perform a variety of functions such as digestion of food, metabolism of drugs, detoxification of toxic compounds, production of essential vitamins, prevention of attachment of pathogenic bacteria to the gut wall, and maintenance of homeostasis in the gastrointestinal tract. A subset of patients with IBS may have a quantitative increase in bacteria in the small bowel (small intestinal bacterial overgrowth. Qualitative changes in gut microbiota have also been associated with IBS. Targeting the gut microbiota using probiotics and antibiotics has emerged as a potentially effective approach to the treatment of this, hitherto enigmatic, functional bowel disorder. The gut microbiota in health, quantitative and qualitative microbiota changes, and therapeutic manipulations targeting the microbiota in patients with IBS are reviewed in this paper.

  17. Microbiota-based treatments in alcoholic liver disease.

    Science.gov (United States)

    Sung, Hotaik; Kim, Seung Woo; Hong, Meegun; Suk, Ki Tae

    2016-08-01

    Gut microbiota plays a key role in the pathogenesis of alcoholic liver disease (ALD). Consumption of alcohol leads to increased gut permeability, small intestinal bacterial overgrowth, and enteric dysbiosis. These factors contribute to the increased translocation of microbial products to the liver via the portal tract. Subsequently, bacterial endotoxins such as lipopolysaccharide, in association with the Toll-like receptor 4 signaling pathway, induce a gamut of damaging immune responses in the hepatic milieu. Because of the close association between deleterious inflammation and ALD-induced microbiota imbalance, therapeutic approaches that seek to reestablish gut homeostasis should be considered in the treatment of alcoholic patients. To this end, a number of preliminary studies on probiotics have confirmed their effectiveness in suppressing proinflammatory cytokines and improving liver function in the context of ALD. In addition, there have been few studies linking the administration of prebiotics and antibiotics with reduction of alcohol-induced liver damage. Because these preliminary results are promising, large-scale randomized studies are warranted to elucidate the impact of these microbiota-based treatments on the gut flora and associated immune responses, in addition to exploring questions about optimal delivery. Finally, fecal microbiota transplant has been shown to be an effective method of modulating gut microbiota and deserve further investigation as a potential therapeutic option for ALD. PMID:27547010

  18. Gut Microbiota: Modulate its Complexity to Restore the Balance

    Directory of Open Access Journals (Sweden)

    Fermín Mearin

    2015-12-01

    Full Text Available The importance of the gut microbiota to health is becoming more widely appreciated. The range of commensal microorganisms in healthy individuals and in patients with a variety of digestive diseases is under active investigation, and evidence is accumulating to suggest that both the diversity and balance of bacterial species are important for health. Disturbance of the balance of microorganisms – dysbiosis – is associated with obesity and a variety of diseases. Restoring the balance by modulating the microbiota through diet, probiotics, or drugs is now being developed as a potential treatment for digestive diseases. Rifaximin has been shown to increase levels of beneficial bacterial species without perturbing the overall composition of the microbiota in patients with a variety of digestive diseases, making it a ‘eubiotic’ rather than an antibiotic. Rifaximin has demonstrated clinical benefit in the treatment of symptomatic uncomplicated diverticular disease, where changes in the colonic microbiota contribute to the pathogenesis of this disease. Modulating the microbiota is also a promising treatment for some types of irritable bowel syndrome (IBS that have been linked to an overgrowth of coliform and Aeromonas species in the small intestine. Rifaximin has demonstrated efficacy in relieving symptoms and reducing relapses in diarrhoeal IBS in the TARGET-1, 2, and 3 trials, without reducing microbial diversity or increasing antimicrobial resistance. While many aspects of the balance of gut microbiota in disease are not yet fully understood, the new understanding of rifaximin as a modulator of gut microbiota may open up new treatment options in digestive disease.

  19. Bacterial diversity in Philippine fermented mustard (burong mustasa) as revealed by 16S rRNA gene analysis.

    Science.gov (United States)

    Larcia, L L H; Estacio, R C; Dalmacio, L M M

    2011-12-01

    Previous studies on the bacterial profile of burong mustasa, a traditional Philippine fermented food, had been conducted using culture-dependent techniques. Since these methods may underestimate the total microbiota of a sample, a culture-independent study was done to determine the bacterial diversity in burong mustasa through molecular biology techniques. Bacterial DNA was isolated from fermented mustard samples at different stages of fermentation. The isolated genomic DNA was amplified by PCR using specific primers for the 16S ribosomal RNA gene (16S rDNA). The 1.5 kb amplicons obtained were subjected to nested PCR using primers for the internal variable region of the 16S rDNA. The 585 bp nested PCR amplicons were then subjected to denaturing gradient gel electrophoresis (DGGE) to separate the different bacteria present in each sample. Distinct and unique bands in the DGGE profile were excised, reamplified, purified and sequenced for bacterial identification. Molecular cloning of the 1.5 kb 16S rDNA was also performed using the pGEM-T Easy Vector System. The cloned gene was sequenced for bacterial identification. The identified microbiota in burong mustasa at different stages of fermentation include lactic acid bacteria and several uncultured bacteria (initial up to the final stages); acetic acid bacteria (middle stage); and Streptobacillus and Fusobacterium species (initial stage). The potential probiotic bacteria found in burong mustasa are Weissella and Lactobacillus. PMID:22146686

  20. Diet, microbiota, and dysbiosis: a 'recipe' for colorectal cancer.

    Science.gov (United States)

    Vipperla, Kishore; O'Keefe, Stephen J

    2016-04-20

    The food we consume feeds not only us, but also a vast and diverse community of microbiota within our gastrointestinal tract. In a process of symbiotic co-evolution, the gut microbiota became essential for the maintenance of the health and integrity of our colon. The advent of next-generation DNA sequencing technology and metabolic profiling have, in the recent years, revealed the remarkable complexity of microbial diversity and function, and that the microbiota produce a wide variety of bioactive products that are not only active at the mucosal surface, but also absorbed and circulated throughout the body, influencing distant organ health and function. As a result, several microbiota compositional patterns and their associations with both health and disease states have been identified. Importantly, a disturbed microbiota-host relationship, termed dysbiosis, is now recognized to be the root cause for a growing list of diseases, including colorectal cancer (CRC). There is mounting in vitro and in vivo evidence to suggest that diet selects for the microbiota composition and several health promoting and deleterious effects of diet are, in fact, mediated by the microbiota. Recent findings of the feasibility of dietary fiber to boost the colonic microbial synthesis of anti-proliferative and counter carcinogenic metabolites, particularly butyrate, underscores the prerequisite of dietary modification as a key measure to curb the pandemic of CRC in westernized countries. Better understanding of the diet-microbiota interplay and large-scale studies to evaluate the efficacy of dietary modification and gut microbiota modulation in reversing dysbiosis and restoring health could offer novel preventative and/or therapeutic strategies against westernized diseases, which are now considered the chief threat to public health. PMID:26840037

  1. Rhizosphere bacterial communities of potato cultivars evaluated through PCR-DGGE profiles Comunidades bacterianas associadas à rizosfera de cultivares de batata avaliadas por perfis de PCR-DGGE

    OpenAIRE

    Enderson Petrônio de Brito Ferreira; André Nepomuceno Dusi; Gustavo Ribeiro Xavier; Norma Gouvêa Rumjanek

    2008-01-01

    The objective of this work was to determine the shifts on the PCR-DGGE profiles of bacterial communities associated to the rhizosphere of potato cultivars, in order to generate baseline information for further studies of environmental risk assessment of genetically modified potato plants. A greenhouse experiment was carried out with five potato cultivars (Achat, Bintje, Agata, Monalisa and Asterix), cultivated in pots containing soil from an integrated system for agroecological production. Th...

  2. [First part: the intestinal microbiota].

    Science.gov (United States)

    Capurso, Lucio

    2016-06-01

    The human gastrointestinal tract contains a large number of commensal (non pathogenic) and pathogenic microbial species that have co-evolved with the human genome and differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host and we can in fact consider the human body as a mix of human and bacterial cells. It is now evident that the large intestine is much more than an organ for waste material and absorption of water, salts and drugs, and indeed has a very important impact on human health, for a major part related to the specific composition of the complex microbial community in the colon. In man, the large gut receives material from the ileum which has already been digested and the contents are then mixed and retained for 6-12 hours in the caecum and right colon. Thus, the large intestine is an open system, with nutrients flowing in the caecum, and bacteria, their metabolic products, and undigested foodstuffs being excreted as faeces. The anaerobic brakdown of carbohydrate and protein by bacteria is known conventionally as fermentation. In man the major end products are the short-chain fatty acids (SCFA) acetate, propionate, butirate, the gases H2 and CO2, ammonia, amines, phenols and energy, which the bacteria use for growth and the maintenance of cellular function. The microbiota is also an important factor in the development of the immune response. The interaction between the gastrointestinal tract and resident microbiota is well balanced in healthy individuals, but its breakdown can lead to intestinal and extraintestinal disease. PMID:27362717

  3. Gut Microbiota and Metabolic Disorders

    Directory of Open Access Journals (Sweden)

    Kyu Yeon Hur

    2015-06-01

    Full Text Available Gut microbiota plays critical physiological roles in the energy extraction and in the control of local or systemic immunity. Gut microbiota and its disturbance also appear to be involved in the pathogenesis of diverse diseases including metabolic disorders, gastrointestinal diseases, cancer, etc. In the metabolic point of view, gut microbiota can modulate lipid accumulation, lipopolysaccharide content and the production of short-chain fatty acids that affect food intake, inflammatory tone, or insulin signaling. Several strategies have been developed to change gut microbiota such as prebiotics, probiotics, certain antidiabetic drugs or fecal microbiota transplantation, which have diverse effects on body metabolism and on the development of metabolic disorders.

  4. The commensal microbiota drives immune homeostasis

    Directory of Open Access Journals (Sweden)

    Marie-Claire eArrieta

    2012-03-01

    Full Text Available For millions of years, microbes have coexisted with eukaryotic cells at the mucosal surfaces of vertebrates in a complex, yet usually harmonious symbiosis. An ever-expanding number of reports describe how eliminating or shifting the intestinal microbiota has profound effects on the development and functionality of the mucosal and systemic immune systems. Here, we examine some of the mechanisms by which bacterial signals affect immune homeostasis. Focusing on the strategies that microbes use to keep our immune system healthy, as opposed to trying to correct the immune imbalances caused by dysbiosis, may prove to be a more astute and efficient way of treating immune-mediated disease.

  5. The diet-microbiota-metabolite axis regulates the host physiology.

    Science.gov (United States)

    Yamada, Takahiro; Takahashi, Daisuke; Hase, Koji

    2016-07-01

    The intestinal microbiota has been implicated in a wide range of diseases, including inflammatory bowel disease, obesity and cancer. Food ingredients are considered a major determinant of gut microbial composition, as exemplified by high-fat diet-induced dysbiosis that can affect host physiology. Accumulating studies show that microbial metabolites are key regulators of the intestinal epithelial barrier and gut immunity. In particular, short-chain fatty acids produced by bacterial fermentation of indigestible polysaccharides have profound impacts on host physiology beyond the gut. In this review, we describe the influences of the diet-microbiota-metabolite axis on host physiology, and especially on the immune and metabolic systems. PMID:26970281

  6. Gut microbiota and probiotics in chronic liver diseases.

    Science.gov (United States)

    Cesaro, Claudia; Tiso, Angelo; Del Prete, Anna; Cariello, Rita; Tuccillo, Concetta; Cotticelli, Gaetano; Del Vecchio Blanco, Camillo; Loguercio, Carmelina

    2011-06-01

    There is a strong relationship between liver and gut: the portal system receives blood from the gut, and intestinal blood content activates liver functions. The liver, in turn, affects intestinal functions through bile secretion into the intestinal lumen. Alterations of intestinal microbiota seem to play an important role in induction and promotion of liver damage progression, in addition to direct injury resulting from different causal agents. Bacterial overgrowth, immune dysfunction, alteration of the luminal factors, and altered intestinal permeability are all involved in the pathogenesis of complications of liver cirrhosis, such as infections, hepatic encephalopathy, spontaneous bacterial peritonitis, and renal failure. Probiotics have been suggested as a useful integrative treatment of different types of chronic liver damage, for their ability to augment intestinal barrier function and prevent bacterial translocation. This review summarizes the main literature findings about the relationships between gut microbiota and chronic liver disease, both in the pathogenesis and in the treatment by probiotics of the liver damage. PMID:21163715

  7. Associations between bacterial communities of house dust and infant gut

    Energy Technology Data Exchange (ETDEWEB)

    Konya, T.; Koster, B. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Maughan, H. [Department of Cell and Systems Biology, University of Toronto (Canada); Escobar, M. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Azad, M.B. [Department of Pediatrics, University of Alberta (Canada); Guttman, D.S. [Department of Cell and Systems Biology, University of Toronto (Canada); Sears, M.R. [Department of Medicine, McMaster University (Canada); Becker, A.B. [University of Manitoba (Canada); Brook, J.R. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Environment Canada (Canada); Takaro, T.K. [Faculty of Health Science, Simon Fraser University (Canada); Kozyrskyj, A.L. [Department of Pediatrics, University of Alberta (Canada); Scott, J.A., E-mail: james.scott@utoronto.ca [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada)

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  8. Associations between bacterial communities of house dust and infant gut

    International Nuclear Information System (INIS)

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership

  9. Associations between bacterial communities of house dust and infant gut.

    Science.gov (United States)

    Konya, T; Koster, B; Maughan, H; Escobar, M; Azad, M B; Guttman, D S; Sears, M R; Becker, A B; Brook, J R; Takaro, T K; Kozyrskyj, A L; Scott, J A

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  10. Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae).

    Science.gov (United States)

    Snyman, Maxi; Gupta, Arvind Kumar; Bezuidenhout, Cornelius Carlos; Claassens, Sarina; van den Berg, Johnnie

    2016-07-01

    Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is a stemborer pest that attacks maize (Zea mays) throughout sub-Saharan Africa. Genetically modified maize has been shown to be effective against B. fusca. However, resistance of B. fusca against Bt-maize has developed and spread throughout South Africa. Previous studies suggested that gut microbiota contribute to mortality across a range of Lepidoptera. To fully assess the role of microbiota within the gut, it is essential to understand the microbiota harboured by natural B. fusca populations. This study aimed to identify the gut-associated bacteria by 16S rRNA gene sequencing. A total of 78 bacterial strains were characterised from the midgut of B. fusca larvae that were collected from 30 sites across the maize producing region of South Africa. Molecular phylogenetic analyses revealed bacteria affiliated to Proteobacteria, Actinobacteria, and Firmicutes. Taxonomic distribution placed these isolates into 15 different genera representing 20 species. The majority of bacteria identified belong to the genera Bacillus, Enterococcus, and Klebsiella. The B. fusca gut represents an intriguing and unexplored niche for analysing microbial ecology. The study could provide opportunities for developing new targets for pest management and contribute to understanding the phenomenon of resistance evolution of this species. PMID:27263010

  11. Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan

    Science.gov (United States)

    David, Mariana Rocha; dos Santos, Lilha Maria Barbosa; Vicente, Ana Carolina Paulo; Maciel-de-Freitas, Rafael

    2016-01-01

    Abstract Mosquito midgut microbiota is a key component of vector competence, as gut bacteria can disturb pathogen development. In this study, we addressed the microbiota composition of Aedes aegypti during its lifespan, under field conditions. We also investigated the possible effects of environment, dietary regime and ageing on the gut community composition. We employed culture independent and dependent approaches to characterise vector microbiota. There was evidence of a lifelong stable core microbiota after mosquitoes were released into an urban settlement, where they presumably fed on a range of vertebrate hosts and carbohydrate sources. This core was formed mainly of bacteria belonging to the genera Pseudomonas, Acinetobacter, Aeromonas and Stenotrophomonas and to the families Oxalobacteraceae, Enterobacteriaceae and Comamonadaceae. We showed that both dietary regime and age were associated with the abundance of some bacterial groups in the Ae. aegypti microbiota. The majority of the bacterial groups we identified have been detected in the midgut of Ae. aegypti from laboratory and wild populations, indicating a possible core microbiota associated with this mosquito species. Our findings suggest that Ae. aegypti harbours a stable bacterial community during its adult life, similar to mosquito populations from distinct geographic areas, which may be further explored for arbovirus biocontrol strategies. PMID:27580348

  12. Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan.

    Science.gov (United States)

    David, Mariana Rocha; Santos, Lilha Maria Barbosa Dos; Vicente, Ana Carolina Paulo; Maciel-de-Freitas, Rafael

    2016-09-01

    Mosquito midgut microbiota is a key component of vector competence, as gut bacteria can disturb pathogen development. In this study, we addressed the microbiota composition of Aedes aegypti during its lifespan, under field conditions. We also investigated the possible effects of environment, dietary regime and ageing on the gut community composition. We employed culture independent and dependent approaches to characterise vector microbiota. There was evidence of a lifelong stable core microbiota after mosquitoes were released into an urban settlement, where they presumably fed on a range of vertebrate hosts and carbohydrate sources. This core was formed mainly of bacteria belonging to the genera Pseudomonas, Acinetobacter, Aeromonas and Stenotrophomonas and to the families Oxalobacteraceae, Enterobacteriaceae and Comamonadaceae. We showed that both dietary regime and age were associated with the abundance of some bacterial groups in the Ae. aegypti microbiota. The majority of the bacterial groups we identified have been detected in the midgut of Ae. aegypti from laboratory and wild populations, indicating a possible core microbiota associated with this mosquito species. Our findings suggest that Ae. aegypti harbours a stable bacterial community during its adult life, similar to mosquito populations from distinct geographic areas, which may be further explored for arbovirus biocontrol strategies. PMID:27580348

  13. Perfil etiológico das meningites bacterianas em crianças Etiological profile of bacterial meningitis in children

    Directory of Open Access Journals (Sweden)

    Orlando C. Mantese

    2002-12-01

    meningite bacteriana continua tendo uma importante mortalidade entre as crianças, principalmente quando causada pelo pneumococo.Objective: To determine the etiologic profile and analyze some epidemiological aspects of children with bacterial meningitis admitted to a public teaching hospital. Methods: A prospective study was conducted on children with clinical and laboratory diagnosis of bacterial meningitis, admitted to Hospital das Clínicas da Universidade Federal de Uberlândia, from January 1987 to January 2001. Patients with meningitis associated with trauma, intracranial devices or malformations of the neural tube, and tuberculosis, were not included in the study. Results: From a total of 415 children with bacterial meningitis, the etiologic agent was detected in 315 (75.9%: Haemophilus influenzae b in 54.2%, meningococci in 20.6%, pneumococci in 18.1% and other agents, in 6.9%. Previous antibiotic treatment, observed in 47.2% of the cases, led to a significant decrease in positive blood cultures (from 50.8% to 38.7% and in cerebrospinal fluid cultures (from 71.7% to 57.6%. Among children younger than 48 months Haemophilus influenzae b was predominant, particularly when compared to meningococci. The overall mortality was 10.1%, with a significant difference between the rates of pneumococcal (17.5% and meningococcal meningitis (4.6%. Conclusions: Children affected by Haemophilus influenzae b and by pneumococci were younger than those with meningitis caused by meningococci. The blood and/or cerebrospinal fluid culture remains an important laboratory tool for etiologic diagnosis, despite the negative impact caused by antibiotic previous treatment. The agents most commonly detected were Haemophilus influenzae b, meningococci and pneumococci. Bacterial meningitis continues to present an important mortality among children, particularly when caused by pneumococci.

  14. Cystic fibrosis transmembrane conductance regulator (CFTR allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients.

    Directory of Open Access Journals (Sweden)

    Serena Schippa

    Full Text Available INTRODUCTION: In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF. CFTR mutations (F508del is the most common lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age. METHODS: Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure. RESULTS: Patients were classified by two different criteria: 1 presence/absence of F508del mutation; 2 disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum were reduced. CONCLUSIONS: This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a 'systemic disease', linking the lung and the gut in a joined axis.

  15. Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

    Institute of Scientific and Technical Information of China (English)

    Yue-Jian Hu; Qian Wang; Yun-Tao Jiang; Rui Ma; Wen-Wei Xia; Zi-Sheng Tang; Zheng Liu; Jing-Ping Liang; Zheng-Wei Huang

    2013-01-01

    The objective of this study was to investigate the compositional profiles and microbial shifts of oral microbiota during head-and-neck radiotherapy. Bioinformatic analysis based on 16S rRNA gene pyrosequencing was performed to assess the diversity and variation of oral microbiota of irradiated patients. Eight patients with head and neck cancers were involved in this study. For each patient, supragingival plaque samples were collected at seven time points before and during radiotherapy. A total of 147232 qualified sequences were obtained through pyrosequencing and bioinformatic analysis, representing 3460 species level operational taxonomic units (OTUs) and 140 genus level taxa. Temporal variations were observed across different time points and supported by cluster analysis based on weighted UniFrac metrics, Moreover, the low evenness of oral microbial communities in relative abundance was revealed by Lorenz curves. This study contributed to a better understanding of the detailed characterization of oral bacterial diversity of irradiated patients.

  16. Reshaping faecal gut microbiota composition by the intake of trans-resveratrol and quercetin in high-fat sucrose diet-fed rats.

    Science.gov (United States)

    Etxeberria, U; Arias, N; Boqué, N; Macarulla, M T; Portillo, M P; Martínez, J A; Milagro, F I

    2015-06-01

    Diet-induced obesity is associated to an imbalance in the normal gut microbiota composition. Resveratrol and quercetin, widely known for their health beneficial properties, have low bioavailability, and when they reach the colon, they are targets of the gut microbial ecosystem. Hence, the use of these molecules in obesity might be considered as a potential strategy to modulate intestinal bacterial composition. The purpose of this study was to determine whether trans-resveratrol and quercetin administration could counteract gut microbiota dysbiosis produced by high-fat sucrose diet (HFS) and, in turn, improve gut health. Wistar rats were randomised into four groups fed an HFS diet supplemented or not with trans-resveratrol [15 mg/kg body weight (BW)/day], quercetin (30 mg/kg BW/day) or a combination of both polyphenols at those doses. Administration of both polyphenols together prevented body weight gain and reduced serum insulin levels. Moreover, individual supplementation of trans-resveratrol and quercetin effectively reduced serum insulin levels and insulin resistance. Quercetin supplementation generated a great impact on gut microbiota composition at different taxonomic levels, attenuating Firmicutes/Bacteroidetes ratio and inhibiting the growth of bacterial species previously associated to diet-induced obesity (Erysipelotrichaceae, Bacillus, Eubacterium cylindroides). Overall, the administration of quercetin was found to be effective in lessening HFS-diet-induced gut microbiota dysbiosis. In contrast, trans-resveratrol supplementation alone or in combination with quercetin scarcely modified the profile of gut bacteria but acted at the intestinal level, altering the mRNA expression of tight-junction proteins and inflammation-associated genes. PMID:25762527

  17. Reshaping faecal gut microbiota composition by the intake of trans-resveratrol and quercetin in high-fat sucrose diet-fed rats.

    Science.gov (United States)

    Etxeberria, U; Arias, N; Boqué, N; Macarulla, M T; Portillo, M P; Martínez, J A; Milagro, F I

    2015-06-01

    Diet-induced obesity is associated to an imbalance in the normal gut microbiota composition. Resveratrol and quercetin, widely known for their health beneficial properties, have low bioavailability, and when they reach the colon, they are targets of the gut microbial ecosystem. Hence, the use of these molecules in obesity might be considered as a potential strategy to modulate intestinal bacterial composition. The purpose of this study was to determine whether trans-resveratrol and quercetin administration could counteract gut microbiota dysbiosis produced by high-fat sucrose diet (HFS) and, in turn, improve gut health. Wistar rats were randomised into four groups fed an HFS diet supplemented or not with trans-resveratrol [15 mg/kg body weight (BW)/day], quercetin (30 mg/kg BW/day) or a combination of both polyphenols at those doses. Administration of both polyphenols together prevented body weight gain and reduced serum insulin levels. Moreover, individual supplementation of trans-resveratrol and quercetin effectively reduced serum insulin levels and insulin resistance. Quercetin supplementation generated a great impact on gut microbiota composition at different taxonomic levels, attenuating Firmicutes/Bacteroidetes ratio and inhibiting the growth of bacterial species previously associated to diet-induced obesity (Erysipelotrichaceae, Bacillus, Eubacterium cylindroides). Overall, the administration of quercetin was found to be effective in lessening HFS-diet-induced gut microbiota dysbiosis. In contrast, trans-resveratrol supplementation alone or in combination with quercetin scarcely modified the profile of gut bacteria but acted at the intestinal level, altering the mRNA expression of tight-junction proteins and inflammation-associated genes.

  18. In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors

    Directory of Open Access Journals (Sweden)

    Peter David Newell

    2014-11-01

    Full Text Available Symbiosis is often characterized by co-evolutionary changes in the genomes of the partners involved. An understanding of these changes can provide insight into the nature of the relationship, including the mechanisms that initiate and maintain an association between organisms. In this study we examined the genome sequences of bacteria isolated from the Drosophila melanogaster gut with the objective of identifying genes that are important for function in the host. We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. First the phenotype of germ-free Drosophila (axenic flies was compared to that of flies colonized with specific bacteria (gnotobiotic flies as a measure of symbiotic function. Non-fly isolates were functionally distinct from bacteria isolated from flies, conferring slower development and an altered nutrient profile in the host, traits known to be microbiota-dependent. Comparative genomic methods were next employed to identify putative symbiosis factors: genes found in bacteria that restore microbiota-dependent traits to gnotobiotic flies, but absent from those that do not. Factors identified include riboflavin synthesis and stress resistance. We also used a phylogenomic approach to identify protein coding genes for which fly-isolate sequences were more similar to each other than to other sequences, reasoning that these genes may have a shared function unique to the fly environment. This method identified genes in Acetobacter species that cluster in two distinct genomic loci: one predicted to be involved in oxidative stress detoxification and another encoding an efflux pump. In summary, we leveraged genomic and in vivo functional comparisons to identify candidate traits that distinguish symbiotic bacteria. These candidates can serve as the basis for further work investigating the genetic requirements of bacteria for function and persistence in the Drosophila gut.

  19. Ascites bacterial burden and immune cell profile are associated with poor clinical outcomes in the absence of overt infection.

    Directory of Open Access Journals (Sweden)

    Kevin J Fagan

    Full Text Available Bacterial infections, most commonly spontaneous bacterial peritonitis in patients with ascites, occur in one third of admitted patients with cirrhosis, and account for a 4-fold increase in mortality. Bacteria are isolated from less than 40% of ascites infections by culture, necessitating empirical antibiotic treatment, but culture-independent studies suggest bacteria are commonly present, even in the absence of overt infection. Widespread detection of low levels of bacteria in ascites, in the absence of peritonitis, suggests immune impairment may contribute to higher susceptibility to infection in cirrhotic patients. However, little is known about the role of ascites leukocyte composition and function in this context. We determined ascites bacterial composition by quantitative PCR and 16S rRNA gene sequencing in 25 patients with culture-negative, non-neutrocytic ascites, and compared microbiological data with ascites and peripheral blood leukocyte composition and phenotype. Bacterial DNA was detected in ascitic fluid from 23 of 25 patients, with significant positive correlations between bacterial DNA levels and poor 6-month clinical outcomes (death, readmission. Ascites leukocyte composition was variable, but dominated by macrophages or T lymphocytes, with lower numbers of B lymphocytes and natural killer cells. Consistent with the hypothesis that impaired innate immunity contributes to susceptibility to infection, high bacterial DNA burden was associated with reduced major histocompatibility complex class II expression on ascites (but not peripheral blood monocytes/macrophages. These data indicate an association between the presence of ascites bacterial DNA and early death and readmission in patients with decompensated cirrhosis. They further suggest that impairment of innate immunity contributes to increased bacterial translocation, risk of peritonitis, or both.

  20. Urinary infection in patients of public health care of Campo Mourão-PR, Brazil: bacterial prevalence and sensitivity profile

    Directory of Open Access Journals (Sweden)

    Josiane dos Santos Bitencourt

    2014-10-01

    Full Text Available Introduction: Cases of bacterial resistance in urinary tract infections (UTIs have increased significantly, mainly due to indiscriminate use of antimicrobials. Objective: Objective: To evaluate the prevalence and antimicrobial susceptibility of microorganisms isolated in urine cultures of patients of Consórcio Intermunicipal de Saúde da Comunidade dos Municípios da Região de Campo Mourão (CISCOMCAM clinical laboratory. Method: We performed a retrospective study of data from urine culture and sensitivity done between January 2012 and December 2013. Results: The most prevalent bacteria were Escherichia coli; women were the most affected gender and people 16-45 years, the most affected age group. The sensitivity profile showed that the antimicrobial combination trimethoprim/ sulfamethoxazole was not associated with the highest rate of bacterial resistance (59.7% and the combination of amoxicillin/clavulanic acid showed the lowest resistance rate (15.3%. For most antimicrobials, including ciprofloxacin and norfloxacin, the rates of bacterial resistance have increased from 2012 to 2013 with statistical significance (p < 0.05 in some cases. Discussion: The prevalence of Gram-negative bacilli in urinary infections is due to the fact that intestinal flora is rich in enterobacteria, and women are most affected by anatomical factors. The development of bacterial resistance to antimicrobials probably arises from their indiscriminate use. Conclusion: The rate of microbial resistance has risen, showing the need for a more effective control of antimicrobial use.

  1. Diet, Gut Microbiota and Obesity

    Directory of Open Access Journals (Sweden)

    Hongjie Li and Chuanxian Wei

    2015-09-01

    Full Text Available Increasing evidence suggests that alteration of gut microbiota ('dysbiosis' can lead to a number of diseases, including obesity, which affects a large population in the world and is now a global health issue. The mechanisms of gut microbiota-mediated obesity are just being explored and characterized in recent years. It has been suggested that dysbiosis of gut microbiota contributes to obesity development mainly in three ways: affecting energy harvest, altering host gene expression, and triggering chronic inflammation. Among the factors that determine and influence gut microbiota composition, diet is one of the best characterized in human and animal studies, and has been long linked with weight gain or loss. In this review, we will discuss recent advances of mechanisms through which gut microbiota dysbiosis leads to obesity. We will further discuss the underlying causes of obesity-related gut microbiota, highlighting dietary effects.

  2. Assessment of the Microbiota in Microdissected Tissues of Crohn's Disease Patients

    Directory of Open Access Journals (Sweden)

    Gert De Hertogh

    2012-01-01

    Full Text Available The microbiota of the gastrointestinal tract is frequently mentioned as one of the key players in the etiopathogenesis of Crohn's disease (CD. Four hypotheses have been suggested: the single, still unknown bacterial pathogen, an abnormal overall composition of the bowel microbiota (“dysbiosis”, an abnormal immunological reaction to an essentially normally composed microbiota, and increased bacterial translocation. We propose that laser capture microdissection of selected microscopic structures, followed by broad-range 16S rRNA gene sequencing, is an excellent method to assess spatiotemporal alterations in the composition of the bowel microbiota in CD. Using this approach, we demonstrated significant changes of the composition, abundance, and location of the gut microbiome in this disease. Some of these abnormal findings persisted even after macroscopic mucosal healing. Further investigations along these lines may lead to a better understanding of the possible involvement of the bowel bacteria in the development of clinical Crohn's disease.

  3. Bacterial microbiome of lungs in COPD.

    Science.gov (United States)

    Sze, Marc A; Hogg, James C; Sin, Don D

    2014-01-01

    Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the bacterial microbiota at different body sites in human beings. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Although traditionally the lung has been viewed as a sterile organ, by using highly sensitive genomic techniques, recent reports have identified diverse bacterial communities in the human lung that may change in COPD. This review summarizes the current knowledge concerning the lung microbiota in COPD and its potential implications for pathogenesis of the disease.

  4. Galacto‐oligosaccharides attenuate renal injury with microbiota modification

    Science.gov (United States)

    Furuse, Satoshi U.; Ohse, Takamoto; Jo‐Watanabe, Airi; Shigehisa, Akira; Kawakami, Koji; Matsuki, Takahiro; Chonan, Osamu; Nangaku, Masaomi

    2014-01-01

    Abstracts Tubulointerstitial injury is central to the progression of end‐stage renal disease. Recent studies have revealed that one of the most investigated uremic toxins, indoxyl sulfate (IS), caused tubulointerstitial injury through oxidative stress and endoplasmic reticulum (ER) stress. Because indole, the precursor of IS, is synthesized from dietary tryptophan by the gut microbiota, we hypothesized that the intervention targeting the gut microbiota in kidney disease with galacto‐oligosaccharides (GOS) would attenuate renal injury. After 2 weeks of GOS administration for 5/6 nephrectomized (Nx) or sham‐operated (Sham) rats, cecal indole and serum IS were measured, renal injury was evaluated, and the effects of GOS on the gut microbiota were examined using pyrosequencing methods. Cecal indole and serum IS were significantly decreased and renal injury was improved with decreased infiltrating macrophages in GOS‐treated Nx rats. The expression levels of ER stress markers and apoptosis were significantly increased in the Nx rats and decreased with GOS. The microbiota analysis indicated that GOS significantly increased three bacterial families and decreased five families in the Nx rats. In addition, the analysis also revealed that the bacterial family Clostridiaceae was significantly increased in the Nx rats compared with the Sham rats and decreased with GOS. Taken altogether, our data show that GOS decreased cecal indole and serum IS, attenuated renal injury, and modified the gut microbiota in the Nx rats, and that the gut microbiota were altered in kidney disease. GOS could be a novel therapeutic agent to protect against renal injury. PMID:24994892

  5. Repertoire of intensive care unit pneumonia microbiota.

    Directory of Open Access Journals (Sweden)

    Sabri Bousbia

    Full Text Available Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs. During a three-year period, we tested the bronchoalveolar lavage (BAL of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls. Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥ 98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77 ± 2.93. Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented.

  6. The Gut Microbiota of Wild Mice

    OpenAIRE

    Weldon, L; Abolins, S; Lenzi, L.; Bourne, C; Riley, EM; Viney, M

    2015-01-01

    The gut microbiota profoundly affects the biology of its host. The composition of the microbiota is dynamic and is affected by both host genetic and many environmental effects. The gut microbiota of laboratory mice has been studied extensively, which has uncovered many of the effects that the microbiota can have. This work has also shown that the environments of different research institutions can affect the mouse microbiota. There has been relatively limited study of the microbiota of wild m...

  7. Gut Microbiota and Metabolic Disorders

    OpenAIRE

    Kyu Yeon Hur; Myung-Shik Lee

    2015-01-01

    Gut microbiota plays critical physiological roles in the energy extraction and in the control of local or systemic immunity. Gut microbiota and its disturbance also appear to be involved in the pathogenesis of diverse diseases including metabolic disorders, gastrointestinal diseases, cancer, etc. In the metabolic point of view, gut microbiota can modulate lipid accumulation, lipopolysaccharide content and the production of short-chain fatty acids that affect food intake, inflammatory tone, or...

  8. Hot topics in gut microbiota

    OpenAIRE

    Doré, Joël; Simrén, Magnus; Buttle, Lisa; Guarner, Francisco

    2013-01-01

    The study of gut microbiota is a rapidly moving field of research, and the impact of gut microbial communities on human health is widely perceived as one of the most exciting advancements in biomedicine in recent years. The gut microbiota plays a key role in digestion, metabolism and immune function, and has widespread impact beyond the gastrointestinal tract. Changes in the biodiversity of the gut microbiota are associated with far reaching consequences on host health and development. Furthe...

  9. Gastrointestinal function development and microbiota

    OpenAIRE

    Di Mauro, Antonio; Neu, Josef; Riezzo, Giuseppe; Raimondi, Francesco; Martinelli, Domenico; Francavilla, Ruggiero; Indrio, Flavia

    2013-01-01

    The intestinal microbiota plays an important role in the development of post-natal gastrointestinal functions of the host. Recent advances in our capability to identify microbes and their function offer exciting opportunities to evaluate the complex cross talk between microbiota, intestinal barrier, immune system and the gut-brain axis. This review summarizes these interactions in the early colonization of gastrointestinal tract with a major focus on the role of intestinal microbiota in the p...

  10. Probiotics and microbiota composition.

    Science.gov (United States)

    Sanders, Mary Ellen

    2016-06-02

    Accumulated evidence, corroborated by a new systematic review by Kristensen et al. (Genome Med 8:52, 2016), suggests that probiotics do not significantly impact the fecal microbiota composition of healthy subjects. Nevertheless, physiological benefits have been associated with probiotic consumption by healthy people. Some studies have suggested that probiotics may impact the function of colonizing microbes, although this needs to be further studied. An alternative hypothesis is that probiotics may promote homeostasis of the gut microbiota, rather than change its composition. This hypothesis warrants investigation as a possible mechanism for how probiotics may benefit healthy people.Please see related article: http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0300-5 .

  11. Microbiota of kefir grains

    Directory of Open Access Journals (Sweden)

    Tomislav Pogačić

    2013-03-01

    Full Text Available Kefir grains represent the unique microbial community consisting of bacteria, yeasts, and sometimes filamentous moulds creating complex symbiotic community. The complexity of their physical and microbial structures is the reason that the kefir grains are still not unequivocally elucidated. Microbiota of kefir grains has been studied by many microbiological and molecular approaches. The development of metagenomics, based on the identification without cultivation, is opening new possibilities for identification of previously nonisolated and non-identified microbial species from the kefir grains. Considering recent studies, there are over 50 microbial species associated with kefir grains. The aim of this review is to summarise the microbiota composition of kefir grains. Moreover, because of technological and microbiological significance of the kefir grains, the paper provides an insight into the microbiological and molecular methods applied to study microbial biodiversity of kefir grains.

  12. Nod2: A Critical Regulator of Ileal Microbiota and Crohn’s Disease

    Science.gov (United States)

    Sidiq, Tabasum; Yoshihama, Sayuri; Downs, Isaac; Kobayashi, Koichi S.

    2016-01-01

    The human intestinal tract harbors large bacterial community consisting of commensal, symbiotic, and pathogenic strains, which are constantly interacting with the intestinal immune system. This interaction elicits a non-pathological basal level of immune responses and contributes to shaping both the intestinal immune system and bacterial community. Recent studies on human microbiota are revealing the critical role of intestinal bacterial community in the pathogenesis of both systemic and intestinal diseases, including Crohn’s disease (CD). NOD2 plays a key role in the regulation of microbiota in the small intestine. NOD2 is highly expressed in ileal Paneth cells that provide critical mechanism for the regulation of ileal microbiota through the secretion of anti-bacterial compounds. Genome mapping of CD patients revealed that loss of function mutations in NOD2 are associated with ileal CD. Genome-wide association studies further demonstrated that NOD2 is one of the most critical genetic factor linked to ileal CD. The bacterial community in the ileum is indeed dysregulated in Nod2-deficient mice. Nod2-deficient ileal epithelia exhibit impaired ability of killing bacteria. Thus, altered interactions between ileal microbiota and mucosal immunity through NOD2 mutations play significant roles in the disease susceptibility and pathogenesis in CD patients, thereby depicting NOD2 as a critical regulator of ileal microbiota and CD. PMID:27703457

  13. Subcutaneous adipose fatty acid profiles and related rumen bacterial populations of steers fed red clover or grass hay diets containing flax or sunflower-seed.

    Directory of Open Access Journals (Sweden)

    Renee M Petri

    Full Text Available Steers were fed 70∶30 forage∶concentrate diets for 205 days, with either grass hay (GH or red clover silage (RC, and either sunflower-seed (SS or flaxseed (FS, providing 5.4% oil in the diets. Compared to diets containing SS, FS diets had elevated (P<0.05 subcutaneous trans (t-18:1 isomers, conjugated linoleic acids and n-6 polyunsaturated fatty acid (PUFA. Forage and oilseed type influenced total n-3 PUFA, especially α-linolenic acid (ALA and total non-conjugated diene biohydrogenation (BH in subcutaneous fat with proportions being greater (P<0.05 for FS or GH as compared to SS or RC. Of the 25 bacterial genera impacted by diet, 19 correlated with fatty acids (FA profile. Clostridium were most abundant when levels of conjugated linolenic acids, and n-3 PUFA's were found to be the lowest in subcutaneous fat, suggestive of their role in BH. Anerophaga, Fibrobacter, Guggenheimella, Paludibacter and Pseudozobellia were more abundant in the rumen when the levels of VA in subcutaneous fat were low. This study clearly shows the impact of oilseeds and forage source on the deposition of subcutaneous FA in beef cattle. Significant correlations between rumen bacterial genera and the levels of specific FA in subcutaneous fat maybe indicative of their role in determining the FA profile of adipose tissue. However, despite numerous correlations, the dynamics of rumen bacteria in the BH of unsaturated fatty acid and synthesis of PUFA and FA tissue profiles require further experimentation to determine if these correlations are consistent over a range of diets of differing composition. Present results demonstrate that in order to achieve targeted FA profiles in beef, a multifactorial approach will be required that takes into consideration not only the PUFA profile of the diet, but also the non-oil fraction of the diet, type and level of feed processing, and the role of rumen microbes in the BH of unsaturated fatty acid.

  14. Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine

    OpenAIRE

    Letícia Bianca Pereira; Renato Vicentini; Laura M. M. Ottoboni

    2015-01-01

    Abstract The core microbiota of a neutral mine drainage and the surrounding high heavy metal content soil at a Brazilian copper mine were characterized by 16S rDNA pyrosequencing. The core microbiota of the drainage was dominated by the generalist genus Meiothermus. The soil samples contained a more heterogeneous bacterial community, with the presence of both generalist and specialist bacteria. Both environments supported mainly heterotrophic bacteria, including organisms resistant to heavy m...

  15. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

    OpenAIRE

    Adamberg, Kaarel; Tomson, Katrin; Talve, Tiina; Pudova, Ksenia; Puurand, Marju; Visnapuu, Triinu; Alamäe, Tiina; Adamberg, Signe

    2015-01-01

    The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, change...

  16. Metabolomics Analysis Identifies Intestinal Microbiota-Derived Biomarkers of Colonization Resistance in Clindamycin-Treated Mice

    OpenAIRE

    Jump, Robin L. P.; Polinkovsky, Alex; Hurless, Kelly; Sitzlar, Brett; Eckart, Kevin; Tomas, Myreen; Deshpande, Abhishek; Nerandzic, Michelle M.; Donskey, Curtis J.

    2014-01-01

    Background The intestinal microbiota protect the host against enteric pathogens through a defense mechanism termed colonization resistance. Antibiotics excreted into the intestinal tract may disrupt colonization resistance and alter normal metabolic functions of the microbiota. We used a mouse model to test the hypothesis that alterations in levels of bacterial metabolites in fecal specimens could provide useful biomarkers indicating disrupted or intact colonization resistance after antibioti...

  17. Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili

    OpenAIRE

    Tytgat, Hanne L. P.; van Teijlingen, Nienke H.; Sullan, Ruby May A.; Douillard, François P.; Pia Rasinkangas; Marcel Messing; Justus Reunanen; Reetta Satokari; Jos Vanderleyden; Yves F Dufrêne; Geijtenbeek, Teunis B. H.; de Vos, Willem M.; Sarah Lebeer

    2016-01-01

    Mapping of the microbial molecules underlying microbiota-host interactions is key to understand how microbiota preserve mucosal homeostasis. A pivotal family of such bacterial molecules are pili. Pili are proteinaceous cell wall appendages with a well-documented role in adhesion, whilst their role in immune interaction with the host is less established. Gram-positive pili are often posttranslationally modified by sortase-specific cleavage reactions and the formation of intramolecular peptide ...

  18. Composition, variability, and temporal stability of the intestinal microbiota of the elderly.

    LENUS (Irish Health Repository)

    Claesson, Marcus J

    2011-03-15

    Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

  19. Dynamics of the surgical microbiota along the cardiothoracic surgery pathway

    Directory of Open Access Journals (Sweden)

    Sara eRomano-Bertrand

    2015-01-01

    Full Text Available Human skin associated microbiota are increasingly described by culture-independent methods that showed an unexpected diversity with variation correlated with several pathologies. A role of microbiota disequilibrium in infection occurrence is hypothesized, particularly in surgical site infections. We study the diversities of operative site microbiota and its dynamics during surgical pathway of patients undergoing coronary-artery by-pass graft (CABG. Pre-, per- and post-operative samples were collected from 25 patients: skin before the surgery, superficially and deeply during the intervention, and healing tissues. Bacterial diversity was assessed by DNA fingerprint using 16S rRNA gene PCR and Temporal Temperature Gel Electrophoresis (TTGE. The diversity of Operational Taxonomic Units (OTUs at the surgical site was analyzed according to the stage of surgery.From all patients and samples, we identified 147 different OTUs belonging to the 6 phyla Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria and Fusobacteria. High variations were observed among patients but common themes can be observed. The Firmicutes dominated quantitatively but were largely encompassed by the Proteobacteria regarding the OTUs diversity. The genera Propionibacterium and Staphylococcus predominated on the preoperative skin, whereas very diverse Proteobacteria appeared selected in peri-operative samples. The resilience in scar skin was partial with depletion in Actinobacteria and Firmicutes and increase of Gram-negative bacteria. Finally, the thoracic operative site presents an unexpected bacterial diversity, which is partially common to skin microbiota but presents particular dynamics. We described a complex bacterial community that gathers pathobiontes and bacteria deemed to be environmental, opportunistic pathogens and non-pathogenic bacteria. These data stress to consider surgical microbiota as a pathobiome rather than a reservoir of individual

  20. Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015.

    Science.gov (United States)

    Blumberg, Jeffrey B; Basu, Arpita; Krueger, Christian G; Lila, Mary Ann; Neto, Catherine C; Novotny, Janet A; Reed, Jess D; Rodriguez-Mateos, Ana; Toner, Cheryl D

    2016-07-01

    Recent advances in cranberry research have expanded the evidence for the role of this Vaccinium berry fruit in modulating gut microbiota function and cardiometabolic risk factors. The A-type structure of cranberry proanthocyanidins seems to be responsible for much of this fruit's efficacy as a natural antimicrobial. Cranberry proanthocyanidins interfere with colonization of the gut by extraintestinal pathogenic Escherichia coli in vitro and attenuate gut barrier dysfunction caused by dietary insults in vivo. Furthermore, new studies indicate synergy between these proanthocyanidins, other cranberry components such as isoprenoids and xyloglucans, and gut microbiota. Together, cranberry constituents and their bioactive catabolites have been found to contribute to mechanisms affecting bacterial adhesion, coaggregation, and biofilm formation that may underlie potential clinical benefits on gastrointestinal and urinary tract infections, as well as on systemic anti-inflammatory actions mediated via the gut microbiome. A limited but growing body of evidence from randomized clinical trials reveals favorable effects of cranberry consumption on measures of cardiometabolic health, including serum lipid profiles, blood pressure, endothelial function, glucoregulation, and a variety of biomarkers of inflammation and oxidative stress. These results warrant further research, particularly studies dedicated to the elucidation of dose-response relations, pharmacokinetic/metabolomics profiles, and relevant biomarkers of action with the use of fully characterized cranberry products. Freeze-dried whole cranberry powder and a matched placebo were recently made available to investigators to facilitate such work, including interlaboratory comparability. PMID:27422512

  1. In vitro evaluation of the microbiota modulation abilities of different sized whole oat grain flakes.

    Science.gov (United States)

    Connolly, Michael L; Lovegrove, Julie A; Tuohy, Kieran M

    2010-10-01

    Epidemiological studies and healthy eating guidelines suggest a positive correlation between ingestion of whole grain cereal and food rich in fibre with protection from chronic diseases. The prebiotic potential of whole grains may be related, however, little is known about the microbiota modulatory capability of oat grain or the impact processing has on this ability. In this study the fermentation profile of whole grain oat flakes, processed to produce two different sized flakes (small and large), by human faecal microbiota was investigated in vitro. Simulated digestion and subsequent fermentation by gut bacteria was investigated using pH controlled faecal batch cultures inoculated with human faecal slurry. The different sized oat flakes, Oat 23's (0.53-0.63 mm) and Oat 25's/26's (0.85-1.0 mm) were compared to oligofructose, a confirmed prebiotic, and cellulose, a poorly fermented carbohydrate. Bacterial enumeration was carried out using the culture independent technique, fluorescent in situ hybridisation, and short chain fatty acid (SCFA) production monitored by gas chromatography. Significant changes in total bacterial populations were observed after 24 h incubation for all substrates except Oat 23's and cellulose. Oats 23's fermentation resulted in a significant increase in the Bacteroides-Prevotella group. Oligofructose and Oats 25's/26's produced significant increases in Bifidobacterium in the latter stages of fermentation while numbers declined for Oats 23's between 5 h and 24 h. This is possibly due to the smaller surface area of the larger flakes inhibiting the simulated digestion, which may have resulted in increased levels of resistant starch (Bifidobacterium are known to ferment this dietary fibre). Fermentation of Oat 25's/26's resulted in a propionate rich SCFA profile and a significant increase in butyrate, which have both been linked to benefiting host health. The smaller sized oats did not produce a significant increase in butyrate

  2. Contrast-enhanced MR imaging in bacterial meningitis in children. Temporal profile and correlation with the prognosis

    International Nuclear Information System (INIS)

    Treatment periods for bacterial meningitis are often very long, and often this prolonged treatment is based on the judgment of its effectiveness by the degree of enhancement on brain magnetic resonance imaging (MRI). In this study, we analyzed the contrast MRI in the acute and recovery phases of bacterial meningitis in twelve patients, and graded the contrast level of the subdural space and subarachnoid space separately. While the contrast level of the subarachnoid space increased with time in 4 cases, that of the subdural space increased in 10 cases, and 9 of them revealed a good prognosis without continuation of the treatment. These findings indicate that increased contrast level of the subdural space is common in the recovery phase of bacterial meningitis, and that repetitive MRI investigation is not valuable to determine the duration of treatment. (author)

  3. Gut microbiota and the development of obesity La microbiota intestinal y el desarrollo de la obesidad

    Directory of Open Access Journals (Sweden)

    A. P. Boroni Moreira

    2012-10-01

    Full Text Available Introduction: Advances in tools for molecular investigations have allowed deeper understanding of how microbes can influence host physiology. A very interesting field of research that has gained attention recently is the possible role of gut microbiota in the development of obesity and metabolic disorders. Objective: The aim of this review is to discuss mechanisms that explain the influence of gut microbiota on host metabolism. Results and discussion: The gut microbiota is important for normal physiology of the host. However, differences in their composition may have different impacts on host metabolism. It has been shown that obese and lean subjects present different microbiota composition profile. These differences in microbiota composition may contribute to weight imbalance and impaired metabolism. The evidences from animal models suggest that it is possible that the microbiota of obese subjects has higher capacity to harvest energy from the diet providing substrates that can activate lipogenic pathways. In addition, microorganisms can also influence the activity of lipoprotein lipase interfering in the accumulation of triglycerides in the adipose tissue. The interaction of gut microbiota with the endocannabinoid system provides a route through which intestinal permeability can be altered. Increased intestinal permeability allows the entrance of endotoxins to the circulation, which are related to the induction of inflammation and insulin resistance in mice. The impact of the proposed mechanisms for humans still needs further investigations. However, the fact that gut microbiota can be modulated through dietary components highlights the importance to study how fatty acids, carbohydrates, micronutrients, prebiotics, and probiotics can influence gut microbiota composition and the management of obesity. Gut microbiota seems to be an important and promising target in the prevention and treatment of obesity and its related metabolic disturbances in

  4. Gut Microbiota-brain Axis

    Science.gov (United States)

    Wang, Hong-Xing; Wang, Yu-Ping

    2016-01-01

    Objective: To systematically review the updated information about the gut microbiota-brain axis. Data Sources: All articles about gut microbiota-brain axis published up to July 18, 2016, were identified through a literature search on PubMed, ScienceDirect, and Web of Science, with the keywords of “gut microbiota”, “gut-brain axis”, and “neuroscience”. Study Selection: All relevant articles on gut microbiota and gut-brain axis were included and carefully reviewed, with no limitation of study design. Results: It is well-recognized that gut microbiota affects the brain's physiological, behavioral, and cognitive functions although its precise mechanism has not yet been fully understood. Gut microbiota-brain axis may include gut microbiota and their metabolic products, enteric nervous system, sympathetic and parasympathetic branches within the autonomic nervous system, neural-immune system, neuroendocrine system, and central nervous system. Moreover, there may be five communication routes between gut microbiota and brain, including the gut-brain's neural network, neuroendocrine-hypothalamic-pituitary-adrenal axis, gut immune system, some neurotransmitters and neural regulators synthesized by gut bacteria, and barrier paths including intestinal mucosal barrier and blood-brain barrier. The microbiome is used to define the composition and functional characteristics of gut microbiota, and metagenomics is an appropriate technique to characterize gut microbiota. Conclusions: Gut microbiota-brain axis refers to a bidirectional information network between the gut microbiota and the brain, which may provide a new way to protect the brain in the near future. PMID:27647198

  5. Antibiotic Administration and Factors Influencing the Vaginal Microbiota during Pregnancy

    DEFF Research Database (Denmark)

    Stokholm, Jakob

    2012-01-01

    with a following increase in pH level can lead to an overgrowth of certain microbiota resulting in bacterial vaginosis or vaginal candidiasis. Humans are continuously exposed to a large amount of environmental factors providing a possible influence on their microbial ecology. Antibiotic administration is one......, and in women with a lower parity. These predictors for antibiotic administration may be used as general health indicators. In study II we analyzed the effect of antibiotic administration during pregnancy on the commensal vaginal microbiota. Vaginal samples were cultured at 36th week of pregnancy and described...... treatment in pregnancy.A changed vaginal flora in pregnant women may lead to infections with potential morbidity to woman and fetus. In study III we studied the associations between exposure to cat and dog during pregnancy and the vaginal bacterial flora at 36th week of pregnancy, antibiotic usage, and self...

  6. Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

    Science.gov (United States)

    Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

    2015-12-30

    The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY.

  7. Bacterial Etiology and Antibiotic Resistance Profile of Community-Acquired Urinary Tract Infections in a Cameroonian City

    Science.gov (United States)

    Gonsu, Hortense Kamga; Koulla-Shiro, Sinata

    2016-01-01

    Introduction. Community-acquired urinary tract infections (CAUTIs) are usually treated empirically. Geographical variations in etiologic agents and their antibiotic sensitivity patterns are common. Knowledge of antibiotic resistance trends is important for improving evidence-based recommendations for empirical treatment of UTIs. Our aim was to determine the major bacterial etiologies of CAUTIs and their antibiotic resistance patterns in a cosmopolitan area of Cameroon for comparison with prescription practices of local physicians. Methods. We performed a cross-sectional descriptive study at two main hospitals in Yaoundé, collecting a clean-catch mid-stream urine sample from 92 patients having a clinical diagnosis of UTI. The empirical antibiotherapy was noted, and identification of bacterial species was done on CLED agar; antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Results. A total of 55 patients had samples positive for a UTI. Ciprofloxacin and amoxicillin/clavulanic acid were the most empirically prescribed antibiotics (30.9% and 23.6%, resp.); bacterial isolates showed high prevalence of resistance to both compounds. Escherichia coli (50.9%) was the most common pathogen, followed by Klebsiella pneumoniae (16.4%). Prevalence of resistance for ciprofloxacin was higher compared to newer quinolones. Conclusions. E. coli and K. pneumoniae were the predominant bacterial etiologies; the prevalence of resistance to commonly prescribed antibiotics was high. PMID:27667998

  8. Bacterial Etiology and Antibiotic Resistance Profile of Community-Acquired Urinary Tract Infections in a Cameroonian City.

    Science.gov (United States)

    Nzalie, Rolf Nyah-Tuku; Gonsu, Hortense Kamga; Koulla-Shiro, Sinata

    2016-01-01

    Introduction. Community-acquired urinary tract infections (CAUTIs) are usually treated empirically. Geographical variations in etiologic agents and their antibiotic sensitivity patterns are common. Knowledge of antibiotic resistance trends is important for improving evidence-based recommendations for empirical treatment of UTIs. Our aim was to determine the major bacterial etiologies of CAUTIs and their antibiotic resistance patterns in a cosmopolitan area of Cameroon for comparison with prescription practices of local physicians. Methods. We performed a cross-sectional descriptive study at two main hospitals in Yaoundé, collecting a clean-catch mid-stream urine sample from 92 patients having a clinical diagnosis of UTI. The empirical antibiotherapy was noted, and identification of bacterial species was done on CLED agar; antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Results. A total of 55 patients had samples positive for a UTI. Ciprofloxacin and amoxicillin/clavulanic acid were the most empirically prescribed antibiotics (30.9% and 23.6%, resp.); bacterial isolates showed high prevalence of resistance to both compounds. Escherichia coli (50.9%) was the most common pathogen, followed by Klebsiella pneumoniae (16.4%). Prevalence of resistance for ciprofloxacin was higher compared to newer quinolones. Conclusions. E. coli and K. pneumoniae were the predominant bacterial etiologies; the prevalence of resistance to commonly prescribed antibiotics was high. PMID:27667998

  9. The gut microbiota and host health

    OpenAIRE

    Marchesi, Julian R.; David H Adams; Fava, Francesca; Hermes, Gerben D A; Hirschfield, Gideon M; Hold, Georgina; Quraishi, Mohammed N.; Kinross, James; Smidt, Hauke; Tuohy, Kieran M.; Thomas, Linda V.; Zoetendal, Erwin G.; Hart, Ailsa

    2015-01-01

    Over the last 10-15 years, our understanding of the composition and functions of the human gut microbiota has increased exponentially. To a large extent, this has been due to new 'omic' technologies that have facilitated large-scale analysis of the genetic and metabolic profile of this microbial community, revealing it to be comparable in influence to a new organ in the body and offering the possibility of a new route for therapeutic intervention. Moreover, it might be more accurate to think ...

  10. Celecoxib Alters the Intestinal Microbiota and Metabolome in Association with Reducing Polyp Burden.

    Science.gov (United States)

    Montrose, David C; Zhou, Xi Kathy; McNally, Erin M; Sue, Erika; Yantiss, Rhonda K; Gross, Steven S; Leve, Nitai D; Karoly, Edward D; Suen, Chen S; Ling, Lilan; Benezra, Robert; Pamer, Eric G; Dannenberg, Andrew J

    2016-09-01

    Treatment with celecoxib, a selective COX-2 inhibitor, reduces formation of premalignant adenomatous polyps in the gastrointestinal tracts of humans and mice. In addition to its chemopreventive activity, celecoxib can exhibit antimicrobial activity. Differing bacterial profiles have been found in feces from colon cancer patients compared with those of normal subjects. Moreover, preclinical studies suggest that bacteria can modulate intestinal tumorigenesis by secreting specific metabolites. In the current study, we determined whether celecoxib treatment altered the luminal microbiota and metabolome in association with reducing intestinal polyp burden in mice. Administration of celecoxib for 10 weeks markedly reduced intestinal polyp burden in APC(Min/+) mice. Treatment with celecoxib also altered select luminal bacterial populations in both APC(Min/+) and wild-type mice, including decreased Lactobacillaceae and Bifidobacteriaceae as well as increased Coriobacteriaceae Metabolomic analysis demonstrated that celecoxib caused a strong reduction in many fecal metabolites linked to carcinogenesis, including glucose, amino acids, nucleotides, and lipids. Ingenuity Pathway Analysis suggested that these changes in metabolites may contribute to reduced cell proliferation. To this end, we showed that celecoxib reduced cell proliferation in the base of normal appearing ileal and colonic crypts of APC(Min/+) mice. Consistent with this finding, lineage tracing indicated that celecoxib treatment reduced the rate at which Lgr5-positive stem cells gave rise to differentiated cell types in the crypts. Taken together, these results demonstrate that celecoxib alters the luminal microbiota and metabolome along with reducing epithelial cell proliferation in mice. We hypothesize that these actions contribute to its chemopreventive activity. Cancer Prev Res; 9(9); 721-31. ©2016 AACR. PMID:27432344

  11. Role of Gut Microbiota in Liver Disease.

    Science.gov (United States)

    Brenner, David A; Paik, Yong-Han; Schnabl, Bernd

    2015-01-01

    Many lines of research have established a relationship between the gut microbiome and patients with liver disease. For example, patients with cirrhosis have increased bacteremia, increased blood levels of lipopolysaccharide, and increased intestinal permeability. Patients with cirrhosis have bacterial overgrowth in the small intestine. Selective intestinal decontamination with antibiotics is beneficial for patients with decompensated cirrhosis. In experimental models of chronic liver injury with fibrosis, several toll-like receptors (TLR) are required to make mice sensitive to liver fibrosis. The presumed ligand for the TLRs are bacterial products derived from the gut microbiome, and TLR knockout mice are resistant to liver inflammation and fibrosis. We and others have characterized the association between preclinical models of liver disease in mice with the microbial diversity in their gut microbiome. In each model, including intragastric alcohol, bile duct ligation, chronic carbon tetrachloride (CCl4), administration, and genetic obesity, there is a significant change in the gut microbiome from normal control mice. However, there is not a single clear bacterial strain or pattern that distinguish mice with liver injury from controlled mice. So how can the gut microbiota affect liver disease? We can identify at least 6 changes that would result in liver injury, inflammation, and/or fibrosis. These include: (1) changes in caloric yield of diet; (2) regulation of gut permeability to release bacterial products; (3) modulation of choline metabolism; (4) production of endogenous ethanol; (5) regulation of bile acid metabolism; and (6) regulation in lipid metabolism.

  12. Intestinal microbiota and ulcerative colitis.

    Science.gov (United States)

    Ohkusa, Toshifumi; Koido, Shigeo

    2015-11-01

    There is a close relationship between the human host and the intestinal microbiota, which is an assortment of microorganisms, protecting the intestine against colonization by exogenous pathogens. Moreover, the intestinal microbiota play a critical role in providing nutrition and the modulation of host immune homeostasis. Recent reports indicate that some strains of intestinal bacteria are responsible for intestinal ulceration and chronic inflammation in inflammatory bowel diseases (IBD) such as ulcerative colitis (UC) and Crohn's disease (CD). Understanding the interaction of the intestinal microbiota with pathogens and the human host might provide new strategies treating patients with IBD. This review focuses on the important role that the intestinal microbiota plays in maintaining innate immunity in the pathogenesis and etiology of UC and discusses new antibiotic therapies targeting the intestinal microbiota.

  13. Gut Microbiota: Modulate its Complexity to Restore the Balance

    OpenAIRE

    Fermín Mearin; Speakers Fermín Mearin; Antonio Gasbarrini; Peter Malfertheiner; Mark Pimentel

    2015-01-01

    The importance of the gut microbiota to health is becoming more widely appreciated. The range of commensal microorganisms in healthy individuals and in patients with a variety of digestive diseases is under active investigation, and evidence is accumulating to suggest that both the diversity and balance of bacterial species are important for health. Disturbance of the balance of microorganisms – dysbiosis – is associated with obesity and a variety of diseases. Restoring the balance by modulat...

  14. Molecular characterization of the cloacal microbiota of wild and captive parrots.

    Science.gov (United States)

    Xenoulis, Panagiotis G; Gray, Patricia L; Brightsmith, Donald; Palculict, Blake; Hoppes, Sharman; Steiner, Jörg M; Tizard, Ian; Suchodolski, Jan S

    2010-12-15

    The gastrointestinal microbiota plays a fundamental role in health and disease. Only limited data are available about the composition of the intestinal microbiota of captive animals compared to those of wild animals. The aim of the present study was to characterize the cloacal microbiota of apparently healthy wild and captive parrots. A total of 16 parrots, 8 wild and 8 captive, belonging to 3 different species, were used in this study. Cloacal material was collected via cloacal swabbing. DNA was extracted and 16S rRNA genes were amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. A total of 518 clones were analyzed, and 49 operational taxonomic units (OTUs) were identified. The OTUs were classified in 4 bacterial phyla: Firmicutes (72.9%), Proteobacteria (14.9%), Actinobacteria (12%), and Bacteroidetes (0.2%). Bacterial diversity was significantly lower in wild birds than in captive birds. Principal component analysis based on the Unifrac distance metric indicated that the cloacal microbiota differed between wild and captive parrots. Staphylococcus saprophyticus was significantly more abundant in wild birds, while Escherichia coli was significantly more abundant in captive birds. In conclusion, wild and captive parrots appear to have differences in the composition of their cloacal bacterial microbiota. The clinical significance of these differences remains to be determined.

  15. Substratum-Associated Microbiota.

    Science.gov (United States)

    Furey, Paula C; Liess, Antonia

    2015-10-01

    This review of literature on substratumassociated microbiota from 2014 highlights topics on benthic algae and bacteria from a range of aquatic environments, but focuses on freshwater habitats. Advances in pollution and toxin detection, assessment methods, and applications of new technologies are highlighted as are updates in taxonomy and systematics. Aspects of general ecology, water quality, nutrient cycling, trophic interactions, land use changes, biofuels, biofouling, and environmental challenges such as climate change, pollutants, tar sands and fracking, oil spills and nuisance blooms are presented. PMID:26420102

  16. Substratum-Associated Microbiota.

    Science.gov (United States)

    Furey, Paula C; Deininger, Anne; Liess, Antonia

    2016-10-01

    This survey of literature on substratum associated microbiota from 2015 highlights research findings associated with benthic algae and bacteria from a variety of aquatic environments, but primarily freshwaters. It focuses on topics of interest to the Water Environment Federation along with those of current emerging interest such as global change, oil spills, and environmental contaminants like pharmaceutical compounds, microplastics, nanoparticles and organic pollutants. Other interesting findings briefly covered include areas of general ecology, nutrient cycling, trophic interactions, water quality, nuisance and invasive species, bioindicators, and bioremediation. PMID:27620106

  17. Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity

    DEFF Research Database (Denmark)

    Laursen, Martin Frederik; Andersen, Louise B. B.; Michaelsen, Kim F.;

    2016-01-01

    The first years of life are paramount in establishing our endogenous gut microbiota, which is strongly affected by diet and has repeatedly been linked with obesity. However, very few studies have addressed the influence of maternal obesity on infant gut microbiota, which may occur either through...... vertically transmitted microbes or through the dietary habits of the family. Additionally, very little is known about the effect of diet during the complementary feeding period, which is potentially important for gut microbiota development. Here, the gut microbiotas of two different cohorts of infants, born...... either of a random sample of healthy mothers (n = 114), or of obese mothers (n = 113), were profiled by 16S rRNA amplicon sequencing. Gut microbiota data were compared to breastfeeding patterns and detailed individual dietary recordings to assess effects of the complementary diet. We found that maternal...

  18. Antimicrobial profiles of bacterial clinical isolates from the Gabonese National Laboratory of Public Health: data from routine activity

    Directory of Open Access Journals (Sweden)

    Léonard Kouegnigan Rerambiah

    2014-12-01

    Conclusions: The antimicrobial resistance profiles seen here are of concern. To control the spread of drug-resistant bacteria, clinicians should be cognizant of their local antimicrobial resistance patterns.

  19. Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

    OpenAIRE

    Roder, Cornelia; Arif, Chatchanit; Daniels, Camille; Weil, Ernesto; Voolstra, Christian R.

    2014-01-01

    Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differential...

  20. Pathophysiological role of host microbiota in the development of obesity.

    Science.gov (United States)

    Kobyliak, Nazarii; Virchenko, Oleksandr; Falalyeyeva, Tetyana

    2016-04-23

    Overweight and obesity increase the risk for a number of diseases, namely, cardiovascular diseases, type 2 diabetes, dyslipidemia, premature death, non-alcoholic fatty liver disease as well as different types of cancer. Approximately 1.7 billion people in the world suffer from being overweight, most notably in developed countries. Current research efforts have focused on host and environmental factors that may affect energy balance. It was hypothesized that a microbiota profile specific to an obese host with increased energy-yielding behavior may exist. Consequently, the gut microbiota is becoming of significant research interest in relation to obesity in an attempt to better understand the aetiology of obesity and to develop new methods of its prevention and treatment. Alteration of microbiota composition may stimulate development of obesity and other metabolic diseases via several mechanisms: increasing gut permeability with subsequent metabolic inflammation; increasing energy harvest from the diet; impairing short-chain fatty acids synthesis; and altering bile acids metabolism and FXR/TGR5 signaling. Prebiotics and probiotics have physiologic functions that contribute to the health of gut microbiota, maintenance of a healthy body weight and control of factors associated with obesity through their effects on mechanisms that control food intake, body weight, gut microbiota and inflammatory processes.

  1. Microbial transformation from normal oral microbiota to acute endodontic infections

    Directory of Open Access Journals (Sweden)

    Hsiao William WL

    2012-07-01

    Full Text Available Abstract Background Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial diversity. Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections. Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites. Results On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample. All sequences fell into 11 different bacterial phyla. The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples. Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples. The microbiota community structures of root canal and abscess samples were, however, more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples. Conclusions We used a novel approach and high-throughput methodologies to characterize the microbiota associated normal and diseased oral sites in the same individuals.

  2. The Intestinal Microbiota in Metabolic Disease

    Directory of Open Access Journals (Sweden)

    Anni Woting

    2016-04-01

    Full Text Available Gut bacteria exert beneficial and harmful effects in metabolic diseases as deduced from the comparison of germfree and conventional mice and from fecal transplantation studies. Compositional microbial changes in diseased subjects have been linked to adiposity, type 2 diabetes and dyslipidemia. Promotion of an increased expression of intestinal nutrient transporters or a modified lipid and bile acid metabolism by the intestinal microbiota could result in an increased nutrient absorption by the host. The degradation of dietary fiber and the subsequent fermentation of monosaccharides to short-chain fatty acids (SCFA is one of the most controversially discussed mechanisms of how gut bacteria impact host physiology. Fibers reduce the energy density of the diet, and the resulting SCFA promote intestinal gluconeogenesis, incretin formation and subsequently satiety. However, SCFA also deliver energy to the host and support liponeogenesis. Thus far, there is little knowledge on bacterial species that promote or prevent metabolic disease. Clostridium ramosum and Enterococcus cloacae were demonstrated to promote obesity in gnotobiotic mouse models, whereas bifidobacteria and Akkermansia muciniphila were associated with favorable phenotypes in conventional mice, especially when oligofructose was fed. How diet modulates the gut microbiota towards a beneficial or harmful composition needs further research. Gnotobiotic animals are a valuable tool to elucidate mechanisms underlying diet–host–microbe interactions.

  3. Effect of two different housing systems on the gut microbiota of germ-free SW mice reconstituted with a complex murine microbiota

    DEFF Research Database (Denmark)

    Lundberg, Randi; Toft, Martin Fitzner; Bahl, Martin I;

    to the inoculum to see the effect of housing and time on the relative bacterial abundances and the appearance of contaminants and their ability to change the overall community picture. With this work, we explore the possibility of housing mice with a complex microbiota over a time period of 5 months in a less...

  4. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology

    Science.gov (United States)

    Chen, Yanfei; Ji, Feng; Guo, Jing; Shi, Ding; Fang, Daiqiong; Li, Lanjuan

    2016-01-01

    Cirrhosis-associated duodenal dysbiosis is not yet clearly defined. In this research, duodenal mucosal microbiota was analyzed in 30 cirrhotic patients and 28 healthy controls using 16S rRNA gene pyrosequencing methods. The principal coordinate analysis revealed that cirrhotic patients were colonized by remarkable different duodenal mucosal microbiota in comparison with controls. At the genus level, Veillonella, Megasphaera, Dialister, Atopobium, and Prevotella were found overrepresented in cirrhotic duodenum. And the duodenal microbiota of healthy controls was enriched with Neisseria, Haemophilus, and SR1 genera incertae sedis. On the other hand, based on predicted metagenomes analyzed, gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism) were highly abundant in cirrhosis duodenal microbiota, and functional modules involved in bacterial proliferation and colonization (e.g. bacterial motility proteins and secretion system) were overrepresented in controls. When considering the etiology of cirrhosis, two operational taxonomic units (OTUs), OTU-23 (Neisseria) and OTU-36 (Gemella), were found discriminative between hepatitis-B-virus related cirrhosis and primary biliary cirrhosis. The results suggest that the structure of duodenal mucosa microbiota in cirrhotic patients is dramatically different from healthy controls. The duodenum dysbiosis might be related to alterations of oral microbiota and changes in duodenal micro-environment. PMID:27687977

  5. Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria.

    Science.gov (United States)

    Hubert, Jan; Kamler, Martin; Nesvorna, Marta; Ledvinka, Ondrej; Kopecky, Jan; Erban, Tomas

    2016-08-01

    The ectoparasitic mite Varroa destructor is a major pest of the honeybee Apis mellifera. In a previous study, bacteria were found in the guts of mites collected from winter beehive debris and were identified using Sanger sequencing of their 16S rRNA genes. In this study, community comparison and diversity analyses were performed to examine the microbiota of honeybees and mites at the population level. The microbiota of the mites and honeybees in 26 colonies in seven apiaries in Czechia was studied. Between 10 and 50 Varroa females were collected from the bottom board, and 10 worker bees were removed from the peripheral comb of the same beehive. Both bees and mites were surface sterilized. Analysis of the 16S rRNA gene libraries revealed significant differences in the Varroa and honeybee microbiota. The Varroa microbiota was less diverse than was the honeybee microbiota, and the relative abundances of bacterial taxa in the mite and bee microbiota differed. The Varroa mites, but not the honeybees, were found to be inhabited by Diplorickettsia. The relative abundance of Arsenophonus, Morganella, Spiroplasma, Enterococcus, and Pseudomonas was higher in Varroa than in honeybees, and the Diplorickettsia symbiont detected in this study is specific to Varroa mites. The results demonstrated that there are shared bacteria between Varroa and honeybee populations but that these bacteria occur in different relative proportions in the honeybee and mite bacteriomes. These results support the suggestion of bacterial transfer via mites, although only some of the transferred bacteria may be harmful.

  6. Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria.

    Science.gov (United States)

    Hubert, Jan; Kamler, Martin; Nesvorna, Marta; Ledvinka, Ondrej; Kopecky, Jan; Erban, Tomas

    2016-08-01

    The ectoparasitic mite Varroa destructor is a major pest of the honeybee Apis mellifera. In a previous study, bacteria were found in the guts of mites collected from winter beehive debris and were identified using Sanger sequencing of their 16S rRNA genes. In this study, community comparison and diversity analyses were performed to examine the microbiota of honeybees and mites at the population level. The microbiota of the mites and honeybees in 26 colonies in seven apiaries in Czechia was studied. Between 10 and 50 Varroa females were collected from the bottom board, and 10 worker bees were removed from the peripheral comb of the same beehive. Both bees and mites were surface sterilized. Analysis of the 16S rRNA gene libraries revealed significant differences in the Varroa and honeybee microbiota. The Varroa microbiota was less diverse than was the honeybee microbiota, and the relative abundances of bacterial taxa in the mite and bee microbiota differed. The Varroa mites, but not the honeybees, were found to be inhabited by Diplorickettsia. The relative abundance of Arsenophonus, Morganella, Spiroplasma, Enterococcus, and Pseudomonas was higher in Varroa than in honeybees, and the Diplorickettsia symbiont detected in this study is specific to Varroa mites. The results demonstrated that there are shared bacteria between Varroa and honeybee populations but that these bacteria occur in different relative proportions in the honeybee and mite bacteriomes. These results support the suggestion of bacterial transfer via mites, although only some of the transferred bacteria may be harmful. PMID:27129319

  7. Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management.

    Science.gov (United States)

    Lee, Min-Jung; Lee, Jin-Jae; Chung, Han Young; Choi, Sang Ho; Kim, Bong-Soo

    2016-10-01

    Abalone is a popular seafood in South Korea; however, because it contains various microorganisms, its ingestion can cause food poisoning. Therefore, analysis of the microbiota on abalone can improve understanding of outbreaks and causes of food poisoning and help to better manage seafood products. In this study, we collected a total of 40 abalones from four different regions in March and July, which are known as the maximum abalone production areas in Korea. The microbiota were analyzed using high-throughput sequencing, and bacterial loads on abalone were quantified by real-time PCR. Over 2700 species were detected in the samples, and Alpha- and Gammaproteobacteria were the predominant classes. The differences in microbiota among regions and at each sampling time were also investigated. Although Psychrobacter was the dominant genus detected on abalone in both March and July, the species compositions were different between the two sampling times. Five potential pathogens (Lactococcus garvieae, Yersinia kristensenii, Staphylococcus saprophyticus, Staphylococcus warneri, and Staphylococcus epidermidis) were detected among the abalone microbiota. In addition, we analyzed the influence of Vibrio parahaemolyticus infection on shifts in abalone microbiota during storage at different temperatures. Although the proportion of Vibrio increased over time in infected and non-infected abalone, the shifts of microbiota were more dynamic in infected abalone. These results can be used to better understand the potential of food poisoning caused by abalone consumption and manage abalone products according to the microbiota composition. PMID:27371902

  8. Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene.

    Directory of Open Access Journals (Sweden)

    G Estruch

    Full Text Available Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata, the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043 and Photobacterium (p-value: 0.025 were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of

  9. Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene.

    Science.gov (United States)

    Estruch, G; Collado, M C; Peñaranda, D S; Tomás Vidal, A; Jover Cerdá, M; Pérez Martínez, G; Martinez-Llorens, S

    2015-01-01

    Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata), the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043) and Photobacterium (p-value: 0.025) were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of the microbiota to

  10. Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert.

    Science.gov (United States)

    Piubeli, Francine; de Lourdes Moreno, María; Kishi, Luciano Takeshi; Henrique-Silva, Flavio; García, María Teresa; Mellado, Encarnación

    2015-12-01

    The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations . PMID:26543264

  11. Gut Microbiota, Inflammation, and Colorectal Cancer.

    Science.gov (United States)

    Brennan, Caitlin A; Garrett, Wendy S

    2016-09-01

    Colorectal cancer is the second-leading cause of cancer-related deaths in the United States and fourth-leading cause of cancer-related deaths worldwide. While cancer is largely considered to be a disease of genetic and environmental factors, increasing evidence has demonstrated a role for the microbiota (the microorganisms associated with the human body) in shaping inflammatory environments and promoting tumor growth and spread. Herein, we discuss both human data from meta'omics analyses and data from mechanistic studies in cell culture and animal models that support specific bacterial agents as potentiators of tumorigenesis-including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli. Further, we consider how microbes can be used in diagnosing colorectal cancer and manipulating the tumor environment to encourage better patient outcomes in response to immunotherapy treatments. PMID:27607555

  12. Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer

    Science.gov (United States)

    Ray, Debolina; Kidane, Dawit

    2016-01-01

    Gut microbiota are required for host nutrition, energy balance, and regulating immune homeostasis, however, in some cases, this mutually beneficial relationship becomes twisted (dysbiosis), and the gut flora can incite pathological disorders including colon cancer. Microbial dysbiosis promotes the release of bacterial genotoxins, metabolites, and causes chronic inflammation, which promote oxidative DNA damage. Oxidized DNA base lesions are removed by base excision repair (BER), however, the role of this altered function of BER, as well as microbiota-mediated genomic instability and colon cancer development, is still poorly understood. In this review article, we will discuss how dysbiotic microbiota induce DNA damage, its impact on base excision repair capacity, the potential link of host BER gene polymorphism, and the risk of dysbiotic microbiota mediated genomic instability and colon cancer.

  13. The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica.

    Science.gov (United States)

    Wilkinson, Ngare; Hughes, Robert J; Aspden, William J; Chapman, James; Moore, Robert J; Stanley, Dragana

    2016-05-01

    Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2-3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the diversity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT; however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections. PMID:26758298

  14. Staphylococcus epidermidis: A differential trait of the fecal microbiota of breast-fed infants

    Directory of Open Access Journals (Sweden)

    Fernández Leonides

    2008-09-01

    Full Text Available Abstract Background Breast milk is an important source of staphylococci and other bacterial groups to the infant gut. The objective of this work was to analyse the bacterial diversity in feces of breast-fed infants and to compare it with that of formula-fed ones. A total of 23 women and their respective infants (16 breast-fed and 7 formula-fed participated in the study. The 16 women and their infants provided a sample of breast milk and feces, respectively, at days 7, 14, and 35. The samples were plated onto different culture media. Staphylococcal and enterococcal isolates were submitted to genetic profiling and to a characterization scheme, including detection of potential virulence traits and sensitivity to antibiotics. Results The feeding practice had a significant effect on bacterial counts. A total of 1,210 isolates (489 from milk, 531 from breast-fed and 190 from formula-fed infants were identified. Staphylococcus epidermidis was the predominant species in milk and feces of breast-fed infants while it was less prevalent in those of formula fed-infants. Enterococcus faecalis was the second predominant bacterial species among the fecal samples provided by the breast-fed infants but it was also present in all the samples from the formula-fed ones. The biofilm-related icaD gene and the mecA gene were only detected in a low number of the S. epidermidis strains. Several enterococcal isolates were also characterized and none of them contained the cylA or the vanABDEG antibiotic-resistance genes. All were sensitive to vancomycin. Conclusion The presence of S. epidermidis is a differential trait of the fecal microbiota of breast-fed infants. Globally, the staphyloccal isolates obtained from milk and feces of breast-fed infants contain a low number of virulence determinants and are sensitive to most of the antibiotics tested.

  15. Gut Microbiota and Inflammation

    Directory of Open Access Journals (Sweden)

    Goran Molin

    2011-06-01

    Full Text Available Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics.

  16. Nonalcoholic fatty liver disease: for better or worse, blame the gut microbiota?

    Science.gov (United States)

    Li, Ding-You; Yang, Min; Edwards, Sarah; Ye, Shui-Qing

    2013-11-01

    Nonalcoholic fatty liver disease (NAFLD) is a major clinical consequence for people with obesity and metabolic syndrome and is also associated with enteral and parenteral nutrition. Early studies suggested that altered gut microbiota might contribute to obesity by affecting energy harvest from the diet and energy storage in the host. Recent evidence in humans as well as in animal models has linked gut microbiota to the development of NAFLD through the gut-liver axis. With bacterial overgrowth and increased intestinal permeability observed in patients with NAFLD and in animal models, gut-derived bacterial products such as endotoxin (lipopolysaccharide) and bacterial DNA are being delivered to the liver through the portal vein and then activate Toll-like receptors (TLRs), mainly TLR4 and TLR9, and their downstream cytokines and chemokines, leading to the development and progression of NAFLD. Given the limited data in humans, the role of gut microbiota in the pathogenesis of NAFLD is still open to discussion. Prebiotics and probiotics have been attempted to modify the microbiota as preventive or therapeutic strategies on this pathological condition. Their beneficial effects on NALFD have been demonstrated in animal models and limited human studies. However, prospective, appropriately powered, randomized, controlled clinical trials are needed to determine whether prebiotics and probiotics and other integrated strategies to modify intestinal microbiota are efficacious therapeutic modalities to treat NALFD.

  17. Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose

    Science.gov (United States)

    Vainauskas, Saulius; Duke, Rebecca M.; McFarland, James; McClung, Colleen; Ruse, Cristian; Taron, Christopher H.

    2016-01-01

    A novel fucose-binding lectin (SL2-1) from the bacterium Streptomyces rapamycinicus was identified by analysis of metagenomic DNA sequences. SL2-1 belongs to a new group of bacterial fucose-specific lectins that have no similarity to known bacterial fucose-binding proteins, but are related to certain eukaryotic fucose-binding lectins. The 17 kDa protein was expressed recombinantly in E. coli and purified by affinity chromatography. Glycan microarray analysis with fluorescently labeled recombinant SL2-1 demonstrated its ability to bind to core α1-6 fucosylated N-glycans, but not to core α1-3 fucosylated N-glycans, or other α1-2, α1-3 and α1-4 fucosylated oligosaccharides. The minimal high affinity binding epitope of SL2-1 was α1-6 fucosylated di-n-acetylchitobiose. The recombinant lectin was efficient in detection of N-glycan core fucosylation using lectin blotting and lectin ELISA assays. Finally, a workflow using SL2-1 for selective and quantitative profiling of core fucosylated N-glycans using UPLC-HILIC-FLR analysis was established. The approach was validated for selective capture and analysis of core fucosylated N-glycans present in complex glycan mixtures derived from mammalian serum IgG. PMID:27678371

  18. Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome

    OpenAIRE

    Parnell, Jill A.; Reimer, Raylene A.

    2012-01-01

    Prebiotic fibers are non-digestible carbohydrates that promote the growth of beneficial bacteria in the gut. Prebiotic consumption may benefit obesity and associated co-morbidities by improving or normalizing the dysbiosis of the gut microbiota. We evaluated the dose response to a prebiotic diet on the gut microbiota, body composition and obesity associated risk factors in lean and genetically obese rats. Prebiotic fibers increased Firmicutes and decreased Bacteroidetes, a profile often assoc...

  19. Pulp and plaque microbiotas of children with severe early childhood caries

    Directory of Open Access Journals (Sweden)

    Natalia I. Chalmers

    2015-02-01

    Full Text Available Background and objective: Bacterial invasion into pulps of primary teeth can lead to infection and premature tooth loss in children. This pilot study aimed to explore whether the microbiota of carious exposures of dental pulps resembles that of carious dentin or that of infected root canals. Design: Children with severe early childhood caries were studied. Children were consented and extent of caries, plaque, and gingivitis measured. Bacteria were sampled from carious lesion biofilms and vital carious exposures of pulps, and processed by anaerobic culture. Isolates were characterized from partial sequences of the 16S rRNA gene and identified by comparison with taxa in the Human Oral Microbiome Database (http://www.HOMD.org. The microbiotas of carious lesions and dental pulps were compared using univariate and multivariate approaches. Results: The microbiota of cariously exposed pulps was similar in composition to that of carious lesion biofilms except that fewer species/taxa were identified from pulps. The major taxa identified belonged to the phyla Firmicutes (mainly streptococci and Actinobacteria (mainly Actinomyces species. Actinomyces and Selenomonas species were associated with carious lesions whereas Veillonella species, particularly Veillonella dispar was associated with pulps. Other bacteria detected in pulps included Streptococcus mutans, Parascardovia denticolens, Bifidobacterium longum, and several Lactobacillus and Actinomyces species. By principal, component analysis pulp microbiotas grouped together, whereas those in caries biofilms were widely dispersed. Conclusions: We conclude that the microbiota of cariously exposed vital primary pulps is composed of a subset of species associated with carious lesions. Vital primary pulps had a dominant Firmicutes and Actinobacteria microbiota which contrasts with reports of endodontic infections which can harbor a gram-negative microbiota. The microbiota of exposed primary pulps may provide

  20. Temperature and bacterial profile of post chill poultry carcasses stored in processing combo held at room temperature.

    Science.gov (United States)

    Handley, John A; Hanning, Irene; Ricke, Steven C; Johnson, Michael G; Jones, Frank T; Apple, Robert O

    2010-10-01

    Post chill whole poultry carcasses from a commercial processing plant were stored in a processing combo at room temperature (70 °F/21 °C) for 54 h to mimic the scenario of temperature abuse before further processing. Temperature data were collected in 1-min intervals and averaged each hour by 9 temperature data loggers. Two linear regressions were developed for the combo and internal breast temperature and slopes were nearly identical. Microbial data was collected by performing whole bird carcass rinses that were enumerated for aerobic plate count (APC), Enterobacteriaceae, Escherichia coli, and total coliform. Samples were collected from the chiller chute at time zero for initial bacterial counts. Carcass sampling continued once the internal breast temperature achieved 45 °F (7 °C 10 h) and continued every 2 h until the final internal breast temperature was 63 °F (17 °C 54 h). Linear regressions were developed for the first 26 h, which exhibited no statistically significant growth except for Enterobacteriaceae. A 2nd linear regression (28 to 54 h) exhibited significant growth for all analyses. Overall, APC increased from a log(10) colony forming unit (CFU)/mL count of 2.86 to 7.02, Enterobacteriaceae increased from 0.66 to 6.64, coliform increased from 0.72 to 4.81, and E. coli increased from 0.53 to 4.45. Denaturing gradient gel electrophoresis was performed to detect changes in the bacterial populations, which indicated 95% similarity within sampled groups, but the overall percent similarity among samples collected over 54 h was 8%. From the data, microbial growth demonstrates a period of 26 h for minimal growth; therefore, the product could be further processed rather than designated as waste. PMID:21535507

  1. Bacterial profile and patterns of antimicrobial drug resistance in intra-abdominal infections: Current experience in a teaching hospital

    Directory of Open Access Journals (Sweden)

    Neetu Shree

    2013-01-01

    Full Text Available Context: Bacterial isolates from intra-abdominal infections, in particular, peritonitis and their unpredictable antimicrobial resistance patterns, continue to be a matter of concern not only globally but regionally too. Aim: An attempt in the present study was made to study the patterns of drug resistance in bacterial isolates, especially gram negative bacilli in intra-abdominal infections (IAI in our hospital. Materials and Methods: From 100 cases of peritonitis, identification of isolates was done as per recommended methods. Antimicrobial susceptibility and extended-spectrum beta-lactamase (ESBL testing were performed following the CLSI guidelines. Results: A total of 133 clinical isolates were obtained, of which 108 were aerobes and 22 anaerobes. Fungal isolates were recovered in only three cases. Escherichia coli (47/108 emerged as the most predominant pathogen followed by Klebsiella spp. (27/108, while Bacteroides fragilis emerged as the predominant anaerobe (12/22. Among coliforms, 61.7% E. coli and 74.1% Klebsiella spp. were ESBL positive. A high level of resistance was observed for beta lactams, ciprofloxacin, amikacin, and ertapenem. Ertapenem resistance (30-41% seen in coliforms, appears as an important issue. Imipenem, tigecycline, and colistin were the most consistently active agents tested against ESBL producers. Conclusion: Drug resistance continues to be a major concern in isolates from intra-abdominal infections. Treatment with appropriate antibiotics preceded by antimicrobial resistance testing aided by early diagnosis, adequate surgical management, and knowledge of antibiotic - resistant organisms appears effective in reducing morbidity and mortality in IAI cases.

  2. Changes in the Eye Microbiota Associated with Contact Lens Wearing

    Directory of Open Access Journals (Sweden)

    Hakdong Shin

    2016-03-01

    Full Text Available Wearing contact lenses has been identified as a risk factor for the development of eye conditions such as giant papillary conjunctivitis and keratitis. We hypothesized that wearing contact lenses is associated with changes in the ocular microbiota. We compared the bacterial communities of the conjunctiva and skin under the eye from 58 subjects and analyzed samples from 20 subjects (9 lens wearers and 11 non-lens wearers taken at 3 time points using a 16S rRNA gene-based sequencing technique (V4 region; Illumina MiSeq. We found that using anesthetic eye drops before sampling decreases the detected ocular microbiota diversity. Compared to those from non-lens wearers, dry conjunctival swabs from lens wearers had more variable and skin-like bacterial community structures (UniFrac; P value = 3.0. The results indicate that wearing contact lenses alters the microbial structure of the ocular conjunctiva, making it more similar to that of the skin microbiota. Further research is needed to determine whether the microbiome structure provides less protection from ocular infections.

  3. Environmental Arsenic Exposure and Microbiota in Induced Sputum

    Directory of Open Access Journals (Sweden)

    Allison G. White

    2014-02-01

    Full Text Available Arsenic exposure from drinking water is associated with adverse respiratory outcomes, but it is unknown whether arsenic affects pulmonary microbiota. This exploratory study assessed the effect of exposure to arsenic in drinking water on bacterial diversity in the respiratory tract of non-smokers. Induced sputum was collected from 10 subjects with moderate mean household water arsenic concentration (21.1 ± 6.4 ppb and 10 subjects with low household water arsenic (2.4 ± 0.8 ppb. To assess microbiota in sputum, the V6 hypervariable region amplicons of bacterial 16s rRNA genes were sequenced using the Ion Torrent Personal Genome Machine. Microbial community differences between arsenic exposure groups were evaluated using QIIME and Metastats. A total of 3,920,441 sequence reads, ranging from 37,935 to 508,787 per sample for 316 chips after QIIME quality filtering, were taxonomically classified into 142 individual genera and five phyla. Firmicutes (22%, Proteobacteria (17% and Bacteriodetes (12% were the main phyla in all samples, with Neisseriaceae (15%, Prevotellaceae (12% and Veillonellacea (7% being most common at the genus level. Some genera, including Gemella, Lactobacillales, Streptococcus, Neisseria and Pasteurellaceae were elevated in the moderate arsenic exposure group, while Rothia, Prevotella, Prevotellaceae Fusobacterium and Neisseriaceae were decreased, although none of these differences was statistically significant. Future studies with more participants and a greater range of arsenic exposure are needed to further elucidate the effects of drinking water arsenic consumption on respiratory microbiota.

  4. Impact of the gut microbiota on the neuroendocrine and behavioural responses to stress in rodents

    Directory of Open Access Journals (Sweden)

    Rabot Sylvie

    2016-01-01

    Full Text Available The gastro-intestinal tract hosts a complex microbial ecosystem, the gut microbiota, whose collective genome coding capacity exceeds that of the host genome. The gut microbiota is nowadays regarded as a full organ, likely to contribute to the development of pathologies when its dynamic balance is disrupted (dysbiosis. In the last decade, evidence emerged that the gut microbiota influences brain development and function. In particular, comparisons between germ-free and conventional laboratory rodents showed that the absence of the gut microbiota exacerbates the hypothalamic pituitary adrenal (HPA system reactivity to stress and alters the anxiety-like behaviour. Furthermore, the dysfunctions observed in germ-free animals can be corrected if the gut microbiota is restored in early life but not in adulthood, suggesting a critical period for microbiota imprinting on the responsiveness to stress. The modes of action are still to be deciphered. They may involve transport of neuroactive bacterial metabolites to the brain through the bloodstream, stimulation of the vagus nerve or of entero-endocrine cells, or modulation of the immune system and, consequently, of the inflammatory status. The discovery that the gut microbiota regulates the neuroendocrine and behavioural responses to stress paves the way for the hypothesis that gut microbiota dysbioses could contribute to the pathophysiology of anxiety-related disorders. In this regard, treatments of anxiety-prone rodent strains with probiotics or antibiotics aimed at modifying their gut microbiota have shown an anxiolytic-like activity. Clinical trials are now needed to know if results obtained in preclinical studies can translate to humans.

  5. Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures.

    Science.gov (United States)

    Mateos-Aparicio, Inmaculada; Mengíbar, Marian; Heras, Angeles

    2016-02-10

    Chitosan with high number of deacetylated units, its reacetylated derivative and COS obtained through an enzymatic treatment with chitosanase were tested in pH controlled batch cultures to investigate the ability of the human faecal microbiota to utilise them. Chitosan derivatives with high number of deacetylated units decreased the bacterial populations: Bifidobacterium spp., Eubacterium rectale/Clostridium coccoides, C. Histolyticum and Bacteroides/Prevotella. On the other hand, chitosan derivatives with high content of acetylated residues maintained the tested bacterial groups and could increase Lactobacillus/Enterococcus. Regarding short chain fatty acids (SCFA), only low Mw COS increased the production in similar levels than fructo-oligossacharides (FOS). The acetylated chitosans and their COS do not appear as potential prebiotics but did not affect negatively the faecal microbiota, while derivatives with high number of deacetylated units could induce a colonic microbiota imbalance. PMID:26686171

  6. The role of the gut microbiota in nonalcoholic fatty liver disease.

    Science.gov (United States)

    Abu-Shanab, Ahmed; Quigley, Eamonn M M

    2010-12-01

    Important metabolic functions have been identified for the gut microbiota in health and disease. Several lines of evidence suggest a role for the gut microbiota in both the etiology of nonalcoholic fatty liver disease (NAFLD) and progression to its more advanced state, nonalcoholic steatohepatitis (NASH). Both NAFLD and NASH are strongly linked to obesity, type 2 diabetes mellitus and the metabolic syndrome and, accordingly, have become common worldwide problems. Small intestinal bacterial overgrowth of Gram-negative organisms could promote insulin resistance, increase endogenous ethanol production and induce choline deficiency, all factors implicated in NAFLD. Among the potential mediators of this association, lipopolysaccharide (a component of Gram-negative bacterial cell walls) exerts relevant metabolic and proinflammatory effects. Although the best evidence to support a role for the gut microbiota in NAFLD and NASH comes largely from animal models, data from studies in humans (albeit at times contradictory) is accumulating and could lead to new therapeutic avenues for these highly prevalent conditions.

  7. Small intestinal bacterial overgrowth syndrome

    Institute of Scientific and Technical Information of China (English)

    Jan; Bures; Jiri; Cyrany; Darina; Kohoutova; Miroslav; Frstl; Stanislav; Rejchrt; Jaroslav; Kvetina; Viktor; Vorisek; Marcela; Kopacova

    2010-01-01

    Human intestinal microbiota create a complex polymi-crobial ecology. This is characterised by its high population density, wide diversity and complexity of interaction. Any dysbalance of this complex intestinal microbiome, both qualitative and quantitative, might have serious health consequence for a macro-organism, including small intestinal bacterial overgrowth syndrome (SIBO).SIBO is defined as an increase in the number and/or alteration in the type of bacteria in the upper gastro-intestinal tract. There...

  8. The Impact of Environmental Heterogeneity and Life Stage on the Hindgut Microbiota of Holotrichia parallela Larvae (Coleoptera: Scarabaeidae)

    OpenAIRE

    Huang, Shengwei; Zhang, Hongyu

    2013-01-01

    Gut microbiota has diverse ecological and evolutionary effects on its hosts. However, the ways in which it responds to environmental heterogeneity and host physiology remain poorly understood. To this end, we surveyed intestinal microbiota of Holotrichia parallela larvae at different instars and from different geographic regions. Bacterial 16S rRNA gene clone libraries were constructed and clones were subsequently screened by DGGE and sequenced. Firmicutes and Proteobacteria were the major ph...

  9. THE INTESTINAL MICROBIOTA IN RAINBOW TROUT (ONCORHYNCHUS MYKISS) IS INFLUENCED BY DIET TYPE AND YERSINIA RUCKERI CHALLENGE

    OpenAIRE

    Ingerslev, Hans-Christian; Dalsgaard, Inger; Jørgensen, Louise von Gersdorff; Madsen, Lone

    2013-01-01

    In recent years it has become more and more evident that the bacterial flora in the gut of warm-blooded animals modulates physiological processes and the immunological status of the host. Besides effects on growth parameters, commensal intestinal bacteria balance the immune system and prevent colonization of pathogenic bacteria. The question is if the gut microbiota is also important in lower vertebrates such as fish? Is the microbiota related to the diet type and does it play a protective ro...

  10. Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure.

    Science.gov (United States)

    Rungrassamee, Wanilada; Klanchui, Amornpan; Maibunkaew, Sawarot; Karoonuthaisiri, Nitsara

    2016-01-01

    The intestinal microbiota play important roles in health of their host, contributing to maintaining the balance and resilience against pathogen. To investigate effects of pathogen to intestinal microbiota, the bacterial dynamics upon a shrimp pathogen, Vibrio harveyi, exposures were determined in two economically important shrimp species; the black tiger shrimp (BT) and the Pacific white shrimp (PW). Both shrimp species were reared under the same diet and environmental conditions. Shrimp survival rates after the V. harveyi exposure revealed that the PW shrimp had a higher resistance to the pathogen than the BT shrimp. The intestinal bacterial profiles were determined by denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing of the 16S rRNA sequences under no pathogen challenge control and under pathogenic V. harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control in BT and PW intestines. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. The barcoded pyrosequencing analysis showed the similar bacterial community structures in intestines of BT and PW shrimp under a normal condition. However, during the time course exposure to V. harveyi, the relative abundance of bacteria belong to Vibrio genus was higher in the BT intestines at 12h after the exposure, whereas relative abundance of vibrios was more stable in PW intestines. The principle coordinates analysis based on weighted-UniFrac analysis showed that intestinal bacterial population in the BT shrimp lost their ability to restore their bacterial balance during the 72-h period of exposure to the pathogen, while the PW shrimp were able to reestablish their bacterial population to resemble those seen in the unexposed control group. This observation of bacterial disruption might correlate to different mortality rates observed between the two shrimp species

  11. Comparative study of Caspian roach (Rutilus rutilus caspicus fry gut microbiota modulation following administration of galacto- and fructooligosaccharide prebiotics

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Hoseinifar

    2015-12-01

    Full Text Available Introduction: Modulation of intestinal microbiota toward potentially beneficial communities (probiotics positively affects fish physiology and health status. Different prebiotics showed contradictory effects on intestinal microbiota. The present study investigates the effects of different levels of two prebiotics, galacto- and fructooligosaccharide on intestinal microbiota of Caspian roach fry which is a commercially valuable species of Caspian sea. Materials and methods: The study was performed as a randomized design with 5 treatments and 3 replications in which Caspian roach were fed different levels, 0, 1, and 2% of galacto- and fructooligosaccharide prebiotics for 6 weeks. At the end of the trial culture, analysis of intestinal microbiota include lactic acid bacteria levels, total bacteria as well as proportion of LAB were performed by using MRS agar, Plate count agar media. Results: Administration of different levels of galacto- and fructooligosaccharide had no significant effects on total bacteria of intestinal microbiota (P > 0.05. The lactic acid bacteria levels significantly increased compared to control group following prebiotics administration in diet (P > 0.05. LAB levels in galactooligosaccharide treatment were higher than those of fructooligosaccharide treatment. The highest LAB proportion in intestinal microbiota was observed in roach fed diet which contains 2% galactooligosaccharide (P > 0.05. Discussion and conclusion: The results of the present study revealed that prebiotics can be used for modulation of Caspian roach intestinal microbiota toward beneficial bacterial communities. Also, the results showed that galactooligosaccharide was more efficient than fructooligosaccharide in case of modulation of intestinal microbiota and elevation of LAB levels.

  12. Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2.

    Science.gov (United States)

    Uchimura, Yasuhiro; Wyss, Madeleine; Brugiroux, Sandrine; Limenitakis, Julien P; Stecher, Bärbel; McCoy, Kathy D; Macpherson, Andrew J

    2016-01-01

    We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species. PMID:27634994

  13. Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2

    Science.gov (United States)

    Uchimura, Yasuhiro; Wyss, Madeleine; Brugiroux, Sandrine; Limenitakis, Julien P.; Stecher, Bärbel; McCoy, Kathy D.

    2016-01-01

    We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species. PMID:27634994

  14. Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

    NARCIS (Netherlands)

    Ferrer, M.; Martins dos Santos, V.A.P.; Ott, S.J.; Moya, A.

    2014-01-01

    It is known that the gastrointestinal tract (GIT) microbiota responds to different antibiotics in different ways and that while some antibiotics do not induce disturbances of the community, others drastically influence the richness, diversity, and prevalence of bacterial taxa. However, the metabolic

  15. A Fungal Signature in the Gut Microbiota of Pediatric Patients with Inflammatory Bowel Disease

    Science.gov (United States)

    Chehoud, Christel; Albenberg, Lindsey G.; Judge, Colleen; Hoffmann, Christian; Grunberg, Stephanie; Bittinger, Kyle; Baldassano, Robert N.; Lewis, James D.; Bushman, Frederic D.; Wu, Gary D.

    2015-01-01

    Background Inflammatory bowel disease (IBD) involves dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. The bacterial microbiota is often altered in IBD, but the connection to disease is not fully clarified, and gut fungi have recently been suggested to play a role as well. In this study, we compared microbes from all three domains of life–bacteria, archaea, and eukaryota–in pediatric patients with IBD and healthy controls. Methods A stool sample was collected from patients with IBD (n=34) or health control subjects (n=90), and bacterial, archaeal, and fungal communities were characterized by deep sequencing of rRNA gene segments specific to each domain. Results IBD patients (Crohn’s disease or ulcerative colitis) had lower bacterial diversity and distinctive fungal communities. Two lineages annotating as Candida were significantly more abundant in IBD patients (p = 0.0034 and p=0.00038, respectively) while a lineage annotating as Cladosporium was more abundant in healthy subjects (p=0.0025). There were no statistically significant differences in archaea, which were rare in pediatric samples compared to those from adults. Conclusions Pediatric IBD is associated with reduced diversity in both fungal and bacterial gut microbiota. Specific Candida taxa were increased in abundance in the IBD samples. These data emphasize the potential importance of fungal microbiota signatures as biomarkers of pediatric IBD, supporting their possible role in disease pathogenesis. PMID:26083617

  16. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota

    NARCIS (Netherlands)

    Scanlan, P.D.; Stensvold, C.R.; Rajilic-Stojanovic, M.; Heilig, H.G.; Vos, de W.M.; O'Toole, P.W.; Cotter, P.D.

    2014-01-01

    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the mi

  17. Bacterial flora of the sigmoid neovagina

    NARCIS (Netherlands)

    T.A. Toolenaar; I. Freundt (Ingrid); J.H. Wagenvoort; F.J. Huikeshoven (Frans); M. Vogel; J. Jeekel (Hans); A.C. Drogendijk

    1993-01-01

    textabstractThe bacterial microbiota of 15 sigmoid neovaginas, created in patients with congenital vaginal aplasia or male transsexualism, was studied. No specimen was sterile, and only normal inhabitants of the colon were cultured. The total counts of bacteria were low

  18. Effects of Biological Tillage on Soil Microbiota and Bacterial Physiologies Colony%生物耕作对菜田土壤微生物区系及细菌生理类群的影响

    Institute of Scientific and Technical Information of China (English)

    李双喜; 郑宪清; 袁大伟; 张娟琴; 何七勇; 吕卫光

    2012-01-01

    Field plot experiments were carried out to investigate the effect of biological tillage on soil microbiota and microbial physiologies colony. Three treatments which were conventional tillage (CK) ,no tillage (Tl) and biological tillage ( T2) were set up. The results showed that biological tillage could increase the nutrient contents and the soil moisture content compared with CK,especially in the 5 -20 cm layer,in which the contents of soil organic matter,total nitrogen,available phosphorous,and soil moisture content were improved 58.33% ,68.93% ,67.06% and 16. 19% Respectively. The numbers of microbial physiologies colony obviously increased in Tl and T2. The application of maize to soil ( T2 ) gave significantly higher number of bacteria, actinomycete and lower number of fungi (P <0.05) ,so did the numbers of ammonifier.nitrifier, inorganic phosphorus decomposing microbes(P <0.05). Increasing earthworm activity was contributive to improve soil physicochemical properties and enzyme activities in agro-ecosystem, which was very important in improving soil fertilization.%旨在研究生物耕作(接种蚯蚓)对土壤微生物区系及细菌生理类群的影响.结果表明,生物耕作能有效提高不同耕层的土壤养分含量和含水量,其中尤以5~20 cm显著,生物耕作处理土壤有机质、全氮、有效磷以及含水量依次比对照增长了58.33%,68.93%,67.06%,16.19%;与常规旋耕(CK)相比,各土层中免耕(T1)和生物耕作(T2)2种保护性耕作方式可明显增加土壤微生物生理类群的数量,且表层(0~5 cm)土壤微生物数量远远大于下层(5~20 cm).T2处理显著增加了土壤中的细菌和放线菌数量,降低了真菌数量(P<0.05);氮化细菌、硝化细菌以及无机磷分解菌等生理细菌数量得到显著提升(P<0.05).在传统的农业生态系统中,培育土壤有益动物生物数量可以提高土壤微生物和酶活性,对改善农田土壤肥力有着重要意义.

  19. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. PMID:26992100

  20. The Human Microbiota in Early Life

    DEFF Research Database (Denmark)

    Mortensen, Martin Steen

    the already well-defined community state types. In addition, we showed that for most women the vaginal microbiota at week 24 of pregnancy is similar to the microbiota twelve weeks later at week 36. The manuscript also contains a novel description of how mothers’ vaginal microbiota has affected the microbiota.......g. Streptococcus and Moraxella) become increasingly dominant. By defining the core microbiota for each infant, the manuscript shows that 69% of the microbiota, three months after birth, represent bacteria that were present at both one week and one month after birth. Lastly, the manuscript describes how...... the microbiota can be separated into five distinct pneumotypes: four having a single dominating genus and one without a common defining genus. The last manuscript, Manuscript III, compares the microbiota descriptions obtained by classical identification using culturing and high throughput sequencing of amplified...

  1. Microbiota and Metabolome Associated with Immunoglobulin A Nephropathy (IgAN)

    OpenAIRE

    De Angelis, Maria; Montemurno, Eustacchio; Piccolo, Maria; Vannini, Lucia; Lauriero, Gabriella; Maranzano, Valentina; Gozzi, Giorgia; Serrazanetti, Diana; Dalfino, Giuseppe; Gobbetti, Marco; Gesualdo, Loreto

    2014-01-01

    This study aimed at investigating the fecal microbiota, and the fecal and urinary metabolome of non progressor (NP) and progressor (P) patients with immunoglobulin A nephropathy (IgAN). Three groups of volunteers were included in the study: (i) sixteen IgAN NP patients; (ii) sixteen IgAN P patients; and (iii) sixteen healthy control (HC) subjects, without known diseases. Selective media were used to determine the main cultivable bacterial groups. Bacterial tag-encoded FLX-titanium amplicon py...

  2. Gut Microbiota as Potential Orchestrators of Irritable Bowel Syndrome

    OpenAIRE

    Bennet, Sean M.P.; Öhman, Lena; Simrén, Magnus

    2015-01-01

    Irritable bowel syndrome (IBS) is a multifactorial functional disorder with no clearly defined etiology or pathophysiology. Modern culture-independent techniques have improved the understanding of the gut microbiota’s composition and demonstrated that an altered gut microbiota profile might be found in at least some subgroups of IBS patients. Research on IBS from a microbial perspective is gaining momentum and advancing. This review will therefore highlight potential links between the gut mic...

  3. Gut microbiota: a key player in health and disease. A review focused on obesity.

    Science.gov (United States)

    Villanueva-Millán, M J; Pérez-Matute, P; Oteo, J A

    2015-09-01

    Gut microbiota, its evolutive dynamics and influence on host through its protective, trophic and metabolic actions, has a key role in health and opens unique opportunities for the identification of new markers of the physiopathological state of each individual. Alterations in gut microbiota composition have been associated with plenty disorders. Of interest, the vast number of studies demonstrates the role of microbiota in obesity, a serious public health problem that has reached epidemic proportions in many developed and middle-income countries. The economic and health costs of this condition and its comorbidities such as fatty liver, insulin resistance/diabetes, or cardiovascular events are considerable. Therefore, every strategy designed to reduce obesity would imply important savings. Targeting microbiota, in order to restore/modulate the microbiota composition with antibiotics, probiotics, prebiotics, or even fecal transplants, is considered as a promising strategy for the development of new solutions for the treatment of obesity. However, there is still lot to do in this field in order to identify the exact composition of microbiota in "health" and the specific mechanisms that regulate the host-microbiotal crosstalk. In addition, it is important to note that changes not only in the gut microbiota profile (abundance) but also in its metabolism and functions need to be taken into account in the context of contribution in the physiopathology of obesity and related disorders.

  4. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming.

    Science.gov (United States)

    Tveit, Alexander Tøsdal; Urich, Tim; Frenzel, Peter; Svenning, Mette Marianne

    2015-05-12

    Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.

  5. Enterotypes influence temporal changes in gut microbiota

    OpenAIRE

    Roager, Henrik Munch; Licht, Tine Rask; Kellebjerg Poulsen, Sanne; Meinert Larsen, Thomas; Bahl, Martin Iain

    2013-01-01

    The human gut microbiota plays an important role for human health. The question is whether we can modulate the gut microbiota by changing diet. During a 6-month, randomised, controlled dietary intervention, the effect of consuming a diet following the New Nordic Diet recommendations (NND) as opposed to Average Danish Diet (ADD) on the gut microbiota in humans (n=62) was investigated. Quantitative PCR analysis showed that the microbiota did not change significantly by the intervention. Neverth...

  6. Intestinal Microbiota Metabolism and Atherosclerosis

    Institute of Scientific and Technical Information of China (English)

    Tian-Xing Liu; Hai-Tao Niu; Shu-Yang Zhang

    2015-01-01

    Objective:This review aimed to summarize the relationship between intestinal microbiota metabolism and cardiovascular disease (CVD) and to propose a novel CVD therapeutic target.Data Sources:This study was based on data obtained from PubMed and EMBASE up to June 30,2015.Articles were selected using the following search temps:"Intestinal microbiota","trimethylamine N-oxide (TMAO)","trimethylamine (TMA)","cardiovascular",and "atherosclerosis".Study Selection:Studies were eligible if they present information on intestinal microbiota metabolism and atherosclerosis.Studies on TMA-containing nutrients were also included.Results:A new CVD risk factor,TMAO,was recently identified.It has been observed that several TMA-containing compounds may be catabolized by specific intestinal microbiota,resulting in TMA release.TMA is subsequently converted to TMAO in the liver.Several preliminary studies have linked TMAO to CVD,particularly atherosclerosis;however,the details of this relationship remain unclear.Conclusions:Intestinal microbiota metabolism is associated with atherosclerosis and may represent a promising therapeutic target with respect to CVD management.

  7. Infecção do trato urinário relacionada com a utilização do catéter vesical de demora: resultados da bacteriúria e da microbiota estudadas Urinary tract infection related to the use of catheter-delay bladder: results of bacteriuria and microbiota studied

    Directory of Open Access Journals (Sweden)

    João Leão e Souza Neto

    2008-02-01

    Full Text Available OBJETIVO: Avaliar o momento do início da bacteriúria e o germe mais freqüentemente relacionado à infecção urinária nos pacientes submetidos à sondagem vesical de demora. MÉTODO: No período de setembro de 2003 a outubro de 2004, foram avaliados os pacientes com 13 anos ou mais, submetidos à operações eletivas com cateterismo vesical de demora. Na inserção do cateter foi colhida a primeira amostra de urina, denominada Amostra 1, e outras seqüencialmente a cada 12 horas. Estas foram analisadas quanto a bacteriúria, leucocitúria, e cultura. A infecção do trato urinário foi definida como a presença de 100.000 unidades formadoras de colônias ou mais, após o isolamento da mesma bactéria ou fungo em culturas de urina de amostras distintas, desde a inserção até a remoção do cateter urinário; a leucocitúria como contagem de leucócitos igual ou superior a 10.000 leucócitos/mm³; e bacteriúria como presença de bactéria de uma única espécie na amostra analisada. RESULTADOS: A amostra foi composta de 63 pacientes, 46 sexo masculino (73% e 17 sexo feminino (27%. Apenas três deles apresentaram leucocitúria na primeira coleta. Nas Amostras 1 houve variação de 1.000 a 20.000 leucócitos/mm³, todas com cultura negativa. O número de amostras variou de 1 a 8 (84h após a realização do cateterismo vesical. As leucocitúrias nas amostras finais variaram de 1.000 a 204.000 leucócitos/mm³, todas com urocultura e bacteriúria negativa. 62 pacientes (98,4% utilizaram antibioticoterapia de curta duração para o sítio cirúrgico. CONCLUSÃO: Até 84h - 3,5 dias - não houve Infecção em nenhuma das amostras coletadas e cultivadas. A antibioticoterapia de curta duração pode ter contribuído para o resultado observado.BACKGROUND: To evaluate the moment of the beginning of bacteriuria and the most frequently germ related to the urinary infection in patients submitted to delayed vesical catheterization. METHODS: During

  8. Effects of the diet on the microbiota of the red palm weevil (Coleoptera: Dryophthoridae.

    Directory of Open Access Journals (Sweden)

    Matteo Montagna

    Full Text Available Rhynchophorus ferrugineus, also known as the red palm weevil, is regarded as the major pest of palm trees. Although studies of the microbiota associated with this species have been performed in recent years, little attention has been dedicated to the influence of the diet in shaping the host bacterial community. Here, we investigated the influence of food sources (i.e. palm tissues vs apple based substrate on the microbial diversity associated with RPW, which was compared with the microbiota associated with wild individuals of the sister species Rhynchophorus vulneratus. The bacterial characterization was performed using a culture independent approach, i.e. the 16S rRNA pyrotag, and a culture dependent approach for a subset of the samples, in order to obtain bacterial isolates from RPW tissues. The bacterial community appeared significantly influenced by diet. Proteobacteria resulted to be the most abundant clade and was present in all the specimens of the three examined weevil groups. Within Proteobacteria, Enterobacteriaceae were identified in all the organs analysed, including hemolymph and reproductive organs. The apple-fed RPWs and the wild R. vulneratus showed a second dominant taxon within Firmicutes that was scarcely present in the microbiota associated with palm-fed RPWs. A comparative analysis on the bacteria associated with the palm tissues highlighted that 12 bacterial genera out of the 13 identified in the plant tissues were also present in weevils, thus indicating that palm tissues may present a source for bacterial acquisition.

  9. Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae)

    KAUST Repository

    Montagna, Matteo

    2015-01-30

    Rhynchophorus ferrugineus, also known as the red palm weevil, is regarded as the major pest of palm trees. Although studies of the microbiota associated with this species have been performed in recent years, little attention has been dedicated to the influence of the diet in shaping the host bacterial community. Here, we investigated the influence of food sources (i.e. palm tissues vs apple based substrate) on the microbial diversity associated with RPW, which was compared with the microbiota associated with wild individuals of the sister species Rhynchophorus vulneratus. The bacterial characterization was performed using a culture independent approach, i.e. the 16S rRNA pyrotag, and a culture dependent approach for a subset of the samples, in order to obtain bacterial isolates from RPW tissues. The bacterial community appeared significantly influenced by diet. Proteobacteria resulted to be the most abundant clade and was present in all the specimens of the three examined weevil groups. Within Proteobacteria, Enterobacteriaceae were identified in all the organs analysed, including hemolymph and reproductive organs. The apple-fed RPWs and the wild R. vulneratus showed a second dominant taxon within Firmicutes that was scarcely present in the microbiota associated with palm-fed RPWs. A comparative analysis on the bacteria associated with the palm tissues highlighted that 12 bacterial genera out of the 13 identified in the plant tissues were also present in weevils, thus indicating that palm tissues may present a source for bacterial acquisition.

  10. Bacterial profile and drug susceptibility pattern of urinary tract infection in pregnant women at University of Gondar Teaching Hospital, Northwest Ethiopia

    Directory of Open Access Journals (Sweden)

    Alemu Agersew

    2012-04-01

    Full Text Available Abstract Background Urinary tract infection (UTI is a common health problem among pregnant women. Proper investigation and prompt treatment are needed to prevent serious life threatening condition and morbidity due to urinary tract infection that can occur in pregnant women. Recent report in Addis Ababa, Ethiopia indicated the prevalence of UTI in pregnant women was 11.6 % and Gram negative bacteria was the predominant isolates and showed multi drug resistance. This study aimed to assess bacterial profile that causes urinary tract infection and their antimicrobial susceptibility pattern among pregnant women visiting antenatal clinic at University of Gondar Teaching Hospital, Northwest Ethiopia. Methods A cross-sectional study was conducted at University of Gondar Teaching Hospital from March 22 to April 30, 2011. Mid stream urine samples were collected and inoculated into Cystine Lactose Electrolyte Deficient medium (CLED. Colony counts yielding bacterial growth of 105/ml of urine or more of pure isolates were regarded as significant bacteriuria for infection. Colony from CLED was sub cultured onto MacConkey agar and blood agar plates. Identification was done using cultural characteristics and a series of biochemical tests. A standard method of agar disc diffusion susceptibility testing method was used to determine susceptibility patterns of the isolates. Results The overall prevalence of UTI in pregnant women was 10.4 %. The predominant bacterial pathogens were Escherichia coli 47.5 % followed by coagulase-negative staphylococci 22.5 %, Staphylococcus aureus 10 %, and Klebsiella pneumoniae 10 %. Gram negative isolates were resulted low susceptibility to co-trimoxazole (51.9 % and tetracycline (40.7 % whereas Gram positive showed susceptibility to ceftriaxon (84.6 % and amoxicillin–clavulanic acid (92.3 %. Multiple drug resistance (resistance to two or more drugs was observed in 95 % of the isolates. Conclusion

  11. Intestinal microbiota: The explosive mixture at the origin of inflammatory bowel disease?

    Institute of Scientific and Technical Information of China (English)

    Roberto; Bringiotti; Enzo; Ierardi; Rosa; Lovero; Giuseppe; Losurdo; Alfredo; Di; Leo; Mariabeatrice; Principi

    2014-01-01

    Inflammatory bowel diseases(IBDs), namely Crohn’s disease and ulcerative colitis, are lifelong chronic disorders arising from interactions among genetic, immunological and environmental factors. Although the origin of IBDs is closely linked to immune response alterations, which governs most medical decision-making, recent findings suggest that gut microbiota may be involved in IBD pathogenesis. Epidemiologic evidence and several studies have shown that a dysregulation of gut microbiota(i.e., dysbiosis) may trigger the onset of intestinal disorders such as IBDs. Animal and human investigations focusing on the microbiota-IBD relationship have suggested an altered balance of the intestinal microbial population in the active phase of IBD. Rigorous microbiota typing could, therefore, soon become part of a complete phenotypic analysis of IBD patients. Moreover, individual susceptibility and environmental triggers such as nutrition, medications, age or smoking could modify bacterial strains in the bowel habitat. Pharmacological manipulation of bowel microbiota is somewhat controversial. The employment of antibiotics, probiotics, prebiotics and synbiotics has been widely addressed in theliterature worldwide, with the aim of obtaining positive results in a number of IBD patient settings, and determining the appropriate timing and modality of this intervention. Recently, novel treatments for IBDs, such as fecal microbiota transplantation, when accepted by patients, have shown promising results. Controlled studies are being designed. In the near future, new therapeutic strategies can be expected, with non-pathogenic or modified food organisms that can be genetically modified to exert anti-inflammatory properties.

  12. Intestinal microbiota: The explosive mixture at the origin of inflammatory bowel disease?

    Science.gov (United States)

    Bringiotti, Roberto; Ierardi, Enzo; Lovero, Rosa; Losurdo, Giuseppe; Di Leo, Alfredo; Principi, Mariabeatrice

    2014-11-15

    Inflammatory bowel diseases (IBDs), namely Crohn's disease and ulcerative colitis, are lifelong chronic disorders arising from interactions among genetic, immunological and environmental factors. Although the origin of IBDs is closely linked to immune response alterations, which governs most medical decision-making, recent findings suggest that gut microbiota may be involved in IBD pathogenesis. Epidemiologic evidence and several studies have shown that a dysregulation of gut microbiota (i.e., dysbiosis) may trigger the onset of intestinal disorders such as IBDs. Animal and human investigations focusing on the microbiota-IBD relationship have suggested an altered balance of the intestinal microbial population in the active phase of IBD. Rigorous microbiota typing could, therefore, soon become part of a complete phenotypic analysis of IBD patients. Moreover, individual susceptibility and environmental triggers such as nutrition, medications, age or smoking could modify bacterial strains in the bowel habitat. Pharmacological manipulation of bowel microbiota is somewhat controversial. The employment of antibiotics, probiotics, prebiotics and synbiotics has been widely addressed in the literature worldwide, with the aim of obtaining positive results in a number of IBD patient settings, and determining the appropriate timing and modality of this intervention. Recently, novel treatments for IBDs, such as fecal microbiota transplantation, when accepted by patients, have shown promising results. Controlled studies are being designed. In the near future, new therapeutic strategies can be expected, with non-pathogenic or modified food organisms that can be genetically modified to exert anti-inflammatory properties. PMID:25400998

  13. The composition of the gut microbiota throughout life, with an emphasis on early life

    Directory of Open Access Journals (Sweden)

    Juan Miguel Rodríguez

    2015-02-01

    Full Text Available The intestinal microbiota has become a relevant aspect of human health. Microbial colonization runs in parallel with immune system maturation and plays a role in intestinal physiology and regulation. Increasing evidence on early microbial contact suggest that human intestinal microbiota is seeded before birth. Maternal microbiota forms the first microbial inoculum, and from birth, the microbial diversity increases and converges toward an adult-like microbiota by the end of the first 3–5 years of life. Perinatal factors such as mode of delivery, diet, genetics, and intestinal mucin glycosylation all contribute to influence microbial colonization. Once established, the composition of the gut microbiota is relatively stable throughout adult life, but can be altered as a result of bacterial infections, antibiotic treatment, lifestyle, surgical, and a long-term change in diet. Shifts in this complex microbial system have been reported to increase the risk of disease. Therefore, an adequate establishment of microbiota and its maintenance throughout life would reduce the risk of disease in early and late life. This review discusses recent studies on the early colonization and factors influencing this process which impact on health.

  14. The composition of the gut microbiota throughout life, with an emphasis on early life.

    Science.gov (United States)

    Rodríguez, Juan Miguel; Murphy, Kiera; Stanton, Catherine; Ross, R Paul; Kober, Olivia I; Juge, Nathalie; Avershina, Ekaterina; Rudi, Knut; Narbad, Arjan; Jenmalm, Maria C; Marchesi, Julian R; Collado, Maria Carmen

    2015-01-01

    The intestinal microbiota has become a relevant aspect of human health. Microbial colonization runs in parallel with immune system maturation and plays a role in intestinal physiology and regulation. Increasing evidence on early microbial contact suggest that human intestinal microbiota is seeded before birth. Maternal microbiota forms the first microbial inoculum, and from birth, the microbial diversity increases and converges toward an adult-like microbiota by the end of the first 3-5 years of life. Perinatal factors such as mode of delivery, diet, genetics, and intestinal mucin glycosylation all contribute to influence microbial colonization. Once established, the composition of the gut microbiota is relatively stable throughout adult life, but can be altered as a result of bacterial infections, antibiotic treatment, lifestyle, surgical, and a long-term change in diet. Shifts in this complex microbial system have been reported to increase the risk of disease. Therefore, an adequate establishment of microbiota and its maintenance throughout life would reduce the risk of disease in early and late life. This review discusses recent studies on the early colonization and factors influencing this process which impact on health.

  15. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis

    Science.gov (United States)

    Koeth, Robert A.; Wang, Zeneng; Levison, Bruce S.; Buffa, Jennifer A.; Org, Elin; Sheehy, Brendan T.; Britt, Earl B.; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D.; DiDonato, Joseph A.; Chen, Jun; Li, Hongzhe; Wu, Gary D.; Lewis, James D.; Warrier, Manya; Brown, J. Mark; Krauss, Ronald M.; Tang, W. H. Wilson; Bushman, Frederic D.; Lusis, Aldons J.; Hazen, Stanley L.

    2013-01-01

    Intestinal microbiota metabolism of choline/phosphatidylcholine produces trimethylamine (TMA), which is further metabolized to a proatherogenic species, trimethylamine-N-oxide (TMAO). Herein we demonstrate that intestinal microbiota metabolism of dietary L-carnitine, a trimethylamine abundant in red meat, also produces TMAO and accelerates atherosclerosis. Omnivorous subjects are shown to produce significantly more TMAO than vegans/vegetarians following ingestion of L-carnitine through a microbiota-dependent mechanism. Specific bacterial taxa in human feces are shown to associate with both plasma TMAO and dietary status. Plasma L-carnitine levels in subjects undergoing cardiac evaluation (n = 2,595) predict increased risks for both prevalent cardiovascular disease (CVD) and incident major adverse cardiac events (MI, stroke or death), but only among subjects with concurrently high TMAO levels. Chronic dietary L-carnitine supplementation in mice significantly altered cecal microbial composition, markedly enhanced synthesis of TMA/TMAO, and increased atherosclerosis, but not following suppression of intestinal microbiota. Dietary supplementation of TMAO, or either carnitine or choline in mice with intact intestinal microbiota, significantly reduced reverse cholesterol transport in vivo. Intestinal microbiota may thus participate in the well-established link between increased red meat consumption and CVD risk. PMID:23563705

  16. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.

    Science.gov (United States)

    Koeth, Robert A; Wang, Zeneng; Levison, Bruce S; Buffa, Jennifer A; Org, Elin; Sheehy, Brendan T; Britt, Earl B; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D; DiDonato, Joseph A; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Warrier, Manya; Brown, J Mark; Krauss, Ronald M; Tang, W H Wilson; Bushman, Frederic D; Lusis, Aldons J; Hazen, Stanley L

    2013-05-01

    Intestinal microbiota metabolism of choline and phosphatidylcholine produces trimethylamine (TMA), which is further metabolized to a proatherogenic species, trimethylamine-N-oxide (TMAO). We demonstrate here that metabolism by intestinal microbiota of dietary L-carnitine, a trimethylamine abundant in red meat, also produces TMAO and accelerates atherosclerosis in mice. Omnivorous human subjects produced more TMAO than did vegans or vegetarians following ingestion of L-carnitine through a microbiota-dependent mechanism. The presence of specific bacterial taxa in human feces was associated with both plasma TMAO concentration and dietary status. Plasma L-carnitine levels in subjects undergoing cardiac evaluation (n = 2,595) predicted increased risks for both prevalent cardiovascular disease (CVD) and incident major adverse cardiac events (myocardial infarction, stroke or death), but only among subjects with concurrently high TMAO levels. Chronic dietary L-carnitine supplementation in mice altered cecal microbial composition, markedly enhanced synthesis of TMA and TMAO, and increased atherosclerosis, but this did not occur if intestinal microbiota was concurrently suppressed. In mice with an intact intestinal microbiota, dietary supplementation with TMAO or either carnitine or choline reduced in vivo reverse cholesterol transport. Intestinal microbiota may thus contribute to the well-established link between high levels of red meat consumption and CVD risk. PMID:23563705

  17. Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome.

    Science.gov (United States)

    Tejesvi, M V; Uhari, M; Tapiainen, T; Pirttilä, A M; Suokas, M; Lantto, U; Koivunen, P; Renko, M

    2016-06-01

    Periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) is a childhood febrile syndrome of unknown origin that is often cured with tonsillectomy. We aimed to compare the bacterial microbiota of the tonsils removed from PFAPA patients with those of controls. We used next-generation sequencing technology to investigate the bacterial microbiota of the tonsils of 30 PFAPA patients and 24 controls. We found significant differences in the presence and relative abundance of many bacteria between PFAPA cases and controls. For example, cyanobacteria, potential producers of microcystins and other toxins, were more common in the case samples (14/30, 47 %) than in the controls (4/24, 17 %, p = 0.02), and the mean relative abundance of cyanobacteria was higher in the case samples (0.2 %) than in the controls (0.01 %, p = 0.01). Streptococci were present in all samples in both groups, but their mean relative abundance was lower in the case samples (3.7 %) than in the controls (9.6 %, p = 0.01). Typical nasopharyngeal microbes such as fusobacteria, Prevotella, Tannerella, Porphyromonas, and Parvimonas dominated the microbiota of the tonsils in both groups. The microbiota of the tonsils removed from PFAPA patients differed significantly from those of the controls. Tonsillar microbiota may play a role in triggering the inflammatory processes that lead to symptoms of PFAPA. PMID:27025724

  18. In Vitro Culture Conditions for Maintaining a Complex Population of Human Gastrointestinal Tract Microbiota

    Directory of Open Access Journals (Sweden)

    Bong-Soo Kim

    2011-01-01

    Full Text Available A stable intestinal microbiota is important in maintaining human physiology and health. Although there have been a number of studies using in vitro and in vivo approaches to determine the impact of diet and xenobiotics on intestinal microbiota, there is no consensus for the best in vitro culture conditions for growth of the human gastrointestinal microbiota. To investigate the dynamics and activities of intestinal microbiota, it is important for the culture conditions to support the growth of a wide range of intestinal bacteria and maintain a complex microbial community representative of the human gastrointestinal tract. Here, we compared the bacterial community in three culture media: brain heart infusion broth and high- and low-carbohydrate medium with different growth supplements. The bacterial community was analyzed using denaturing gradient gel electrophoresis (DGGE, pyrosequencing and real-time PCR. Based on the molecular analysis, this study indicated that the 3% fecal inoculum in low-concentration carbohydrate medium with 1% autoclaved fecal supernatant provided enhanced growth conditions to conduct in vitro studies representative of the human intestinal microbiota.

  19. Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity

    DEFF Research Database (Denmark)

    Laursen, Martin Frederik; Andersen, Louise B. B.; Michaelsen, Kim F.;

    2016-01-01

    The first years of life are paramount in establishing our endogenous gut microbiota, which is strongly affected by diet and has repeatedly been linked with obesity. However, very few studies have addressed the influence of maternal obesity on infant gut microbiota, which may occur either through...... either of a random sample of healthy mothers (n = 114), or of obese mothers (n = 113), were profiled by 16S rRNA amplicon sequencing. Gut microbiota data were compared to breastfeeding patterns and detailed individual dietary recordings to assess effects of the complementary diet. We found that maternal...... obesity did not influence microbial diversity or specific taxon abundances during the complementary feeding period. Across cohorts, breastfeeding duration and composition of the complementary diet were found to be the major determinants of gut microbiota development. In both cohorts, gut microbial...

  20. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome.

    Science.gov (United States)

    Chassaing, Benoit; Koren, Omry; Goodrich, Julia K; Poole, Angela C; Srinivasan, Shanthi; Ley, Ruth E; Gewirtz, Andrew T

    2015-03-01

    The intestinal tract is inhabited by a large and diverse community of microbes collectively referred to as the gut microbiota. While the gut microbiota provides important benefits to its host, especially in metabolism and immune development, disturbance of the microbiota-host relationship is associated with numerous chronic inflammatory diseases, including inflammatory bowel disease and the group of obesity-associated diseases collectively referred to as metabolic syndrome. A primary means by which the intestine is protected from its microbiota is via multi-layered mucus structures that cover the intestinal surface, thereby allowing the vast majority of gut bacteria to be kept at a safe distance from epithelial cells that line the intestine. Thus, agents that disrupt mucus-bacterial interactions might have the potential to promote diseases associated with gut inflammation. Consequently, it has been hypothesized that emulsifiers, detergent-like molecules that are a ubiquitous component of processed foods and that can increase bacterial translocation across epithelia in vitro, might be promoting the increase in inflammatory bowel disease observed since the mid-twentieth century. Here we report that, in mice, relatively low concentrations of two commonly used emulsifiers, namely carboxymethylcellulose and polysorbate-80, induced low-grade inflammation and obesity/metabolic syndrome in wild-type hosts and promoted robust colitis in mice predisposed to this disorder. Emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. Use of germ-free mice and faecal transplants indicated that such changes in microbiota were necessary and sufficient for both low-grade inflammation and metabolic syndrome. These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects

  1. Characterization of the gut microbiota in leptin deficient obese mice – Correlation to inflammatory and diabetic parameters

    DEFF Research Database (Denmark)

    Ellekilde, Merete; Krych, L.; Hansen, C.H.F.;

    2014-01-01

    Gut microbiota have been implicated as a relevant factor in the development of type 2 diabetes mellitus (T2DM), and its diversity might be a cause of variation in animal models of T2DM. In this study, we aimed to characterise the gut microbiota of a T2DM mouse model with a long term vision of being...... able to target the gut microbiota to reduce the number of animals used in experiments. Male B6.V-Lep(ob)/J mice were characterized according to a number of characteristics related to T2DM, inflammation and gut microbiota. All findings were thereafter correlated to one another in a linear regression...... model. The total gut microbiota profile correlated to glycated haemoglobin, and high proportions of Prevotellaceae and Lachnospiraceae correlated to impaired or improved glucose intolerance, respectively. In addition, Akkermansia muciniphila disappeared with age as glucose intolerance worsened. A high...

  2. Investigation of bacterial microbiota and risk factors in dogs with external ocular diseases from Bandeirantes, Paraná State, BrazilInvestigação da microbiota bacteriana e associações de risco em cães com afecções oculares externas atendidos em Bandeirantes, Paraná, Brasil

    Directory of Open Access Journals (Sweden)

    João Luis Garcia

    2012-02-01

    Full Text Available For the determination of the bacterial etiology of the external ocular diseases and sensitivity to antimicrobials, 38 dogs with external ocular diseases, unilateral or bilateral, and 120 dogs without ocular diseases (control group, were studied between 08/2008 and 07/2009 in the Veterinary Hospital of North Paraná State University, Brazil. The collected samples of the inferior conjunctival sac were incubated at 37ºC in an aerobic environment, in blood agar and MacConkey agar, for 120 hours. After the presumptive identification, the bacterial species were identified by the systems APISTAPH (bio- Merieux, Incorporation, API 20 STREP (bio-Merieux, Incorporation and BACTRAY (Laborclin, Ltd. and incubated in Mueller-Hinton agar with antimicrobials disks, for sensitivity determination. For the risk factors, the owners answered a questionnaire with epidemiological variables. There was microorganism growth in 46 (73.02% samples, with isolation of one microorganism in 42 samples and two microorganisms in four. Gram-positive bacteria corresponded to 76% of the isolated, Gramnegative 20% and yeasts fungi 4%. Staphylococcus spp totalized 66% of isolated, with S. aureus (24% and S. intermedius (24% the most prevalent. With the exception of S. intermedius (91.67% and S. epidermidis (66.67%, the isolated bacterial species presented 100% resistance to the sulfonamide. The S. aureus isolated presented 91,67% sensitivity to chloranphenicol, tobramycin and amoxicillin/clavulanic acid, and the same percentile of resistance to tetracycline. The S. intermedius presented 100% sensitivity to amoxicillin/ clavulanic acid and 91,67% to gentamicin and 75% resistance to tetracycline and ceftriaxone. The associations of risk for external ocular diseases were clinical returns (OR=59,50, 7,29Para a determinação da etiologia bacteriana das afecções oculares externas e perfil de sensibilidade a antimicrobianos, 38 cães com doenças oculares externas, unilaterais ou

  3. Long-term exposure to antibiotics has caused accumulation of resistance determinants in the gut microbiota of honeybees.

    Science.gov (United States)

    Tian, Baoyu; Fadhil, Nibal H; Powell, J Elijah; Kwong, Waldan K; Moran, Nancy A

    2012-01-01

    Antibiotic treatment can impact nontarget microbes, enriching the pool of resistance genes available to pathogens and altering community profiles of microbes beneficial to hosts. The gut microbiota of adult honeybees, a distinctive community dominated by eight bacterial species, provides an opportunity to examine evolutionary responses to long-term treatment with a single antibiotic. For decades, American beekeepers have routinely treated colonies with oxytetracycline for control of larval pathogens. Using a functional metagenomic screen of bacteria from Maryland bees, we detected a high incidence of tetracycline/oxytetracycline resistance. This resistance is attributable to known resistance loci for which nucleotide sequences and flanking mobility genes were nearly identical to those from human pathogens and from bacteria associated with farm animals. Surveys using diagnostic PCR and sequencing revealed that gut bacteria of honeybees from diverse localities in the United States harbor eight tetracycline resistance loci, including efflux pump genes (tetB, tetC, tetD, tetH, tetL, and tetY) and ribosome protection genes (tetM and tetW), often at high frequencies. Isolates of gut bacteria from Connecticut bees display high levels of tetracycline resistance. Resistance genes were ubiquitous in American samples, though rare in colonies unexposed for 25 years. In contrast, only three resistance loci, at low frequencies, occurred in samples from countries not using antibiotics in beekeeping and samples from wild bumblebees. Thus, long-term antibiotic treatment has caused the bee gut microbiota to accumulate resistance genes, drawn from a widespread pool of highly mobile loci characterized from pathogens and agricultural sites. We found that 50 years of using antibiotics in beekeeping in the United States has resulted in extensive tetracycline resistance in the gut microbiota. These bacteria, which form a distinctive community present in healthy honeybees worldwide, may

  4. Long-term exposure to antibiotics has caused accumulation of resistance determinants in the gut microbiota of honeybees.

    Science.gov (United States)

    Tian, Baoyu; Fadhil, Nibal H; Powell, J Elijah; Kwong, Waldan K; Moran, Nancy A

    2012-10-30

    Antibiotic treatment can impact nontarget microbes, enriching the pool of resistance genes available to pathogens and altering community profiles of microbes beneficial to hosts. The gut microbiota of adult honeybees, a distinctive community dominated by eight bacterial species, provides an opportunity to examine evolutionary responses to long-term treatment with a single antibiotic. For decades, American beekeepers have routinely treated colonies with oxytetracycline for control of larval pathogens. Using a functional metagenomic screen of bacteria from Maryland bees, we detected a high incidence of tetracycline/oxytetracycline resistance. This resistance is attributable to known resistance loci for which nucleotide sequences and flanking mobility genes were nearly identical to those from human pathogens and from bacteria associated with farm animals. Surveys using diagnostic PCR and sequencing revealed that gut bacteria of honeybees from diverse localities in the United States harbor eight tetracycline resistance loci, including efflux pump genes (tetB, tetC, tetD, tetH, tetL, and tetY) and ribosome protection genes (tetM and tetW), often at high frequencies. Isolates of gut bacteria from Connecticut bees display high levels of tetracycline resistance. Resistance genes were ubiquitous in American samples, though rare in colonies unexposed for 25 years. In contrast, only three resistance loci, at low frequencies, occurred in samples from countries not using antibiotics in beekeeping and samples from wild bumblebees. Thus, long-term antibiotic treatment has caused the bee gut microbiota to accumulate resistance genes, drawn from a widespread pool of highly mobile loci characterized from pathogens and agricultural sites. We found that 50 years of using antibiotics in beekeeping in the United States has resulted in extensive tetracycline resistance in the gut microbiota. These bacteria, which form a distinctive community present in healthy honeybees worldwide, may

  5. Microbiota conjuntival em pacientes com alergia ocular Conjunctival microbiota in patients with ocular allergy

    Directory of Open Access Journals (Sweden)

    Alexandre Mattoso Libório

    2005-12-01

    Full Text Available OBJETIVO: Avaliar a presença de microbiota aeróbia da conjuntiva de portadores de alergia ocular e comparar a um grupo controle. MÉTODOS: Foram examinados 133 pacientes no período de abril a junho de 2001 divididos em 2 grupos. O grupo A foi composto de 63 portadores de conjuntivite alérgica (sem uso de medicação e o grupo B de 70 pacientes do ambulatório geral (controle. Foram coletadas amostras do fundo de saco conjuntival do olho direito de todos os pacientes e o material foi semeado em meios sólidos de cultura (ágar sangue, chocolate e Sabouraud. RESULTADOS: No grupo A, 30 culturas (47,7% foram positivas e no grupo B, 6 (8,6%. Sete bactérias foram isoladas no grupo A e 4 no B. A análise estatística revelou associação significante entre a positividade dos cultivos e conjuntivite alérgica. CONCLUSÃO: Microbiota bacteriana foi mais freqüentemente encontrada nos pacientes com alergia ocular.PURPOSE: To evaluate de presence of conjunctival aerobic microbiota in patients with ocular allergy as compared to a control group. METHODS: One hundred and thirty-three patients were evaluated from April to June 2001 and divided into 2 groups. Sixty-three patients with allergic conjunctivitis (without medication were in group A and 70 patients from the general outpatient clinic were in group B (control group. Samples from the conjunctival sac of the right eye were collected and cultured in solid media (blood, chocolate and Sabouraud agar. RESULTS: In group A, 30 cultures (47.7% were positive and 6 (8.6% in group B. Seven bacteria were isolated from group A and 4 from group B. Statistical analysis revealed significant association between positive cultures and allergic conjunctivitis. CONCLUSION: Bacterial microbiota was more frequently found in patients with ocular allergy.

  6. The influence of diet on the gut microbiota.

    Science.gov (United States)

    Scott, Karen P; Gratz, Silvia W; Sheridan, Paul O; Flint, Harry J; Duncan, Sylvia H

    2013-03-01

    Diet is a major factor driving the composition and metabolism of the colonic microbiota. The amount, type and balance of the main dietary macronutrients (carbohydrates, proteins and fats) have a great impact on the large intestinal microbiota. The human colon contains a dense population of bacterial cells that outnumber host cells 10-fold. Bacteroidetes, Firmicutes and Actinobacteria are the three major phyla that inhabit the human large intestine and these bacteria possess a fascinating array of enzymes that can degrade complex dietary substrates. Certain colonic bacteria are able to metabolise a remarkable variety of substrates whilst other species carry out more specialised activities, including primary degradation of plant cell walls. Microbial metabolism of dietary carbohydrates results mainly in the formation of short chain fatty acids and gases. The major bacterial fermentation products are acetate, propionate and butyrate; and the production of these tends to lower the colonic pH. These weak acids influence the microbial composition and directly affect host health, with butyrate the preferred energy source for the colonocytes. Certain bacterial species in the colon survive by cross-feeding, using either the breakdown products of complex carbohydrate degradation or fermentation products such as lactic acid for growth. Microbial protein metabolism results in additional fermentation products, some of which are potentially harmful to host health. The current 'omic era promises rapid progress towards understanding how diet can be used to modulate the composition and metabolism of the gut microbiota, allowing researchers to provide informed advice, that should improve long-term health status. PMID:23147033

  7. Evaluation of an oral subchronic exposure of deoxynivalenol on the composition of human gut microbiota in a model of human microbiota-associated rats.

    Directory of Open Access Journals (Sweden)

    Manuel J Saint-Cyr

    Full Text Available BACKGROUND: Deoxynivalenol (DON, a mycotoxin produced by Fusarium species, is one of the most prevalent mycotoxins present in cereal crops worldwide. Due to its toxic properties, high stability and prevalence, the presence of DON in the food chain represents a health risk for both humans and animals. The gastrointestinal microbiota represents potentially the first target for these food contaminants. Thus, the effects of mycotoxins on the human gut microbiota is clearly an issue that needs to be addressed in further detail. Using a human microbiota-associated rat model, the aim of the present study was to evaluate the impact of a chronic exposure of DON on the composition of human gut microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Four groups of 5 germ free male rats each, housed in 4 sterile isolators, were inoculated with a different fresh human fecal flora. Rats were then fed daily by gavage with a solution of DON at 100 µg/kg bw for 4 weeks. Fecal samples were collected at day 0 before the beginning of the treatment; days 7, 16, 21, and 27 during the treatment; and 10 days after the end of the treatment at day 37. DON effect was assessed by real-time PCR quantification of dominant and subdominant bacterial groups in feces. Despite a different intestinal microbiota in each isolator, similar trends were generally observed. During oral DON exposure, a significant increase of 0.5 log10 was observed for the Bacteroides/Prevotella group during the first 3 weeks of administration. Concentration levels for Escherichia coli decreased at day 27. This significant decrease (0.9 log10 CFU/g remained stable until the end of the experiment. CONCLUSIONS/SIGNIFICANCE: We have demonstrated an impact of oral DON exposure on the human gut microbiota composition. These findings can serve as a template for risk assessment studies of food contaminants on the human gut microbiota.

  8. Enterotypes influence temporal changes in gut microbiota

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Licht, Tine Rask; Kellebjerg Poulsen, Sanne;

    The human gut microbiota plays an important role for the health of the host. The question is whether we can modulate the gut microbiota by changing diet. During a 6-month, randomised, controlled dietary intervention, the effect of a moderate diet shift from Average Danish Diet to New Nordic Diet on...... the gut microbiota in humans (n=62) was investigated. Quantitative PCR analysis showed that the microbiota did not change significantly by the intervention. Nevertheless, by stratifying subjects into two enterotypes, distinguished by the Prevotella/Bacteroides ratio (P/B), we were able to detect...... significant changes in the gut microbiota composition resulting from the interventions. Subjects with a high-P/B experienced more pronounced changes in the gut microbiota composition than subjects with a low-P/B. The study is the first to indicate that enterotypes influence microbiota response to a dietary...

  9. High-fat diet alters gut microbiota physiology in mice

    OpenAIRE

    Daniel, Hannelore; Gholami, Amin Moghaddas; Berry, David; Desmarchelier, Charles; Hahne, Hannes; Loh, Gunnar; Mondot, Stanislas; Lepage, Patricia; Rothballer, Michael; Walker, Alesia; Böhm, Christoph; Wenning, Mareike; Wagner, Michael; Blaut, Michael; Schmitt-Kopplin, Philippe

    2013-01-01

    The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by...

  10. Helminth colonization is associated with increased diversity of the gut microbiota.

    Directory of Open Access Journals (Sweden)

    Soo Ching Lee

    2014-05-01

    Full Text Available Soil-transmitted helminths colonize more than 1.5 billion people worldwide, yet little is known about how they interact with bacterial communities in the gut microbiota. Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths, since they predominantly infect individuals from developing countries, such as the indigenous communities in Malaysia we examine in this work. We compared the composition and diversity of bacterial communities from the fecal microbiota of 51 people from two villages in Malaysia, of which 36 (70.6% were infected by helminths. The 16S rRNA V4 region was sequenced at an average of nineteen thousand sequences per samples. Helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection. We developed a new approach of combining centered log-ratio (clr transformation for OTU relative abundances with sparse Partial Least Squares Discriminant Analysis (sPLS-DA to enable more robust predictions of OTU interrelationships. These results suggest that helminths may have an impact on the diversity, bacterial community structure and function of the gut microbiota.

  11. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.

    Science.gov (United States)

    Browne, Hilary P; Forster, Samuel C; Anonye, Blessing O; Kumar, Nitin; Neville, B Anne; Stares, Mark D; Goulding, David; Lawley, Trevor D

    2016-05-26

    Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability. PMID:27144353

  12. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    Science.gov (United States)

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  13. Bacterial microbiome of lungs in COPD

    Directory of Open Access Journals (Sweden)

    Sze MA

    2014-02-01

    Full Text Available Marc A Sze,1 James C Hogg,2 Don D Sin1 1Department of Medicine, 2Department of Pathology and Laboratory Medicine, The James Hogg Research Centre, Providence Heart-Lung Institute, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada Abstract: Chronic obstructive pulmonary disease (COPD is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the bacterial microbiota at different body sites in human beings. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Although traditionally the lung has been viewed as a sterile organ, by using highly sensitive genomic techniques, recent reports have identified diverse bacterial communities in the human lung that may change in COPD. This review summarizes the current knowledge concerning the lung microbiota in COPD and its potential implications for pathogenesis of the disease. Keywords: chronic obstructive pulmonary disease, bacterial microbiome, lungs

  14. Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

    OpenAIRE

    Berry, David; Schwab, Clarissa; Milinovich, Gabriel; Reichert, Jochen; Ben Mahfoudh, Karim; Decker, Thomas; Engel, Marion; Hai, Brigitte; Hainzl, Eva; Heider, Susanne; Kenner, Lukas; Müller, Mathias; Rauch, Isabella; Strobl, Birgit; Wagner, Michael

    2012-01-01

    Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1−/− and wild-type mice, as determined by 454 pyrosequencing of bacterial...

  15. Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease

    Science.gov (United States)

    Shimizu, Jun; Kubota, Takao; Takada, Erika; Takai, Kenji; Fujiwara, Naruyoshi; Arimitsu, Nagisa; Ueda, Yuji; Wakisaka, Sueshige; Suzuki, Tomoko; Suzuki, Noboru

    2016-01-01

    Gut microbiota compositional alteration may have an association with immune dysfunction in patients with Behcet’s disease (BD). We conducted a fecal metagenomic analysis of BD patients. We analyzed fecal microbiota obtained from 12 patients with BD and 12 normal individuals by sequencing of 16S ribosomal RNA gene. We compared the relative abundance of bacterial taxa. Direct comparison of the relative abundance of bacterial taxa demonstrated that the genera Bifidobacterium and Eggerthella increased significantly and the genera Megamonas and Prevotella decreased significantly in BD patients compared with normal individuals. A linear discriminant analysis of bacterial taxa showed that the phylum Actinobacteria, including Bifidobacterium, and the family Lactobacillaceae exhibited larger positive effect sizes than other bacteria in patients with BD. The phylum Firmicutes and the class Clostridia had large effect sizes in normal individuals. There was no significant difference in annotated species numbers (as numbers of operational taxonomic unit; OTU) and bacterial diversity of each sample (alpha diversity) between BD patients and normal individuals. We next assigned each sample to a position using three axes by principal coordinates analysis of the OTU table. The two groups had a significant distance as beta diversity in the 3-axis space. Fecal sIgA concentrations increased significantly in BD patients but did not correlate with any bacterial taxonomic abundance. These data suggest that the compositional changes of gut microbes may be one type of dysbiosis (unfavorable microbiota alteration) in patients with BD. The dysbiosis may have an association with the pathophysiology of BD. PMID:27105322

  16. Gut indigenous microbiota and epigenetics

    Directory of Open Access Journals (Sweden)

    Boris Arkadievich Shenderov

    2012-03-01

    Full Text Available This review introduces and discusses data regarding fundamental and applied investigations in mammalian epigenomics and gut microbiota received over the last 10 years. Analysis of these data enabled the author first to come to the conclusion that the multiple low molecular weight substances of indigenous gut microbiota origin should be considered one of the main endogenous factors actively participating in epigenomic mechanisms that responsible for the mammalian genome reprogramming and post-translated modifications. Gut microecological imbalance coursed by various biogenic and abiogenic agents and factors can produce the different epigenetic abnormalities and the onset and progression of metabolic diseases associated. The author substantiates the necessity to create an international project ‘Human Gut Microbiota and Epigenomics’ that facilitates interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics investigations as well as in diseases prevention and treatment. Some priority scientific and applied directions in the current omic technologies coupled with gnotobiological approaches are suggested that can open a new era in characterizing the role of the symbiotic microbiota small metabolic and signal molecules in the host epigenomics. Although discussed subject is only at an early stage its validation can open novel approaches in drug discovery studies.

  17. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem?

    Directory of Open Access Journals (Sweden)

    Alexis eMosca

    2016-03-01

    Full Text Available Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. We argue that this phenomenon is similar to the process of ecosystem impoverishment in macro ecology where human activity decreases ecological niches, the size of predator populations and finally the biodiversity. Such pauperization is fundamental since it reverses the evolution processes, drives life backward into diminished complexity, stability and adaptability. A simple therapeutic approach could thus be to reintroduce bacterial predators and restore a bacterial diversity of the host microbiota.

  18. Citrobacter rodentium mouse model of bacterial infection.

    Science.gov (United States)

    Crepin, Valerie F; Collins, James W; Habibzay, Maryam; Frankel, Gad

    2016-10-01

    Infection of mice with Citrobacter rodentium is a robust model to study bacterial pathogenesis, mucosal immunology, the health benefits of probiotics and the role of the microbiota during infection. C. rodentium was first isolated by Barthold from an outbreak of mouse diarrhea in Yale University in 1972 and was 'rediscovered' by Falkow and Schauer in 1993. Since then the use of the model has proliferated, and it is now the gold standard for studying virulence of the closely related human pathogens enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Here we provide a detailed protocol for various applications of the model, including bacterial growth, site-directed mutagenesis, mouse inoculation (from cultured cells and after cohabitation), monitoring of bacterial colonization, tissue extraction and analysis, immune responses, probiotic treatment and microbiota analysis. The main protocol, from mouse infection to clearance and analysis of tissues and host responses, takes ∼5 weeks to complete. PMID:27606775

  19. Metabolism of Cholesterol and Bile Acids by the Gut Microbiota

    Directory of Open Access Journals (Sweden)

    Philippe Gérard

    2013-12-01

    Full Text Available The human gastro-intestinal tract hosts a complex and diverse microbial community, whose collective genetic coding capacity vastly exceeds that of the human genome. As a consequence, the gut microbiota produces metabolites from a large range of molecules that host’s enzymes are not able to convert. Among these molecules, two main classes of steroids, cholesterol and bile acids, denote two different examples of bacterial metabolism in the gut. Therefore, cholesterol is mainly converted into coprostanol, a non absorbable sterol which is excreted in the feces. Moreover, this conversion occurs in a part of the human population only. Conversely, the primary bile acids (cholic and chenodeoxycholic acids are converted to over twenty different secondary bile acid metabolites by the gut microbiota. The main bile salt conversions, which appear in the gut of the whole human population, include deconjugation, oxidation and epimerization of hydroxyl groups at C3, C7 and C12, 7-dehydroxylation, esterification and desulfatation. If the metabolisms of cholesterol and bile acids by the gut microbiota are known for decades, their consequences on human health and disease are poorly understood and only start to be considered.

  20. Metatranscriptomic approach to analyze the functional human gut microbiota.

    Directory of Open Access Journals (Sweden)

    María José Gosalbes

    Full Text Available The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.

  1. Midgut microbiota and host immunocompetence underlie Bacillus thuringiensis killing mechanism.

    Science.gov (United States)

    Caccia, Silvia; Di Lelio, Ilaria; La Storia, Antonietta; Marinelli, Adriana; Varricchio, Paola; Franzetti, Eleonora; Banyuls, Núria; Tettamanti, Gianluca; Casartelli, Morena; Giordana, Barbara; Ferré, Juan; Gigliotti, Silvia; Ercolini, Danilo; Pennacchio, Francesco

    2016-08-23

    Bacillus thuringiensis is a widely used bacterial entomopathogen producing insecticidal toxins, some of which are expressed in insect-resistant transgenic crops. Surprisingly, the killing mechanism of B. thuringiensis remains controversial. In particular, the importance of the septicemia induced by the host midgut microbiota is still debated as a result of the lack of experimental evidence obtained without drastic manipulation of the midgut and its content. Here this key issue is addressed by RNAi-mediated silencing of an immune gene in a lepidopteran host Spodoptera littoralis, leaving the midgut microbiota unaltered. The resulting cellular immunosuppression was characterized by a reduced nodulation response, which was associated with a significant enhancement of host larvae mortality triggered by B. thuringiensis and a Cry toxin. This was determined by an uncontrolled proliferation of midgut bacteria, after entering the body cavity through toxin-induced epithelial lesions. Consequently, the hemolymphatic microbiota dramatically changed upon treatment with Cry1Ca toxin, showing a remarkable predominance of Serratia and Clostridium species, which switched from asymptomatic gut symbionts to hemocoelic pathogens. These experimental results demonstrate the important contribution of host enteric flora in B. thuringiensis-killing activity and provide a sound foundation for developing new insect control strategies aimed at enhancing the impact of biocontrol agents by reducing the immunocompetence of the host.

  2. Midgut microbiota and host immunocompetence underlie Bacillus thuringiensis killing mechanism.

    Science.gov (United States)

    Caccia, Silvia; Di Lelio, Ilaria; La Storia, Antonietta; Marinelli, Adriana; Varricchio, Paola; Franzetti, Eleonora; Banyuls, Núria; Tettamanti, Gianluca; Casartelli, Morena; Giordana, Barbara; Ferré, Juan; Gigliotti, Silvia; Ercolini, Danilo; Pennacchio, Francesco

    2016-08-23

    Bacillus thuringiensis is a widely used bacterial entomopathogen producing insecticidal toxins, some of which are expressed in insect-resistant transgenic crops. Surprisingly, the killing mechanism of B. thuringiensis remains controversial. In particular, the importance of the septicemia induced by the host midgut microbiota is still debated as a result of the lack of experimental evidence obtained without drastic manipulation of the midgut and its content. Here this key issue is addressed by RNAi-mediated silencing of an immune gene in a lepidopteran host Spodoptera littoralis, leaving the midgut microbiota unaltered. The resulting cellular immunosuppression was characterized by a reduced nodulation response, which was associated with a significant enhancement of host larvae mortality triggered by B. thuringiensis and a Cry toxin. This was determined by an uncontrolled proliferation of midgut bacteria, after entering the body cavity through toxin-induced epithelial lesions. Consequently, the hemolymphatic microbiota dramatically changed upon treatment with Cry1Ca toxin, showing a remarkable predominance of Serratia and Clostridium species, which switched from asymptomatic gut symbionts to hemocoelic pathogens. These experimental results demonstrate the important contribution of host enteric flora in B. thuringiensis-killing activity and provide a sound foundation for developing new insect control strategies aimed at enhancing the impact of biocontrol agents by reducing the immunocompetence of the host. PMID:27506800

  3. The health advantage of a vegan diet: exploring the gut microbiota connection.

    Science.gov (United States)

    Glick-Bauer, Marian; Yeh, Ming-Chin

    2014-11-01

    This review examines whether there is evidence that a strict vegan diet confers health advantages beyond that of a vegetarian diet or overall healthy eating. Few studies include vegan subjects as a distinct experimental group, yet when vegan diets are directly compared to vegetarian and omnivorous diets, a pattern of protective health benefits emerges. The relatively recent inclusion of vegan diets in studies of gut microbiota and health allows us the opportunity to assess whether the vegan gut microbiota is distinct, and whether the health advantages characteristic of a vegan diet may be partially explained by the associated microbiota profile. The relationship between diet and the intestinal microbial profile appears to follow a continuum, with vegans displaying a gut microbiota most distinct from that of omnivores, but not always significantly different from that of vegetarians. The vegan gut profile appears to be unique in several characteristics, including a reduced abundance of pathobionts and a greater abundance of protective species. Reduced levels of inflammation may be the key feature linking the vegan gut microbiota with protective health effects. However, it is still unclear whether a therapeutic vegan diet can be prescribed to alter the gut microflora for long-term health benefits. PMID:25365383

  4. The health advantage of a vegan diet: exploring the gut microbiota connection.

    Science.gov (United States)

    Glick-Bauer, Marian; Yeh, Ming-Chin

    2014-10-31

    This review examines whether there is evidence that a strict vegan diet confers health advantages beyond that of a vegetarian diet or overall healthy eating. Few studies include vegan subjects as a distinct experimental group, yet when vegan diets are directly compared to vegetarian and omnivorous diets, a pattern of protective health benefits emerges. The relatively recent inclusion of vegan diets in studies of gut microbiota and health allows us the opportunity to assess whether the vegan gut microbiota is distinct, and whether the health advantages characteristic of a vegan diet may be partially explained by the associated microbiota profile. The relationship between diet and the intestinal microbial profile appears to follow a continuum, with vegans displaying a gut microbiota most distinct from that of omnivores, but not always significantly different from that of vegetarians. The vegan gut profile appears to be unique in several characteristics, including a reduced abundance of pathobionts and a greater abundance of protective species. Reduced levels of inflammation may be the key feature linking the vegan gut microbiota with protective health effects. However, it is still unclear whether a therapeutic vegan diet can be prescribed to alter the gut microflora for long-term health benefits.

  5. The Health Advantage of a Vegan Diet: Exploring the Gut Microbiota Connection

    Directory of Open Access Journals (Sweden)

    Marian Glick-Bauer

    2014-10-01

    Full Text Available This review examines whether there is evidence that a strict vegan diet confers health advantages beyond that of a vegetarian diet or overall healthy eating. Few studies include vegan subjects as a distinct experimental group, yet when vegan diets are directly compared to vegetarian and omnivorous diets, a pattern of protective health benefits emerges. The relatively recent inclusion of vegan diets in studies of gut microbiota and health allows us the opportunity to assess whether the vegan gut microbiota is distinct, and whether the health advantages characteristic of a vegan diet may be partially explained by the associated microbiota profile. The relationship between diet and the intestinal microbial profile appears to follow a continuum, with vegans displaying a gut microbiota most distinct from that of omnivores, but not always significantly different from that of vegetarians. The vegan gut profile appears to be unique in several characteristics, including a reduced abundance of pathobionts and a greater abundance of protective species. Reduced levels of inflammation may be the key feature linking the vegan gut microbiota with protective health effects. However, it is still unclear whether a therapeutic vegan diet can be prescribed to alter the gut microflora for long-term health benefits.

  6. Intestinal microbiota, diet and health.

    Science.gov (United States)

    Power, Susan E; O'Toole, Paul W; Stanton, Catherine; Ross, R Paul; Fitzgerald, Gerald F

    2014-02-01

    The human intestine is colonised by 10¹³ to 10¹⁴ micro-organisms, the vast majority of which belong to the phyla Firmicutes and Bacteroidetes. Although highly stable over time, the composition and activities of the microbiota may be influenced by a number of factors including age, diet and antibiotic treatment. Although perturbations in the composition or functions of the microbiota are linked to inflammatory and metabolic disorders (e.g. inflammatory bowel diseases, irritable bowel syndrome and obesity), it is unclear at this point whether these changes are a symptom of the disease or a contributing factor. A better knowledge of the mechanisms through which changes in microbiota composition (dysbiosis) promote disease states is needed to improve our understanding of the causal relationship between the gut microbiota and disease. While evidence of the preventive and therapeutic effects of probiotic strains on diarrhoeal illness and other intestinal conditions is promising, the exact mechanisms of the beneficial effects are not fully understood. Recent studies have raised the question of whether non-viable probiotic strains can confer health benefits on the host by influencing the immune system. As the potential health effect of these non-viable bacteria depends on whether the mechanism of this effect is dependent on viability, future research needs to consider each probiotic strain on a case-by-case basis. The present review provides a comprehensive, updated overview of the human gut microbiota, the factors influencing its composition and the role of probiotics as a therapeutic modality in the treatment and prevention of diseases and/or restoration of human health. PMID:23931069

  7. Gut Microbiota: From Fundamental Research to Translational Medicine

    Directory of Open Access Journals (Sweden)

    Yujing Bi

    2015-12-01

    aroused strong interest in recent years, is reported to be a highly successful therapy for recurrent Clostridium difficile infection. These studies support novel research ideas that are no longer focused solely on the host, but rather on the intimacy of the host-microbiota relationship. Considering the relative ease of regulating the gut microbiota[1], targeting these organisms through diet, prebiotics, probiotics, or other methods may become a useful strategy for curing diseases. To date, a large number of studies have been devoted to uncovering the relationship between microbial metabolites and human diseases, and it is highly likely that more bacterial or related pathways involved in human disease will be identified. In the future, targeting the microbiome may represent an effective and complementary strategy to current approaches for preventing and treating diseases.

  8. Intestinal Microbiota Is Influenced by Gender and Body Mass Index.

    Directory of Open Access Journals (Sweden)

    Carmen Haro

    Full Text Available Intestinal microbiota changes are associated with the development of obesity. However, studies in humans have generated conflicting results due to high inter-individual heterogeneity in terms of diet, age, and hormonal factors, and the largely unexplored influence of gender. In this work, we aimed to identify differential gut microbiota signatures associated with obesity, as a function of gender and changes in body mass index (BMI. Differences in the bacterial community structure were analyzed by 16S sequencing in 39 men and 36 post-menopausal women, who had similar dietary background, matched by age and stratified according to the BMI. We observed that the abundance of the Bacteroides genus was lower in men than in women (P 33. In fact, the abundance of this genus decreased in men with an increase in BMI (P<0.001, Q<0.001. However, in women, it remained unchanged within the different ranges of BMI. We observed a higher presence of Veillonella (84.6% vs. 47.2%; X2 test P = 0.001, Q = 0.019 and Methanobrevibacter genera (84.6% vs. 47.2%; X2 test P = 0.002, Q = 0.026 in fecal samples in men compared to women. We also observed that the abundance of Bilophila was lower in men compared to women regardless of BMI (P = 0.002, Q = 0.041. Additionally, after correcting for age and sex, 66 bacterial taxa at the genus level were found to be associated with BMI and plasma lipids. Microbiota explained at P = 0.001, 31.17% variation in BMI, 29.04% in triglycerides, 33.70% in high-density lipoproteins, 46.86% in low-density lipoproteins, and 28.55% in total cholesterol. Our results suggest that gut microbiota may differ between men and women, and that these differences may be influenced by the grade of obesity. The divergence in gut microbiota observed between men and women might have a dominant role in the definition of gender differences in the prevalence of metabolic and intestinal inflammatory diseases.

  9. Intestinal Microbiota Is Influenced by Gender and Body Mass Index

    Science.gov (United States)

    Haro, Carmen; Rangel-Zúñiga, Oriol A.; Alcalá-Díaz, Juan F.; Gómez-Delgado, Francisco; Pérez-Martínez, Pablo; Delgado-Lista, Javier; Quintana-Navarro, Gracia M.; Landa, Blanca B.; Navas-Cortés, Juan A.; Tena-Sempere, Manuel; Clemente, José C.; López-Miranda, José

    2016-01-01

    Intestinal microbiota changes are associated with the development of obesity. However, studies in humans have generated conflicting results due to high inter-individual heterogeneity in terms of diet, age, and hormonal factors, and the largely unexplored influence of gender. In this work, we aimed to identify differential gut microbiota signatures associated with obesity, as a function of gender and changes in body mass index (BMI). Differences in the bacterial community structure were analyzed by 16S sequencing in 39 men and 36 post-menopausal women, who had similar dietary background, matched by age and stratified according to the BMI. We observed that the abundance of the Bacteroides genus was lower in men than in women (P 33. In fact, the abundance of this genus decreased in men with an increase in BMI (P<0.001, Q<0.001). However, in women, it remained unchanged within the different ranges of BMI. We observed a higher presence of Veillonella (84.6% vs. 47.2%; X2 test P = 0.001, Q = 0.019) and Methanobrevibacter genera (84.6% vs. 47.2%; X2 test P = 0.002, Q = 0.026) in fecal samples in men compared to women. We also observed that the abundance of Bilophila was lower in men compared to women regardless of BMI (P = 0.002, Q = 0.041). Additionally, after correcting for age and sex, 66 bacterial taxa at the genus level were found to be associated with BMI and plasma lipids. Microbiota explained at P = 0.001, 31.17% variation in BMI, 29.04% in triglycerides, 33.70% in high-density lipoproteins, 46.86% in low-density lipoproteins, and 28.55% in total cholesterol. Our results suggest that gut microbiota may differ between men and women, and that these differences may be influenced by the grade of obesity. The divergence in gut microbiota observed between men and women might have a dominant role in the definition of gender differences in the prevalence of metabolic and intestinal inflammatory diseases. PMID:27228093

  10. Intestinal microbiota in inflammatory bowel disease: Friend of foe?

    Institute of Scientific and Technical Information of China (English)

    Francesca Fava; Silvio Danese

    2011-01-01

    Inflammatory bowel disease (IBD) arises from disruption of immune tolerance to the gut commensal microbiota,leading to chronic intestinal inflammation and mucosal damage in genetically predisposed hosts. In healthy individuals the intestinal microbiota have a symbiotic relationship with the host organism and possess important and unique functions, including a metabolic function (i.e.digestion of dietary compounds and xenobiotics, fermentation of undigestible carbohydrates with production of short chain fatty acids), a mucosal barrier function (i.e. by inhibiting pathogen invasion and strengthening epithelial barrier integrity), and an immune modulatory function (i.e. mucosal immune system priming and maintenance of intestinal epithelium homeostasis). A fine balance regulates the mechanism that allows coexistence of mammals with their commensal bacteria.In IBD this mechanism of immune tolerance is impaired because of several potential causative factors. The gut microbiota composition and activity of IBD patients are abnormal, with a decreased prevalence of dominant members of the human commensal microbiota (i.e.Clostridium Ⅸa and Ⅳ groups, Bacteroides , bifidobacteria)and a concomitant increase in detrimental bacteria (i.e. sulphate-reducing bacteria, Escherichia coli ).The observed dysbiosis is concomitant with defective innate immunity and bacterial killing (i.e. reduced mucosal defensins and IgA, malfunctioning phagocytosis)and overaggressive adaptive immune response (due to ineffective regulatory T cells and antigen presenting cells), which are considered the basis of IBD pathogenesis.However, we still do not know how the interplay between these parameters causes the disease. Studies looking at gut microbial composition, epithelial integrity and mucosal immune markers in genotyped IBD populations are therefore warranted to shed light on this obscure pathogenesis.

  11. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota.

    Directory of Open Access Journals (Sweden)

    Tatsuki Ogura

    Full Text Available Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an "ECOMICS" web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.

  12. Effect of diet supplementation with Ascophyllum nodosum on cow milk composition and microbiota.

    Science.gov (United States)

    Chaves Lopez, Clemencia; Serio, Annalisa; Rossi, Chiara; Mazzarrino, Giovanni; Marchetti, Sonia; Castellani, Federica; Grotta, Lisa; Fiorentino, Francesco Paolo; Paparella, Antonello; Martino, Giuseppe

    2016-08-01

    Iodine deficiency remains a major public health concern in many countries, including some European regions. This study aimed at understanding the effect of a supplement of marine alga Ascophyllum nodosum as a iodine fortifier in the cow diet, on the compositional and microbiological quality of milk. The results obtained in this work indicated that the dietary inclusion of A. nodosum exerted significant effects on cow milk composition. In particular, it increased iodine content and reduced the quantity of free amino acids without modifying the free fatty acid content. From a microbiological point of view, statistically significant differences were found in presumptive mesophilic lactobacilli, mesophilic lactococci, and Pseudomonas spp. counts. Based on a culture-independent method, milk obtained after dietary inclusion of A. nodosum harbored the highest number of Firmicutes (e.g., Lactococcus lactis) and the lowest number of Proteobacteria (e.g., Pseudomonas). In addition to changes in bacterial population, diet supplementation with A. nodosum changed the catabolic profiles of the milk community, according to Biolog Ecoplate (Biolog Inc., Hayward, CA) results. The results of this study suggest that the dietary inclusion of the marine alga A. nodosum led to an improvement of the iodine content in milk, and to a modification of its microbiota with a positive effect on milk hygiene and transformation. PMID:27320666

  13. Impact of Kefir Derived Lactobacillus kefiri on the Mucosal Immune Response and Gut Microbiota

    Directory of Open Access Journals (Sweden)

    P. Carasi

    2015-01-01

    Full Text Available The evaluation of the impact of probiotics on host health could help to understand how they can be used in the prevention of diseases. On the basis of our previous studies and in vitro assays on PBMC and Caco-2 ccl20:luc reporter system presented in this work, the strain Lactobacillus kefiri CIDCA 8348 was selected and administrated to healthy Swiss mice daily for 21 days. The probiotic treatment increased IgA in feces and reduced expression of proinflammatory mediators in Peyer Patches and mesenteric lymph nodes, where it also increased IL-10. In ileum IL-10, CXCL-1 and mucin 6 genes were upregulated; meanwhile in colon mucin 4 was induced whereas IFN-γ, GM-CSF, and IL-1β genes were downregulated. Moreover, ileum and colon explants showed the anti-inflammatory effect of L. kefiri since the LPS-induced increment of IL-6 and GM-CSF levels in control mice was significantly attenuated in L. kefiri treated mice. Regarding fecal microbiota, DGGE profiles allowed differentiation of experimental groups in two separated clusters. Quantitative PCR analysis of different bacterial groups revealed only significant changes in Lactobacillus population. In conclusion, L. kefiri is a good candidate to be used in gut inflammatory disorders.

  14. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque.

    Directory of Open Access Journals (Sweden)

    Miriam E Martin

    Full Text Available Helicobacter pylori colonization is highly prevalent among humans and causes significant gastric disease in a subset of those infected. When present, this bacterium dominates the gastric microbiota of humans and induces antimicrobial responses in the host. Since the microbial context of H. pylori colonization influences the disease outcome in a mouse model, we sought to assess the impact of H. pylori challenge upon the pre-existing gastric microbial community members in the rhesus macaque model. Deep sequencing of the bacterial 16S rRNA gene identified a community profile of 221 phylotypes that was distinct from that of the rhesus macaque distal gut and mouth, although there were taxa in common. High proportions of both H. pylori and H. suis were observed in the post-challenge libraries, but at a given time, only one Helicobacter species was dominant. However, the relative abundance of non-Helicobacter taxa was not significantly different before and after challenge with H. pylori. These results suggest that while different gastric species may show competitive exclusion in the gastric niche, the rhesus gastric microbial community is largely stable despite immune and physiological changes due to H. pylori infection.

  15. Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants.

    Science.gov (United States)

    Lee, Eun; Kim, Byoung Ju; Kang, Mi Jin; Choi, Kil Yong; Cho, Hyun Ju; Kim, Yeongho; Yang, Song I; Jung, Young Ho; Kim, Hyung Young; Seo, Ju Hee; Kwon, Ji Won; Kim, Hyo Bin; Lee, So Yeon; Hong, Soo Jong

    2016-09-01

    Microbial colonization of the infant gut is unstable and shows a wide range of diversity between individuals. Gut microbiota play an important role in the development of the immune system, and an imbalance in these organisms can affect health, including an increased risk of allergic diseases. Microbial colonization of young infants is affected by the delivery mode at birth and the consequent alterations of gut microbiota in early life affect the development of allergic diseases. We investigated the effects of the delivery mode on the temporal dynamics of gut microbiota in healthy Korean infants. Fecal samples were collected at 1-3 days, 1 month, and 6 months after birth in six healthy infants. Microbiota were characterized by 16S rRNA shotgun sequencing. At the first and third days of life, infants born by vaginal delivery showed a higher richness and diversity of gut microbiota compared with those born by cesarean section. However, these differences disappeared with age. The Bacteroides genus and Bacteroidetes phylum were abundant in infants born by vaginal delivery, whereas Bacilli and Clostridium g4 were increased in infants born by cesarean section. The Firmicutes phylum and Bacteroides genus showed convergent dynamics with age. This study demonstrated the effect of delivery mode on the dynamics of gut microbiota profiles in healthy Korean infants. PMID:27334787

  16. The effect of high-fat diet on the composition of the gut microbiota in cloned and non-cloned pigs of lean and obese phenotype

    DEFF Research Database (Denmark)

    Pedersen, Rebecca; Andersen, Anders Daniel; Hermann-Bank, Marie Louise;

    2013-01-01

    overall composition of their gut microbiota. The colon of lean cloned pigs contained relatively more bacteria belonging to the phylum Firmicutes and less from the phylum Bacteroidetes than obese cloned pigs as estimated by qPCR. Fluidigm qPCR results revealed differences in specific bacterial groups...... in the gut microbiota of both lean and obese pigs. Our results suggest that high-far-high-energy diet is associated with changes in the gut microbiota even in the absence of obesity. Overall, the cloned pigs had a different gut microbiota from that of non-cloned pigs. To our knowledge this is the first study...... to investigate the gut microbiota of cloned domestic pigs of lean and obese phenotype....

  17. Having older siblings is associated with gut microbiota development during early childhood

    DEFF Research Database (Denmark)

    Laursen, Martin Frederik; Zachariassen, Gitte; Bahl, Martin Iain;

    2015-01-01

    older siblings was associated with increased relative abundance of several bacterial taxa at both 9 and 18 months of age. Compared to the effect of having siblings, presence of household furred pets and early life infections had less pronounced effects on the gut microbiota. Gut microbiota...... hygiene hypothesis. However, no associations were found between gut microbiota and atopic symptoms of eczema and asthmatic bronchitis during early childhood and thus further studies are required to elucidate whether sibling-associated gut microbial changes influence development of allergies later in......Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies...

  18. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  19. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota

    OpenAIRE

    Tatsuki Ogura; Yasuhiro Date; Jun Kikuchi

    2013-01-01

    Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under ...

  20. Comparison of methods and animal models commonly used for investigation of fecal microbiota: Effects of time, host and gender

    DEFF Research Database (Denmark)

    Bernbom, Nete; Nørrung, Birgit; Saadbye, Peter;

    2006-01-01

    Denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and plating on selective agars were used to study variation in the fecal microbiota of rats over time as well as variation between individuals. Investigated rats were either conventional...... and specific pathogen free (SPF). or human flora associated (HFA). A higher variation (p RFLP profiles of fecal microbiota from SPF and HFA rats revealed that variation over time was less significant than...

  1. Toxicity ranking and toxic mode of action evaluation of commonly used agricultural adjuvants on the basis of bacterial gene expression profiles.

    Directory of Open Access Journals (Sweden)

    Ingrid Nobels

    Full Text Available The omnipresent group of pesticide adjuvants are often referred to as "inert" ingredients, a rather misleading term since consumers associate this term with "safe". The upcoming new EU regulation concerning the introduction of plant protection products on the market (EC1107/2009 includes for the first time the demand for information on the possible negative effects of not only the active ingredients but also the used adjuvants. This new regulation requires basic toxicological information that allows decisions on the use/ban or preference of use of available adjuvants. In this study we obtained toxicological relevant information through a multiple endpoint reporter assay for a broad selection of commonly used adjuvants including several solvents (e.g. isophorone and non-ionic surfactants (e.g. ethoxylated alcohols. The used assay allows the toxicity screening in a mechanistic way, with direct measurement of specific toxicological responses (e.g. oxidative stress, DNA damage, membrane damage and general cell lesions. The results show that the selected solvents are less toxic than the surfactants, suggesting that solvents may have a preference of use, but further research on more compounds is needed to confirm this observation. The gene expression profiles of the selected surfactants reveal that a phenol (ethoxylated tristyrylphenol and an organosilicone surfactant (ethoxylated trisiloxane show little or no inductions at EC(20 concentrations, making them preferred surfactants for use in different applications. The organosilicone surfactant shows little or no toxicity and good adjuvant properties. However, this study also illustrates possible genotoxicity (induction of the bacterial SOS response for several surfactants (POEA, AE, tri-EO, EO FA and EO NP and one solvent (gamma-butyrolactone. Although the number of compounds that were evaluated is rather limited (13, the results show that the used reporter assay is a promising tool to rank commonly

  2. Transient and Prolonged Response of Chicken Cecum Mucosa to Colonization with Different Gut Microbiota

    Science.gov (United States)

    Volf, Jiri; Polansky, Ondrej; Varmuzova, Karolina; Gerzova, Lenka; Sekelova, Zuzana; Faldynova, Marcela; Babak, Vladimir; Medvecky, Matej; Smith, Adrian L.; Kaspers, Bernd; Velge, Philippe; Rychlik, Ivan

    2016-01-01

    In this study we determined protein and gene expression in the caeca of newly hatched chickens inoculated with cecal contents sourced from hens of different ages. Over 250 proteins exhibited modified expression levels in response to microbiota inoculation. The most significant inductions were observed for ISG12-2, OASL, ES1, LYG2, DMBT1-L, CDD, ANGPTL6, B2M, CUZD1, IgM and Ig lambda chain. Of these, ISG12-2, ES1 and both immunoglobulins were expressed at lower levels in germ-free chickens compared to conventional chickens. In contrast, CELA2A, BRT-2, ALDH1A1, ADH1C, AKR1B1L, HEXB, ALDH2, ALDOB, CALB1 and TTR were expressed at lower levels following inoculation of microbiota. When chicks were given microbiota preparations from different age donors, the recipients mounted differential responses to the inoculation which also differed from the response profile in naturally colonised birds. For example, B2M, CUZD1 and CELA2A responded differently to the inoculation with microbiota of 4- or 40-week-old hens. The increased or decreased gene expression could be recorded 6 weeks after the inoculation of newly hatched chickens. To characterise the proteins that may directly interact with the microbiota we characterised chicken proteins that co-purified with the microbiota and identified a range of host proteins including CDD, ANGPTL6, DMBT1-L, MEP1A and Ig lambda. We propose that induction of ISG12-2 results in reduced apoptosis of host cells exposed to the colonizing commensal microbiota and that CDD, ANGPTL6, DMBT1-L, MEP1A and Ig lambda reduce contact of luminal microbiota with the gut epithelium thereby reducing the inflammatory response. PMID:27685470

  3. Exometabolomic Profiling of Bacterial Cultures

    DEFF Research Database (Denmark)

    Honoré, Anders Hans

    ‐previously reported metabolites were identified as having antifungal properties (manuscript V). In conclusion, the research conducted in this project demonstrated the potential of untargeted analysis of the exometabolome in combination with multivariate data analysis for building new understanding of biological...... compounds have been identified as antifungal based on a strategy of bioassay guided fractionation, the factors for antifungal effect remain unexplained. Lack of understanding about the mechanism(s) responsible for the effect restricts development of new cultures with antifungal properties as well...... as the application into other food matrices. The scope of the thesis was to develop and apply a chromatography mass spectrometry based metabolomic footprint workflow for the investigation of the mechanisms behind the antifungal properties of a co‐culture, consisting of Lactobacillus paracasei (LAB A...

  4. Enterotypes influence temporal changes in gut microbiota

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Licht, Tine Rask; Kellebjerg Poulsen, Sanne;

    The human gut microbiota plays an important role for human health. The question is whether we can modulate the gut microbiota by changing diet. During a 6-month, randomised, controlled dietary intervention, the effect of consuming a diet following the New Nordic Diet recommendations (NND) as...... opposed to Average Danish Diet (ADD) on the gut microbiota in humans (n=62) was investigated. Quantitative PCR analysis showed that the microbiota did not change significantly by the intervention. Nevertheless, by stratifying subjects into two enterotypes, distinguished by the Prevotella/Bacteroides ratio...... (P/B), we were able to detect significant changes in the gut microbiota composition resulting from the interventions. Subjects with a high-P/B experienced more pronounced changes in the gut microbiota composition than subjects with a low-P/B. The study is the first to indicate that enterotypes...

  5. The gut microbiota and metabolic disease

    DEFF Research Database (Denmark)

    Arora, T; Bäckhed, Gert Fredrik

    2016-01-01

    The human gut microbiota has been studied for more than a century. However, of nonculture-based techniques exploiting next-generation sequencing for analysing the microbiota, development has renewed research within the field during the past decade. The observation that the gut microbiota......, as an environmental factor, contributes to adiposity has further increased interest in the field. The human microbiota is affected by the diet, and macronutrients serve as substrates for many microbially produced metabolites, such as short-chain fatty acids and bile acids, that may modulate host metabolism. Obesity......-producing bacteria might be causally linked to type 2 diabetes. Bariatric surgery, which promotes long-term weight loss and diabetes remission, alters the gut microbiota in both mice and humans. Furthermore, by transferring the microbiota from postbariatric surgery patients to mice, it has been demonstrated...

  6. Microbiota-Produced Succinate Improves Glucose Homeostasis via Intestinal Gluconeogenesis.

    Science.gov (United States)

    De Vadder, Filipe; Kovatcheva-Datchary, Petia; Zitoun, Carine; Duchampt, Adeline; Bäckhed, Fredrik; Mithieux, Gilles

    2016-07-12

    Beneficial effects of dietary fiber on glucose and energy homeostasis have long been described, focusing mostly on the production of short-chain fatty acids by the gut commensal bacteria. However, bacterial fermentation of dietary fiber also produces large amounts of succinate and, to date, no study has focused on the role of succinate on host metabolism. Here, we fed mice a fiber-rich diet and found that succinate was the most abundant carboxylic acid in the cecum. Dietary succinate was identified as a substrate for intestinal gluconeogenesis (IGN), a process that improves glucose homeostasis. Accordingly, dietary succinate improved glucose and insulin tolerance in wild-type mice, but those effects were absent in mice deficient in IGN. Conventional mice colonized with the succinate producer Prevotella copri exhibited metabolic benefits, which could be related to succinate-activated IGN. Thus, microbiota-produced succinate is a previously unsuspected bacterial metabolite improving glycemic control through activation of IGN. PMID:27411015

  7. Fish oil enhances recovery of intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplant.

    Directory of Open Access Journals (Sweden)

    Qiurong Li

    Full Text Available BACKGROUND: The intestinal chronic rejection (CR is the major limitation to long-term survival of transplanted organs. This study aimed to investigate the interaction between intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplantation, and to find out whether fish oil enhances recovery of intestinal microbiota and epithelial integrity. METHODS/PRINCIPAL FINDINGS: The luminal and mucosal microbiota composition of CR rats were characterized by DGGE analysis at 190 days after intestinal transplant. The specific bacterial species were determined by sequence analysis. Furthermore, changes in the localization of intestinal TJ proteins were examined by immunofluorescent staining. PCR-DGGE analysis revealed that gut microbiota in CR rats had a shift towards Escherichia coli, Bacteroides spp and Clostridium spp and a decrease in the abundance of Lactobacillales bacteria in the intestines. Fish oil supplementation could enhance the recovery of gut microbiota, showing a significant decrease of gut bacterial proportions of E. coli and Bacteroides spp and an increase of Lactobacillales spp. In addition, CR rats showed pronounced alteration of tight junction, depicted by marked changes in epithelial cell ultrastructure and redistribution of occuldin and claudins as well as disruption in TJ barrier function. Fish oil administration ameliorated disruption of epithelial integrity in CR, which was associated with an improvement of the mucosal structure leading to improved tight junctions. CONCLUSIONS/SIGNIFICANCE: Our study have presented novel evidence that fish oil is involved in the maintenance of epithelial TJ integrity and recovery of gut microbiota, which may have therapeutic potential against CR in intestinal transplantation.

  8. Cultivable intestinal microbiota of yellowtail juveniles (Seriola lalandi in an aquaculture system

    Directory of Open Access Journals (Sweden)

    Eduardo Aguilera

    2013-07-01

    Full Text Available The yellowtail (Seriola lalandi has been farmed for many years and is becoming a promising aquaculture species. Knowledge of the intestinal microbiota of this species is very limited. Thus, the aim of this study is to describe the bacterial populations associated with the intestinal tract of Seriola lalandi reared in Chile. The microbiota composition was analyzed at two growth stages distinguished by weight and parameters such as Specific Growth Rate (SGR and Feed Conversion Ratio (FCR. Juveniles (mean initial weight 7.33 ± 0.30 g and pre-adults (81.7 ± 19.0 g were fed with commercial diet for 33 and 50 days, respectively. The first intestinal samples were collected at the end of Trial 1 from specimens weighing approximately 50 g while the second samples were obtained at the end of Trial 2 from specimens weighing approximately 370 g. The microbiota composition was examined using conventional isolation in Tryptic Soy Agar (TSA followed by 16S rRNA sequencing and identification. In total, 16 genera were identified. Pseudomonas, Vibrio and Staphylococcus were the predominant genera in fish at the 50 g stage, whereas Microbacterium and Francisella were the predominant genera in the 370 g stage. The microbiota composition showed different assemblages, depending on host size, with Bacillus and Vibrio being the only genera that were shared. Knowledge of the intestinal microbiota of Seriola lalandi is the first step in the exploration of microbiota management and the development of probiotics, as well as in the identification of the bacterial populations in healthy fish under cultured conditions.

  9. Microbiota disbiosis is associated with colorectal cancer

    OpenAIRE

    Zhiguang eGao; Bomin eGuo; Renyuan eGao; Qingchao eZhu; Huanlong eQin

    2015-01-01

    The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent noncancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals...

  10. Microbiota disbiosis is associated with colorectal cancer

    OpenAIRE

    Gao, Zhiguang; Guo, Bomin; Gao, Renyuan; Zhu, Qingchao; Qin, Huanlong

    2015-01-01

    The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individual...

  11. Molecular analysis of gut microbiota in obesity among Indian individuals

    Indian Academy of Sciences (India)

    Deepak P Patil; Dhiraj P Dhotre; Sachin G Chavan; Armiya Sultan; Dhawal S Jain; Vikram B Lanjekar; Jayshree Gangawani; Poonam S Shah; Jayshree S Todkar; Shashank Shah; Dilip R Ranade; Milind S Patole; Yogesh S Shouche

    2012-09-01

    Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR ( > 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.

  12. The bioremediation potential of marine sandy sediment microbiota

    Directory of Open Access Journals (Sweden)

    Dan Răzvan POPOVICIU

    2012-11-01

    Full Text Available The natural microbiota from marine sandy sediments on the Romanian sea coast was tested for resilience in case of hydrocarbon contamination, for estimating the number of (culturable hydrocarbon and lipid oil-degrading microorganisms and for determining the influence of inorganic nitrate and phosphate nutrients on hydrocarbon spill bioremediation process, by microcosm experiments.Results show that hydrocarbon contamination affects the bacteriobenthos both in terms of cell numbers and composition. Bacterial numbers showed a rapid decrease (28% in four days, followed by a relatively fast recovery (two weeks. The pollution favoured the increase of Gram-positive bacterial proportion (from around 25% to 33%Sandy sediment microbiota in both sites studied contained microorganisms able to use mineral or lipid oils as sole carbon sources, usually around 103-104/cm3, with variations according to the sediment grain size and substrate used.The biostimulation experiments showed that, in absence of water dynamism (and, implicitly, an efficient oxygenation, the addition of nitrogen and phosphorus can be ineffective and even inhibit the remediation process, probably due to eutrophication.

  13. The Role of Gut Microbiota on Insulin Resistance

    Directory of Open Access Journals (Sweden)

    Mario J. A. Saad

    2013-03-01

    Full Text Available The development of obesity and insulin resistance has been extensively studied in the last decades, but the mechanisms underlying these alterations are still not completely understood. The gut microbiota has been identified as a potential contributor to metabolic diseases. It has been shown that obese individuals present different proportions of bacterial phyla compared with lean individuals, with an increase in Firmicutes and Actinobacteria and a decrease in Bacteroidetes. This alteration seems to interfere with intestinal permeability, increasing the absorption of lipopolysaccharide (LPS, which reaches circulation and initiates activation of Toll-like receptor (TLR 4 and 2 and LPS receptor CD14, leading to increased activation of inflammatory pathways. With these activations, an impairment of the insulin signaling is observed, with decreased phosphorylation of the insulin receptor, insulin receptor substrate (IRS and Akt, as well as increased inhibitory serine phosphorylation of IRS-1. Altered proportions of bacterial phyla have also been demonstrated to interfere with host’s biochemical pathways, increasing energy extraction and depot in adipose tissue. Therefore, understanding the mechanisms by which the alteration in the gut microbiota produces different signaling activations and phenotype changes may offer an interesting opportunity for the treatment of obesity and type 2 diabetes.

  14. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies.

    Science.gov (United States)

    Distrutti, Eleonora; Monaldi, Lorenzo; Ricci, Patrizia; Fiorucci, Stefano

    2016-02-21

    In the last decade the impressive expansion of our knowledge of the vast microbial community that resides in the human intestine, the gut microbiota, has provided support to the concept that a disturbed intestinal ecology might promote development and maintenance of symptoms in irritable bowel syndrome (IBS). As a correlate, manipulation of gut microbiota represents a new strategy for the treatment of this multifactorial disease. A number of attempts have been made to modulate the gut bacterial composition, following the idea that expansion of bacterial species considered as beneficial (Lactobacilli and Bifidobacteria) associated with the reduction of those considered harmful (Clostridium, Escherichia coli, Salmonella, Shigella and Pseudomonas) should attenuate IBS symptoms. In this conceptual framework, probiotics appear an attractive option in terms of both efficacy and safety, while prebiotics, synbiotics and antibiotics still need confirmation. Fecal transplant is an old treatment translated from the cure of intestinal infective pathologies that has recently gained a new life as therapeutic option for those patients with a disturbed gut ecosystem, but data on IBS are scanty and randomized, placebo-controlled studies are required. PMID:26900286

  15. Rearing and foraging affects bumblebee (Bombus terrestris) gut microbiota.

    Science.gov (United States)

    Newbold, Lindsay K; Oliver, Anna E; Cuthbertson, Leah; Walkington, Sarah E; Gweon, Hyun S; Heard, Matthew S; van der Gast, Christopher J

    2015-08-01

    Bumblebees are ecologically and economically important as pollinators of crop and wild plants, especially in temperate systems. Species, such as the buff-tailed bumblebee (Bombus terrestris), are reared commercially to pollinate high-value crops. Their highly specific gut microbiota, characterized by low diversity, may affect nutrition and immunity and are likely to be important for fitness and colony health. However, little is known about how environmental factors affect bacterial community structure. We analysed the gut microbiota from three groups of worker bumblebees (B. terrestris) from distinct colonies that varied in rearing and foraging characteristics: commercially reared with restricted foraging (RR); commercially reared with outside foraging (RF); and wild-caught workers (W). Contrary to previous studies, which indicate that bacterial communities are highly conserved across workers, we found that RF individuals had an intermediate community structure compared with RR and W types. Further, this was shaped by differences in the abundances of common operational taxonomic units (OTUs) and the diversity of rare OTUs present, which we propose results from an increase in the variety of carbohydrates obtained through foraging. PMID:25994560

  16. Fecal Microbiota Transplantation for Inflammatory Bowel Disease

    Science.gov (United States)

    Lopez, Joanna

    2016-01-01

    The gut bacterial microbiome, particularly its role in disease and inflammation, has gained international attention with the successful use of fecal microbiota transplantation (FMT) in the treatment of Clostridium difficile infection. This success has led to studies exploring the role of FMT in other conditions, including inflammatory bowel disease (IBD). Both Crohn’s disease and ulcerative colitis are chronic inflammatory conditions of the gastrointestinal system that have multifactorial etiologies. A shift in gut microbial composition in genetically susceptible individuals, an altered immune system, and environmental factors are all hypothesized to have a role in the pathogenesis of IBD. While numerous case reports and cohort studies have described the use of FMT in patients with IBD over the last 2 decades, the development of new sequencing techniques and results from 2 recent randomized, controlled trials have allowed for a better understanding of the relationship between the microbiome and the human host. However, despite these efforts, knowledge remains limited and the role of FMT in the management of IBD remains uncertain. Further investigation is necessary before FMT joins the current armamentarium of treatment options in clinical practice. PMID:27493597

  17. Vaginal Microbiota and the Use of Probiotics

    Directory of Open Access Journals (Sweden)

    Sarah Cribby

    2008-01-01

    Full Text Available The human vagina is inhabited by a range of microbes from a pool of over 50 species. Lactobacilli are the most common, particularly in healthy women. The microbiota can change composition rapidly, for reasons that are not fully clear. This can lead to infection or to a state in which organisms with pathogenic potential coexist with other commensals. The most common urogenital infection in premenopausal women is bacterial vaginosis (BV, a condition characterized by a depletion of lactobacilli population and the presence of Gram-negative anaerobes, or in some cases Gram-positive cocci, and aerobic pathogens. Treatment of BV traditionally involves the antibiotics metronidazole or clindamycin, however, the recurrence rate remains high, and this treatment is not designed to restore the lactobacilli. In vitro studies have shown that Lactobacillus strains can disrupt BV and yeast biofilms and inhibit the growth of urogenital pathogens. The use of probiotics to populate the vagina and prevent or treat infection has been considered for some time, but only quite recently have data emerged to show efficacy, including supplementation of antimicrobial treatment to improve cure rates and prevent recurrences.

  18. Obesity, fatty liver disease and intestinal microbiota.

    Science.gov (United States)

    Arslan, Nur

    2014-11-28

    Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disorder that is increasing in prevalence with the worldwide epidemic of obesity. NAFLD is the hepatic manifestation of the metabolic syndrome. The term NAFLD describes a spectrum of liver pathology ranges from simple steatosis to steatosis with inflammation nonalcoholic steatohepatitis and even cirrhosis. Metabolic syndrome and NAFLD also predict hepatocellular carcinoma. Many genetic and environmental factors have been suggested to contribute to the development of obesity and NAFLD, but the exact mechanisms are not known. Intestinal ecosystem contains trillions of microorganisms including bacteria, Archaea, yeasts and viruses. Several studies support the relationship between the intestinal microbial changes and obesity and also its complications, including insulin resistance and NAFLD. Given that the gut and liver are connected by the portal venous system, it makes the liver more vulnerable to translocation of bacteria, bacterial products, endotoxins or secreted cytokines. Altered intestinal microbiota (dysbiosis) may stimulate hepatic fat deposition through several mechanisms: regulation of gut permeability, increasing low-grade inflammation, modulation of dietary choline metabolism, regulation of bile acid metabolism and producing endogenous ethanol. Regulation of intestinal microbial ecosystem by diet modifications or by using probiotics and prebiotics as a treatment for obesity and its complications might be the issue of further investigations.

  19. Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?

    Directory of Open Access Journals (Sweden)

    María Carmen Cenit

    2015-08-01

    Full Text Available It is widely recognized that the intestinal microbiota plays a role in the initiation and perpetuation of intestinal inflammation in numerous chronic conditions. Most studies report intestinal dysbiosis in celiac disease (CD patients, untreated and treated with a gluten-free diet (GFD, compared to healthy controls. CD patients with gastrointestinal symptoms are also known to have a different microbiota compared to patients with dermatitis herpetiformis and controls, suggesting that the microbiota is involved in disease manifestation. Furthermore, a dysbiotic microbiota seems to be associated with persistent gastrointestinal symptoms in treated CD patients, suggesting its pathogenic implication in these particular cases. GFD per se influences gut microbiota composition, and thus constitutes an inevitable confounding factor in studies conducted in CD patients. To improve our understanding of whether intestinal dysbiosis is the cause or consequence of disease, prospective studies in healthy infants at family risk of CD are underway. These studies have revealed that the CD host genotype selects for the early colonizers of the infant’s gut, which together with environmental factors (e.g., breast-feeding, antibiotics, etc. could influence the development of oral tolerance to gluten. Indeed, some CD genes and/or their altered expression play a role in bacterial colonization and sensing. In turn, intestinal dysbiosis could promote an abnormal response to gluten or other environmental CD-promoting factors (e.g., infections in predisposed individuals. Here, we review the current knowledge of host-microbe interactions and how host genetics/epigenetics and environmental factors shape gut microbiota and may influence disease risk. We also summarize the current knowledge about the potential mechanisms of action of the intestinal microbiota and specific components that affect CD pathogenesis.

  20. Paneth cells, defensins, and the commensal microbiota: a hypothesis on intimate interplay at the intestinal mucosa.

    Science.gov (United States)

    Salzman, Nita H; Underwood, Mark A; Bevins, Charles L

    2007-04-01

    Mucosal surfaces are colonized by a diverse and dynamic microbiota. Much investigation has focused on bacterial colonization of the intestine, home to the vast majority of this microbiota. Experimental evidence has highlighted that these colonizing microbes are essential to host development and homeostasis, but less is known about host factors that may regulate the composition of this ecosystem. While evidence shows that IgA has a role in shaping this microbiota, it is likely that effector molecules of the innate immune system are also involved. One hypothesis is that gene-encoded antimicrobial peptides, key elements of innate immunity throughout nature, have an essential role in this regulation. These effector molecules characteristically have activity against a broad spectrum of bacteria and other microbes. At mucosal surfaces, antimicrobial peptides may affect the numbers and/or composition of the colonizing microbiota. In humans and other mammals, defensins are a predominant class of antimicrobial peptides. In the small intestine, Paneth cells (specialized secretory epithelial cells) produce high quantities of defensins and several other antibiotic peptides and proteins. Data from murine models indicate that Paneth cell defensins play a pivotal role in defense from food and water-borne pathogens in the intestinal lumen. Recent studies in humans provide evidence that reduced Paneth cell defensin expression may be a key pathogenic factor in ileal Crohn's disease, a subgroup of inflammatory bowel disease (IBD), and changes in the colonizing microbiota may mediate this pathogenic mechanism. It is also possible that low levels of Paneth cell defensins, characteristic of normal intestinal development, may predispose premature neonates to necrotizing enterocolitis (NEC) through similar close links with the composition of the intestinal microbiota. Future studies to further define mechanisms by which defensins and other host factors regulate the composition of the

  1. The intestinal microbiota plays a role in Salmonella-induced colitis independent of pathogen colonization.

    Directory of Open Access Journals (Sweden)

    Rosana B R Ferreira

    Full Text Available The intestinal microbiota is composed of hundreds of species of bacteria, fungi and protozoa and is critical for numerous biological processes, such as nutrient acquisition, vitamin production, and colonization resistance against bacterial pathogens. We studied the role of the intestinal microbiota on host resistance to Salmonella enterica serovar Typhimurium-induced colitis. Using multiple antibiotic treatments in 129S1/SvImJ mice, we showed that disruption of the intestinal microbiota alters host susceptibility to infection. Although all antibiotic treatments caused similar increases in pathogen colonization, the development of enterocolitis was seen only when streptomycin or vancomycin was used; no significant pathology was observed with the use of metronidazole. Interestingly, metronidazole-treated and infected C57BL/6 mice developed severe pathology. We hypothesized that the intestinal microbiota confers resistance to infectious colitis without affecting the ability of S. Typhimurium to colonize the intestine. Indeed, different antibiotic treatments caused distinct shifts in the intestinal microbiota prior to infection. Through fluorescence in situ hybridization, terminal restriction fragment length polymorphism, and real-time PCR, we showed that there is a strong correlation between the intestinal microbiota composition before infection and susceptibility to Salmonella-induced colitis. Members of the Bacteroidetes phylum were present at significantly higher levels in mice resistant to colitis. Further analysis revealed that Porphyromonadaceae levels were also increased in these mice. Conversely, there was a positive correlation between the abundance of Lactobacillus sp. and predisposition to colitis. Our data suggests that different members of the microbiota might be associated with S. Typhimurium colonization and colitis. Dissecting the mechanisms involved in resistance to infection and inflammation will be critical for the development of

  2. Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity.

    Science.gov (United States)

    Laursen, Martin Frederik; Andersen, Louise B B; Michaelsen, Kim F; Mølgaard, Christian; Trolle, Ellen; Bahl, Martin Iain; Licht, Tine Rask

    2016-01-01

    The first years of life are paramount in establishing our endogenous gut microbiota, which is strongly affected by diet and has repeatedly been linked with obesity. However, very few studies have addressed the influence of maternal obesity on infant gut microbiota, which may occur either through vertically transmitted microbes or through the dietary habits of the family. Additionally, very little is known about the effect of diet during the complementary feeding period, which is potentially important for gut microbiota development. Here, the gut microbiotas of two different cohorts of infants, born either of a random sample of healthy mothers (n = 114), or of obese mothers (n = 113), were profiled by 16S rRNA amplicon sequencing. Gut microbiota data were compared to breastfeeding patterns and detailed individual dietary recordings to assess effects of the complementary diet. We found that maternal obesity did not influence microbial diversity or specific taxon abundances during the complementary feeding period. Across cohorts, breastfeeding duration and composition of the complementary diet were found to be the major determinants of gut microbiota development. In both cohorts, gut microbial composition and alpha diversity were thus strongly affected by introduction of family foods with high protein and fiber contents. Specifically, intake of meats, cheeses, and Danish rye bread, rich in protein and fiber, were associated with increased alpha diversity. Our results reveal that the transition from early infant feeding to family foods is a major determinant for gut microbiota development. IMPORTANCE The potential influence of maternal obesity on infant gut microbiota may occur either through vertically transmitted microbes or through the dietary habits of the family. Recent studies have suggested that the heritability of obesity may partly be caused by the transmission of "obesogenic" gut microbes. However, the findings presented here suggest that maternal obesity per

  3. Human Microbiota and Ophthalmic Disease

    Science.gov (United States)

    Lu, Louise J.; Liu, Ji

    2016-01-01

    The human ocular surface, consisting of the cornea and conjunctiva, is colonized by an expansive, diverse microbial community. Molecular-based methods, such as 16S rRNA sequencing, has allowed for more comprehensive and precise identification of the species composition of the ocular surface microbiota compared to traditional culture-based methods. Evidence suggests that the normal microbiota plays a protective immunological role in preventing the proliferation of pathogenic species and thus, alterations in the homeostatic microbiome may be linked to ophthalmic pathologies. Further investigation of the ocular surface microbiome, as well as the microbiome of other areas of the body such as the oral mucosa and gut, and their role in the pathophysiology of diseases is a significant, emerging field of research, and may someday enable the development of novel probiotic approaches for the treatment and prevention of ophthalmic diseases.

  4. Host species as a strong determinant of the intestinal microbiota of fish larvae.

    Science.gov (United States)

    Li, Xuemei; Yu, Yuhe; Feng, Weisong; Yan, Qingyun; Gong, Yingchun

    2012-02-01

    We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical. PMID:22367934

  5. Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals.

    Science.gov (United States)

    Shang, Qingsen; Yin, Yeshi; Zhu, Liying; Li, Guoyun; Yu, Guangli; Wang, Xin

    2016-05-01

    Oral preparations of chondroitin sulfate (CS) have long been used as anti-osteoarthritis (anti-OA) drugs. However, little is known about the degradation of CS by human gut microbiota. In the present study, degradation profiles of CSA (the main constituent of CS drugs) by the human gut microbiota from six healthy subjects were investigated. Each individual's microbiota had differing degradation activities, but ΔUA-GalNAc4S was the end product in all cases. To elucidate the mechanisms underlying this phenomenon, different CSA-degrading bacteria were isolated from each individual's microbiota and tested for CSA degradation. In addition to Bacteroides thetaiotaomicron J1, Bacteroides thetaiotaomicron 82 and Bacteroides ovatus E3, a new CSA-degrading bacterium, Clostridium hathewayi R4, was isolated and characterized. Interestingly, at least two different CSA-degrading species were identified from each individual's gut microbiota. Predictably, these functional bacteria also had differing degradation rates, but still generated the same end product, ΔUA-GalNAc4S. In addition, the human fecal isolates produced different degradation profiles for CSC, CSD, and CSE, suggesting that CS could be readily metabolized to varying extents by diverse microbial consortiums, which may help to explain the poor bioavailability and unequal efficacy of CS among individuals in OA treatment. PMID:26800901

  6. Clostridium difficile and the microbiota

    OpenAIRE

    Seekatz, Anna M.; Young, Vincent B.

    2014-01-01

    Clostridium difficile infection (CDI) is the leading health care–associated illness. Both human and animal models have demonstrated the importance of the gut microbiota’s capability of providing colonization resistance against C. difficile. Risk factors for disease development include antibiotic use, which disrupts the gut microbiota, leading to the loss of colonization resistance and subsequent CDI. Identification of the specific microbes capable of restoring this function remains elusive. F...

  7. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas

    Science.gov (United States)

    Yang, Yuzhan; Deng, Ye; Cao, Lei

    2016-01-01

    Microorganisms in vertebrate guts have been recognized as important symbionts influencing host life. However, it remains unclear about the gut microbiota in long-distance migratory Anseriformes herbivores, which could be functionally important for these wetland-dependent animals. We collected faeces of the greater white-fronted goose (GWFG), bean goose (BG) and swan goose (SG) from Shengjin Lake (SJL) and Poyang Lake (PYL) in the Yangtze River Floodplain, China. High-throughput sequencing of 16S rRNA V4 region was employed to depict the composition and structure of geese gut microbiota during wintering period. The dominant bacterial phyla across all samples were Firmicutes, Proteobacteria and Actinobacteria, but significant variations were detected among different goose species and sampling sites, in terms of α diversity, community structures and microbial interactions. We found a significant correlation between diet and the microbial community structure in GWFG-SJL samples. These results demonstrated that host species and diet are potential drivers of goose gut microbiota assemblies. Despite these variations, functions of geese gut microbiota were similar, with great abundances of potential genes involved in nutrient metabolism. This preliminary study would be valuable for future, exhaustive investigations of geese gut microbiota and their interactions with host. PMID:27600170

  8. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota.

    Science.gov (United States)

    Engen, Phillip A; Green, Stefan J; Voigt, Robin M; Forsyth, Christopher B; Keshavarzian, Ali

    2015-01-01

    The exces