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Sample records for oral fungal microbiome

  1. Adhesion Forces and Composition of Planktonic and Adhering Oral Microbiomes

    NARCIS (Netherlands)

    Wessel, S. W.; Chen, Y.; Maitra, A.; van den Heuvel, E. R.; Slomp, A. M.; Busscher, H. J.; van der Mei, H. C.

    The oral microbiome consists of a planktonic microbiome residing in saliva and an adhering microbiome (the biofilm adhering to oral hard and soft tissues). Here we hypothesized that possible differences in microbial composition of the planktonic and adhering oral microbiome on teeth can be related

  2. Adhesion Forces and Composition of Planktonic and Adhering Oral Microbiomes

    NARCIS (Netherlands)

    Wessel, S. W.; Chen, Y.; Maitra, A.; van den Heuvel, E. R.; Slomp, A. M.; Busscher, H. J.; van der Mei, H. C.

    2014-01-01

    The oral microbiome consists of a planktonic microbiome residing in saliva and an adhering microbiome (the biofilm adhering to oral hard and soft tissues). Here we hypothesized that possible differences in microbial composition of the planktonic and adhering oral microbiome on teeth can be related t

  3. Understanding Caries From the Oral Microbiome Perspective.

    Science.gov (United States)

    Tanner, Anne C R; Kressirer, Christine A; Faller, Lina L

    2016-07-01

    Dental caries is a major disease of the oral cavity with profound clinical significance. Caries results from a transition of a healthy oral microbiome into an acidogenic community of decreased microbial diversity in response to excessive dietary sugar intake. Microbiological cultivation, molecular identification, gene expression and metabolomic analyses show the importance of the entire microbial community in understanding the role of the microbiome in the pathology of caries.

  4. Key Determinants of the Fungal and Bacterial Microbiomes in Homes

    Science.gov (United States)

    Kettleson, Eric M.; Adhikari, Atin; Vesper, Stephen; Chatterjee, Kanistha; Indugula, Reshmi; Reponen, Tiina

    2015-01-01

    Backgroundy The microbiome of the home is of great interest because of its possible impact on health. Our goal was to identify some of the factors that determine the richness, evenness and diversity of the home's fungal and bacterial microbiomes. Methods Vacuumed settled dust from homes (n=35) in Cincinnati, OH, were analyzed by pyrosequencing to determine the fungal and bacterial relative sequence occurrence. The correlation coefficients between home environmental characteristics, including age of home, Environmental Relative Moldiness Index (ERMI) values, occupant number, relative humidity and temperature, as well as pets (dog and cat) were evaluated for their influence on fungal and bacterial communities. In addition, linear discriminant analysis (LDA) was used for identifying fungal and bacterial genera and species associated with those housing determinants found to be significant. Results The fungal richness was found to be positively correlated with age of home (p=0.002), ERMI value (p=0.003), and relative humidity (p=0.015) in the home. However, fungal evenness and diversity were only correlated with the age of home (p=0.001). Diversity and evenness (not richness) of the bacterial microbiome in the homes were associated with dog ownership. Linear discriminant analysis showed total of 39 putative fungal genera/species with significantly higher LDA scores in high ERMI homes and 47 genera/species with significantly higher LDA scores in homes with high relative humidity. When categorized according to the age of the home, a total of 67 fungal genera/species had LDA scores above the significance threshold. Dog ownership appeared to have the most influence on the bacterial microbiome, since a total of 130 bacterial genera/species had significantly higher LDA scores in homes with dogs. Conclusions Some key determinants of the fungal and bacterial microbiome appear to be excess moisture, age of the home and dog ownership. PMID:25707017

  5. The microbiome of the oral mucosa in irritable bowel syndrome

    OpenAIRE

    2016-01-01

    abstract Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The...

  6. Fungal invasion of the rhizosphere microbiome

    NARCIS (Netherlands)

    Chapelle, E.; Mendes, R.; Bakker, P.A.H.M.; Raaijmakers, Jos

    2015-01-01

    The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongl

  7. Fungal invasion of the rhizosphere microbiome

    NARCIS (Netherlands)

    Chapelle, E.; Mendes, R.; Bakker, P.A.H.M.; Raaijmakers, Jos

    2016-01-01

    The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongl

  8. Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench

    Directory of Open Access Journals (Sweden)

    Patricia I Diaz

    2014-07-01

    Full Text Available High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci. In this perspective, we discuss the current state of the field of fungal-bacterial interactions in the context of the oral cavity. We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression. Such studies need to be coupled with investigations using disease-relevant models to mechanistically test the associations observed in humans and eventually identify fungal-bacterial interactions that could serve as preventive or therapeutic targets for oral diseases.

  9. Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench.

    Science.gov (United States)

    Diaz, Patricia I; Strausbaugh, Linda D; Dongari-Bagtzoglou, Anna

    2014-01-01

    High throughput sequencing has accelerated knowledge on the oral microbiome. While the bacterial component of oral communities has been extensively characterized, the role of the fungal microbiota in the oral cavity is largely unknown. Interactions among fungi and bacteria are likely to influence oral health as exemplified by the synergistic relationship between Candida albicans and oral streptococci. In this perspective, we discuss the current state of the field of fungal-bacterial interactions in the context of the oral cavity. We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression. Such studies need to be coupled with investigations using disease-relevant models to mechanistically test the associations observed in humans and eventually identify fungal-bacterial interactions that could serve as preventive or therapeutic targets for oral diseases.

  10. Oral microbiome in HIV-associated periodontitis

    Science.gov (United States)

    Noguera-Julian, Marc; Guillén, Yolanda; Peterson, Jessica; Reznik, David; Harris, Erica V.; Joseph, Sandeep J.; Rivera, Javier; Kannanganat, Sunil; Amara, Rama; Nguyen, Minh Ly; Mutembo, Simon; Paredes, Roger; Read, Timothy D.; Marconi, Vincent C.

    2017-01-01

    Abstract HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV– individuals at different levels of PD severity. This cross-sectional study included both HIV+ and HIV– patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations. Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV–) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome. HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites. PMID:28328799

  11. The oral microbiome and adverse pregnancy outcomes

    Directory of Open Access Journals (Sweden)

    Cobb CM

    2017-08-01

    Full Text Available Charles M Cobb,1 Patricia J Kelly,2 Karen B Williams,3 Shilpa Babbar,4 Mubashir Angolkar,5 Richard J Derman6 1Department of Periodontics, School of Dentistry, 2Department of Public Health Nursing, School of Nursing and Health Studies, 3Department of Biomedical & Health Informatics, School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 4Department of Obstetrics, Gynecology & Women’s Health, Division of Maternal & Fetal Medicine, School of Medicine, Saint Louis University, St Louis, MO, USA; 5Department of Public Health, Jawaharlal Nehru Medical College (JNMC, KLE University, Karnataka, India; 6Department of Obstetrics & Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA Abstract: Significant evidence supports an association between periodontal pathogenic bacteria and preterm birth and preeclampsia. The virulence properties assigned to specific oral pathogenic bacteria, for example, Fusobacterium nucleatum, Porphyromonas gingivalis, Filifactor alocis, Campylobacter rectus, and others, render them as potential collaborators in adverse outcomes of pregnancy. Several pathways have been suggested for this association: 1 hematogenous spread (bacteremia of periodontal pathogens; 2 hematogenous spread of multiple mediators of inflammation that are generated by the host and/or fetal immune response to pathogenic bacteria; and 3 the possibility of oral microbial pathogen transmission, with subsequent colonization, in the vaginal microbiome resulting from sexual practices. As periodontal disease is, for the most part, preventable, the medical and dental public health communities can address intervention strategies to control oral inflammatory disease, lessen the systemic inflammatory burden, and ultimately reduce the potential for adverse pregnancy outcomes. This article reviews the oral, vaginal, and placental microbiomes, considers their potential impact on preterm labor, and the future

  12. Acquiring and maintaining a normal oral microbiome: current perspective.

    Science.gov (United States)

    Zaura, Egija; Nicu, Elena A; Krom, Bastiaan P; Keijser, Bart J F

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis-a microbial shift toward a disease, e.g., periodontitis or caries. Although processes that underlie oral diseases have been studied extensively, processes involved in maintaining of a normal, healthy microbiome are poorly understood. In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained. We introduce our view on the prenatal development of tolerance for the normal oral microbiome: we propose that development of fetal tolerance toward the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome. We describe the processes that influence the establishment of such microbiome, followed by our perspective on the process of sustaining a healthy oral microbiome. We divide microbiome-maintenance factors into host-derived and microbe-derived, while focusing on the host. Finally, we highlight the need and directions for future research.

  13. Acquiring and maintaining a normal oral microbiome: current perspective

    Directory of Open Access Journals (Sweden)

    Egija eZaura

    2014-06-01

    Full Text Available The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis – a microbial shift towards a disease, e.g., periodontitis or caries. Although processes that underlie oral diseases have been studied extensively, processes involved in maintaining of a normal, healthy microbiome are poorly understood. In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained. We introduce our view on the prenatal development of tolerance for the normal oral microbiome: we propose that development of fetal tolerance towards the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome. We describe the processes that influence the establishment of such microbiome, followed by our perspective on the process of sustaining a healthy oral microbiome. We divide microbiome-maintenance factors into host-derived and microbe-derived, while focusing on the host. Finally, we highlight the need and directions for future research.

  14. Diet may influence the oral microbiome composition in cats.

    Science.gov (United States)

    Adler, Christina J; Malik, Richard; Browne, Gina V; Norris, Jacqueline M

    2016-06-09

    Periodontal disease is highly prevalent amongst domestic cats, causing pain, gingival bleeding, reduced food intake, loss of teeth and possibly impacts on overall systemic health. Diet has been suggested to play a role in the development of periodontal disease in cats. There is a complete lack of information about how diet (composition and texture) affects the feline oral microbiome, the composition of which may influence oral health and the development of periodontal disease. We undertook a pilot study to assess if lifelong feeding of dry extruded kibble or wet (canned and/or fresh meat combinations) diets to cats (n = 10) with variable oral health affected the microbiome. Oral microbiome composition was assessed by amplifying the V1-V3 region of the 16S gene from supragingival dental plaque DNA extracts. These amplicons were sequenced using Illumina technology. This deep sequencing revealed the feline oral microbiome to be diverse, containing 411 bacterial species from 14 phyla. We found that diet had a significant influence on the overall diversity and abundance of specific bacteria in the oral environment. Cats fed a dry diet exclusively had higher bacterial diversity in their oral microbiome than wet-food diet cats (p microbiome between cats on the two diets assessed, the relationship between these differences and gingival health was unclear. Our preliminary results indicate that further analysis of the influence of dietary constituents and texture on the feline oral microbiome is required to reveal the relationship between diet, the oral microbiome and gingival health in cats.

  15. Diet may influence the oral microbiome composition in cats

    National Research Council Canada - National Science Library

    Adler, Christina J; Malik, Richard; Browne, Gina V; Norris, Jacqueline M

    2016-01-01

    .... There is a complete lack of information about how diet (composition and texture) affects the feline oral microbiome, the composition of which may influence oral health and the development of periodontal disease...

  16. Betel nut chewing, oral premalignant lesions, and the oral microbiome

    Science.gov (United States)

    Hernandez, Brenda Y.; Zhu, Xuemei; Goodman, Marc T.; Gatewood, Robert; Mendiola, Paul; Quinata, Katrina; Paulino, Yvette C.

    2017-01-01

    Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed. Oral swabbing and saliva samples were evaluated by 454 pyrosequencing of the V3- V5 region of the 16S rRNA bacterial gene and genotyped for HPV. One hundred twenty-two adults were enrolled including 64 current betel nut chewers, 37 former chewers, and 21 with no history of betel nut use. Oral premalignant lesions, including leukoplakia and submucous fibrosis, were observed in 10 chewers. Within-sample bacterial diversity was significantly lower in long-term (≥10 years) chewers vs. never chewers and in current chewers with oral lesions vs. individuals without lesions. Between-sample bacterial diversity based on Unifrac distances significantly differed by chewing status and oral lesion status. Current chewers had significantly elevated levels of Streptococcus infantis and higher and lower levels of distinct taxa of the Actinomyces and Streptococcus genera. Long-term chewers had reduced levels of Parascardovia and Streptococcus. Chewers with oral lesions had significantly elevated levels of Oribacterium, Actinomyces, and Streptococcus, including Streptococcus anginosus. In multivariate analyses, controlling for smoking, oral HPV, S.anginosus, and S. infantis levels, current betel nut chewing remained the only predictor of oral premalignant lesions. Our study provides evidence that betel nut chewing alters the oral bacterial microbiome including that of chewers who develop oral premalignant lesions. Nonetheless, whether microbial changes

  17. Acquiring and maintaining a normal oral microbiome: current perspective

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.F.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift towa

  18. Acquiring and maintaining a normal oral microbiome : Current perspective

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.F.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift towa

  19. Acquiring and maintaining a normal oral microbiome: current perspective.

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis-a microbial shift towa

  20. Acquiring and maintaining a normal oral microbiome : Current perspective

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.F.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift towa

  1. Acquiring and maintaining a normal oral microbiome: current perspective.

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis-a microbial shift towa

  2. Acquiring and maintaining a normal oral microbiome: current perspective.

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis-a microbial shift

  3. Role of oral microbiome on oral cancers, a review.

    Science.gov (United States)

    Gholizadeh, Pourya; Eslami, Hosein; Yousefi, Mehdi; Asgharzadeh, Mohammad; Aghazadeh, Mohammad; Kafil, Hossein Samadi

    2016-12-01

    The oral cavity is inhibited by many of the bacterial species. Some of them have a key role in the development of oral disease. Interrelationships between oral microbiome and systemic conditions such as head-and-neck cancer have become increasingly appreciated in recent years. Emerging evidence also suggests a link between periodontal disease and oral cancer, and the explanation being that chronic inflammation could be a major factor in both diseases. Squamous cell carcinoma is that the most frequently occurring malignancy of the oral cavity and adjacent sites, representing over 90% of all cancers. The incidence of oral cancer is increasing, significantly among young people and women. Worldwide there are 350,000-400,000 new cases diagnosed every year. Bacteria, viruses, and fungi are strongly implicated as etiological factors in certain cancers. In this review we will discuss the association between the development of oral cancer in potentially malignant oral lesions with chronic periodontitis, chronic Porphyromonas gingivalis, Fusobacterium nucleatum, candida, other microbes and described mechanisms which may be involved in these carcinoma.

  4. Fungal infections of the oral mucosa

    OpenAIRE

    P Anitha Krishnan

    2012-01-01

    Fungal infections in humans occur as a result of defects in the immune system. An increasing emergence in oral Candidal and non-Candidal fungal infections is evident in the past decade owing to the rise in the immunodeficient and immunocompromised population globally. Oral Candidal infection usually involves a compromised host and the compromise may be local or systemic. Local compromising factors include decreased salivation, poor oral hygiene, wearing dentures among others while systemic fa...

  5. Oral microbiome link to neurodegeneration in glaucoma.

    Directory of Open Access Journals (Sweden)

    Konstantin Astafurov

    Full Text Available BACKGROUND: Glaucoma is a progressive optic nerve degenerative disease that often leads to blindness. Local inflammatory responses are implicated in the pathology of glaucoma. Although inflammatory episodes outside the CNS, such as those due to acute systemic infections, have been linked to central neurodegeneration, they do not appear to be relevant to glaucoma. Based on clinical observations, we hypothesized that chronic subclinical peripheral inflammation contributes to neurodegeneration in glaucoma. METHODS: Mouthwash specimens from patients with glaucoma and control subjects were analyzed for the amount of bacteria. To determine a possible pathogenic mechanism, low-dose subcutaneous lipopolysaccharide (LPS was administered in two separate animal models of glaucoma. Glaucomatous neurodegeneration was assessed in the retina and optic nerve two months later. Changes in gene expression of toll-like receptor 4 (TLR4 signaling pathway and complement as well as changes in microglial numbers and morphology were analyzed in the retina and optic nerve. The effect of pharmacologic blockade of TLR4 with naloxone was determined. FINDINGS: Patients with glaucoma had higher bacterial oral counts compared to control subjects (p<0.017. Low-dose LPS administration in glaucoma animal models resulted in enhancement of axonal degeneration and neuronal loss. Microglial activation in the optic nerve and retina as well as upregulation of TLR4 signaling and complement system were observed. Pharmacologic blockade of TLR4 partially ameliorated the enhanced damage. CONCLUSIONS: The above findings suggest that the oral microbiome contributes to glaucoma pathophysiology. A plausible mechanism by which increased bacterial loads can lead to neurodegeneration is provided by experiments in animal models of the disease and involves activation of microglia in the retina and optic nerve, mediated through TLR4 signaling and complement upregulation. The finding that commensal

  6. The Fungal Biome of the Oral Cavity.

    Science.gov (United States)

    Chandra, Jyotsna; Retuerto, Mauricio; Mukherjee, Pranab K; Ghannoum, Mahmoud

    2016-01-01

    Organisms residing in the oral cavity (oral microbiota) contribute to health and disease, and influence diseases like gingivitis, periodontitis, and oral candidiasis (the most common oral complication of HIV-infection). These organisms are also associated with cancer and other systemic diseases including upper respiratory infections. There is limited knowledge regarding how oral microbes interact together and influence the host immune system. Characterizing the oral microbial community (oral microbiota) in health and disease represents a critical step in gaining insight into various members of this community. While most of the studies characterizing oral microbiota have focused on bacterial community, there are few encouraging studies characterizing the oral mycobiome (the fungal component of the oral microbiota). Our group recently characterized the oral mycobiome in health and disease focusing on HIV. In this chapter we will describe the methods used by our group for characterization of the oral mycobiome.

  7. Fungal infections of the oral mucosa.

    Science.gov (United States)

    Krishnan, P Anitha

    2012-01-01

    Fungal infections in humans occur as a result of defects in the immune system. An increasing emergence in oral Candidal and non-Candidal fungal infections is evident in the past decade owing to the rise in the immunodeficient and immunocompromised population globally. Oral Candidal infection usually involves a compromised host and the compromise may be local or systemic. Local compromising factors include decreased salivation, poor oral hygiene, wearing dentures among others while systemic factors include diabetes mellitus, nutritional deficiency, HIV infection/AIDS and others. Oral candidiasis is generally a localized infection and rarely appears as a systemic fungal disease whereas oral non-Candidal fungal infections are usually signs of disseminated disease. Some of the non-Candidal fungi that were once considered exotic and geographically restricted are now seen worldwide, beyond their natural habitat, probably attributed to globalization and travels. Currently infections from these fungi are more prevalent than before and they may present either as primary oral lesions or as oral manifestations of systemic mycoses. This review discusses the various predisposing factors, clinical presentations, clinical differential diagnosis, diagnosis and management of oral candidiasis, as well as briefly highlights upon a few of the more exotic non-Candidal fungi that infect the oral mucosa.

  8. Molecular characterization of the skin fungal microbiome in patients with psoriasis.

    Science.gov (United States)

    Takemoto, Akemi; Cho, Otomi; Morohoshi, Yuka; Sugita, Takashi; Muto, Masahiko

    2015-02-01

    The skin surface is colonized by a wide variety of fungi and bacteria. While many of these organisms, including Malassezia, Candida, Streptococcus and Staphylococcus species, are associated with provocation and/or exacerbation of psoriasis, a detailed analysis of the cutaneous fungal microbiome in psoriatic patients has yet to be performed. To identify the disease-specific fungal microbiota on psoriatic scale samples, fungal rRNA gene sequences from 12 psoriatic patients and 12 healthy controls were analyzed by pyrosequencing. A total of 317 806 high-quality sequences were obtained, representing 142 genera. Malassezia species were the most abundant sequences in both populations (46.9 ± 14.0% in psoriasis vs. 76.0 ± 14.6% for healthy controls). Principal coordinate analysis revealed that the fungal microbiomes were independent. Although an association between the cutaneous fungal microbiome and psoriasis has yet to be established, our data indicate that the microbiome in patients with psoriasis is independent of that in healthy controls.

  9. Defining the healthy "core microbiome" of oral microbial communities

    NARCIS (Netherlands)

    E. Zaura; B.J.F. Keijser; S.M. Huse; W. Crielaard

    2009-01-01

    Background: Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the h

  10. Defining the healthy "core microbiome" of oral microbial communities

    NARCIS (Netherlands)

    Zaura, E.; Keijser, B.J.; Huse, S.M.; Crielaard, W.

    2009-01-01

    Background. Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the h

  11. Next-generation sequencing approaches to understanding the oral microbiome

    NARCIS (Netherlands)

    Zaura, E.

    2012-01-01

    Until recently, the focus in dental research has been on studying a small fraction of the oral microbiome—so-called opportunistic pathogens. With the advent of next-generation sequencing (NGS) technologies, researchers now have the tools that allow for profiling of the microbiomes and metagenomes at

  12. Next-generation sequencing approaches to understanding the oral microbiome

    NARCIS (Netherlands)

    Zaura, E.

    2012-01-01

    Until recently, the focus in dental research has been on studying a small fraction of the oral microbiome—so-called opportunistic pathogens. With the advent of next-generation sequencing (NGS) technologies, researchers now have the tools that allow for profiling of the microbiomes and metagenomes at

  13. The oral microbiome - an update for oral healthcare professionals

    DEFF Research Database (Denmark)

    Kilian, M; Chapple, I L C; Hannig, M

    2016-01-01

    For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology ...

  14. Defining the healthy "core microbiome" of oral microbial communities

    Directory of Open Access Journals (Sweden)

    Crielaard Wim

    2009-12-01

    Full Text Available Abstract Background Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing. Results We sampled and sequenced microbiomes from several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva in three healthy individuals. Within an individual oral cavity, we found over 3600 unique sequences, over 500 different OTUs or "species-level" phylotypes (sequences that clustered at 3% genetic difference and 88 - 104 higher taxa (genus or more inclusive taxon. The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus Granulicatella, Proteobacteria (genus Neisseria, Haemophilus, Actinobacteria (genus Corynebacterium, Rothia, Actinomyces, Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas and Fusobacteria (genus Fusobacterium. Each individual sample harboured on average 266 "species-level" phylotypes (SD 67; range 123 - 326 with cheek samples being the least diverse and the dental samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate from the samples that were obtained from solid surfaces (teeth. There was a large overlap in the higher taxa, "species-level" phylotypes and unique sequences among the three microbiomes: 84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the "core microbiome" contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads

  15. The oral microbiome in health and disease and the potential impact on personalized dental medicine.

    Science.gov (United States)

    Zarco, M F; Vess, T J; Ginsburg, G S

    2012-03-01

    Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The oral microbiome is particularly imperative to health because it can cause both oral and systemic disease. The oral microbiome rests within biofilms throughout the oral cavity, forming an ecosystem that maintains health when in equilibrium. However, certain ecological shifts in the microbiome allow pathogens to manifest and cause disease. Severe forms of oral disease may result in systemic disease at different body sites. Microbiomics and metagenomics are two fields of research that have emerged to identify the presence of specific microbes in the body and understand the nature of the microbiome activity during both health and disease. The analysis of the microbiome and its genomes will pave the way for more effective therapeutic and diagnostic techniques and, ultimately, contribute to the development of personalized medicine and personalized dental medicine.

  16. Bacterial and fungal microbiome analysis of alfalfa rhizosphere soils

    Science.gov (United States)

    Soil microbial communities are increasingly being recognized for their critical roles in agriculture. While microbiome studies enabled by next generation sequencing platforms reveal soils to be some of the most diverse environments known, certain taxa may have disproportionate influence in their fu...

  17. Microbiota, oral microbiome, and pancreatic cancer.

    Science.gov (United States)

    Michaud, Dominique S; Izard, Jacques

    2014-01-01

    Only 30% of patients with a diagnosis of pancreatic cancer survive 1 year after the diagnosis. Progress in understanding the causes of pancreatic cancer has been made, including solidifying the associations with obesity and diabetes, and a proportion of cases should be preventable through lifestyle modifications. Unfortunately, identifying reliable biomarkers of early pancreatic cancer has been extremely challenging, and no effective screening modality is currently available for this devastating form of cancer. Recent data suggest that the microbiota may play a role in the disease process, but many questions remain. Future studies focusing on the human microbiome, both etiologically and as a marker of disease susceptibility, should shed light on how to better tackle prevention, early detection, and treatment of this highly fatal disease.

  18. Uncultured Members of the Oral Microbiome.

    Science.gov (United States)

    Wade, William; Thompson, Hayley; Rybalka, Alexandra; Vartoukian, Sonia

    2016-07-01

    Around one-third of oral bacteria cannot be cultured using conventional methods. Some bacteria have specific requirements for nutrients while others may be inhibited by substances in the culture media or produced by other bacteria. Oral bacteria have evolved as part of multispecies biofilms, and many thus require interaction with other bacterial species to grow. In vitro models have been developed that mimic these interactions and have been used to grow previously uncultivated organisms.

  19. Acquisition and maturation of oral microbiome throughout childhood: An update.

    Science.gov (United States)

    Sampaio-Maia, Benedita; Monteiro-Silva, Filipa

    2014-05-01

    Traditional microbiology concepts are being renewed since the development of new microbiological technologies, such as, sequencing and large-scale genome analysis. Since the entry into the new millennium, a lot of new information has emerged regarding the oral microbiome. This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. Throughout childhood, the oral microbial load increases, but the microbial diversity decreases. The initial colonizers are related to the type of delivery, personal relationships, and living environment. These first colonizers seem to condition the subsequent colonization, which will lead to more complex and stable ecosystems in adulthood. These early oral microbial communities, therefore, play a major role in the development of the adult oral microbiota and may represent a source of both pathogenic and protective microorganisms in a very early stage of human life. The implications of this knowledge on the daily clinical practice of odontopediatrics are highlighted.

  20. Acquisition and maturation of oral microbiome throughout childhood: An update

    Directory of Open Access Journals (Sweden)

    Benedita Sampaio-Maia

    2014-01-01

    Full Text Available Traditional microbiology concepts are being renewed since the development of new microbiological technologies, such as, sequencing and large-scale genome analysis. Since the entry into the new millennium, a lot of new information has emerged regarding the oral microbiome. This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. Throughout childhood, the oral microbial load increases, but the microbial diversity decreases. The initial colonizers are related to the type of delivery, personal relationships, and living environment. These first colonizers seem to condition the subsequent colonization, which will lead to more complex and stable ecosystems in adulthood. These early oral microbial communities, therefore, play a major role in the development of the adult oral microbiota and may represent a source of both pathogenic and protective microorganisms in a very early stage of human life. The implications of this knowledge on the daily clinical practice of odontopediatrics are highlighted.

  1. Systems approaches to computational modeling of the oral microbiome

    Directory of Open Access Journals (Sweden)

    Dimiter V. Dimitrov

    2013-07-01

    Full Text Available Current microbiome research has generated tremendous amounts of data providing snapshots of molecular activity in a variety of organisms, environments, and cell types. However, turning this knowledge into whole system level of understanding on pathways and processes has proven to be a challenging task. In this review we highlight the applicability of bioinformatics and visualization techniques to large collections of data in order to better understand the information that contains related diet – oral microbiome – host mucosal transcriptome interactions. In particular we focus on systems biology of Porphyromonas gingivalis in the context of high throughput computational methods tightly integrated with translational systems medicine. Those approaches have applications for both basic research, where we can direct specific laboratory experiments in model organisms and cell cultures, to human disease, where we can validate new mechanisms and biomarkers for prevention and treatment of chronic disorders

  2. The microbiome and disease: reviewing the links between the oral microbiome, aging, and Alzheimer's disease.

    Science.gov (United States)

    Shoemark, Deborah K; Allen, Shelley J

    2015-01-01

    This review, gathered from diverse sources, shows how our microbiome influences health and ultimately how well we age. Evidence linking oral bacteria to Alzheimer's disease (AD) is discussed in the context of aging, drawing together data from epidemiological, experimental, genetic, and environmental studies. Immunosenescence results in increased bacterial load as cell-mediated and humoral immune responses wane. The innate immune system gradually takes over; contributing to the rise in circulating proinflammatory cytokines such as TNFα. Maintaining the integrity of the blood-brain barrier (BBB) against a backdrop of increasing bacterial load is important. Aging may favor the proliferation of anaerobes in the mouth eliciting a robust TNFα response from the oral epithelium. Prolonged exposure to high levels of circulating TNFα compromises the integrity of the BBB. Sensitive techniques now detect the "asymptomatic" presence of bacteria in areas previously thought to be sterile, providing new insights into the wider distribution of components of the microbiome. These "immune-tolerated" bacteria may slowly multiply elsewhere until they elicit a chronic inflammatory response; some are now considered causal in instances of atherosclerosis and back pain. Inflammatory processes have long been associated with AD. We propose for a subset of AD patients, aging favors the overgrowth of oral anaerobes established earlier in life provoking a pro-inflammatory innate response that weakens the BBB allowing bacteria to spread and quietly influence the pathogenesis of AD. Finally, we suggest that human polymorphisms considered alongside components of the microbiome may provide new avenues of research for the prevention and treatment of disease.

  3. Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression.

    Science.gov (United States)

    Duran-Pinedo, Ana E; Yost, Susan; Frias-Lopez, Jorge

    2015-10-01

    The oral microbiome is one of the most complex microbial communities in the human body, and due to circumstances not completely understood, the healthy microbial community becomes dysbiotic, giving rise to periodontitis, a polymicrobial inflammatory disease. We previously reported the results of community-wide gene expression changes in the oral microbiome during periodontitis progression and identified signatures associated with increasing severity of the disease. Small noncoding RNAs (sRNAs) are key players in posttranscriptional regulation, especially in fast-changing environments such as the oral cavity. Here, we expanded our analysis to the study of the sRNA metatranscriptome during periodontitis progression on the same samples for which mRNA expression changes were analyzed. We observed differential expression of 12,097 sRNAs, identifying a total of 20 Rfam sRNA families as being overrepresented in progression and 23 at baseline. Gene ontology activities regulated by the differentially expressed (DE) sRNAs included amino acid metabolism, ethanolamine catabolism, signal recognition particle-dependent cotranslational protein targeting to membrane, intron splicing, carbohydrate metabolism, control of plasmid copy number, and response to stress. In integrating patterns of expression of protein coding transcripts and sRNAs, we found that functional activities of genes that correlated positively with profiles of expression of DE sRNAs were involved in pathogenesis, proteolysis, ferrous iron transport, and oligopeptide transport. These findings represent the first integrated sequencing analysis of the community-wide sRNA transcriptome of the oral microbiome during periodontitis progression and show that sRNAs are key regulatory elements of the dysbiotic process leading to disease.

  4. The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition

    Science.gov (United States)

    O’Donnell, Lindsay E.; Robertson, Douglas; Nile, Christopher J.; Cross, Laura J.; Riggio, Marcello; Sherriff, Andrea; Bradshaw, David; Lambert, Margaret; Malcolm, Jennifer; Buijs, Mark J.; Zaura, Egija; Crielaard, Wim; Brandt, Bernd W.; Ramage, Gordon

    2015-01-01

    Objectives The composition of dental plaque has been well defined, whereas currently there is limited understanding of the composition of denture plaque and how it directly influences denture related stomatitis (DS). The aims of this study were to compare the microbiomes of denture wearers, and to understand the implications of these towards inter-kingdom and host-pathogen interactions within the oral cavity. Methods Swab samples were obtained from 123 participants wearing either a complete or partial denture; the bacterial composition of each sample was determined using bar-coded illumina MiSeq sequencing of the bacterial hypervariable V4 region of 16S rDNA. Sequencing data processing was undertaken using QIIME, clustered in Operational Taxonomic Units (OTUs) and assigned to taxonomy. The dentures were sonicated to remove the microbial flora residing on the prosthesis, sonicate was then cultured using diagnostic colorex Candida media. Samples of unstimulated saliva were obtained and antimicrobial peptides (AMP) levels were measured by ELISA. Results We have shown that dental and denture plaques are significantly distinct both in composition and diversity and that the oral microbiome composition of a denture wearer is variable and is influenced by the location within the mouth. Dentures and mucosa were predominantly made up of Bacilli and Actinobacteria. Moreover, the presence of natural teeth has a significant impact on the overall microbial composition, when compared to the fully edentulous. Furthermore, increasing levels of Candida spp. positively correlate with Lactobacillus spp. AMPs were quantified, though showed no specific correlations. Conclusions This is the first study to provide a detailed understanding of the oral microbiome of denture wearers and has provided evidence that DS development is more complex than simply a candidal infection. Both fungal and bacterial kingdoms clearly play a role in defining the progression of DS, though we were unable to

  5. The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition.

    Directory of Open Access Journals (Sweden)

    Lindsay E O'Donnell

    Full Text Available The composition of dental plaque has been well defined, whereas currently there is limited understanding of the composition of denture plaque and how it directly influences denture related stomatitis (DS. The aims of this study were to compare the microbiomes of denture wearers, and to understand the implications of these towards inter-kingdom and host-pathogen interactions within the oral cavity.Swab samples were obtained from 123 participants wearing either a complete or partial denture; the bacterial composition of each sample was determined using bar-coded illumina MiSeq sequencing of the bacterial hypervariable V4 region of 16S rDNA. Sequencing data processing was undertaken using QIIME, clustered in Operational Taxonomic Units (OTUs and assigned to taxonomy. The dentures were sonicated to remove the microbial flora residing on the prosthesis, sonicate was then cultured using diagnostic colorex Candida media. Samples of unstimulated saliva were obtained and antimicrobial peptides (AMP levels were measured by ELISA.We have shown that dental and denture plaques are significantly distinct both in composition and diversity and that the oral microbiome composition of a denture wearer is variable and is influenced by the location within the mouth. Dentures and mucosa were predominantly made up of Bacilli and Actinobacteria. Moreover, the presence of natural teeth has a significant impact on the overall microbial composition, when compared to the fully edentulous. Furthermore, increasing levels of Candida spp. positively correlate with Lactobacillus spp. AMPs were quantified, though showed no specific correlations.This is the first study to provide a detailed understanding of the oral microbiome of denture wearers and has provided evidence that DS development is more complex than simply a candidal infection. Both fungal and bacterial kingdoms clearly play a role in defining the progression of DS, though we were unable to show a defined role for

  6. Characterization of the Fungal Microbiome (Mycobiome in Fecal Samples from Dogs

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    M. Lauren Foster

    2013-01-01

    Full Text Available The prevalence and phylogenetic description of fungal organisms and their role as part of the intestinal ecosystem have not yet been studied extensively in dogs. This study evaluated the fungal microbiome of 19 dogs (12 healthy dogs and 7 dogs with acute diarrhea using fungal tag-encoded FLX-Titanium amplicon pyrosequencing. Five distinct fungal phyla were identified, with Ascomycota (medians: 97.9% of obtained sequences in healthy dogs and 98.2% in diseased dogs and Basidiomycota (median 1.0% in healthy dogs and median 0.5% in diseased dogs being the most abundant fungal phyla. A total of 219 fungal genera were identified across all 19 dogs with a median (range of 28 (4–69 genera per sample. Candida was the most abundant genus found in both the diseased dogs (median: 1.9%, range: 0.2%–38.5% of sequences and healthy dogs (median: 5.2%, range: 0.0%–63.1% of sequences. Candida natalensis was the most frequently identified species. No significant differences were observed in the relative proportions of fungal communities between healthy and diseased dogs. In conclusion, fecal samples of healthy dogs and dogs with acute diarrhea harbor various fungal genera, and their role in gastrointestinal health and disease warrants further studies.

  7. The microbiome associated with equine periodontitis and oral health.

    Science.gov (United States)

    Kennedy, Rebekah; Lappin, David Francis; Dixon, Padraic Martin; Buijs, Mark Johannes; Zaura, Egija; Crielaard, Wim; O'Donnell, Lindsay; Bennett, David; Brandt, Bernd Willem; Riggio, Marcello Pasquale

    2016-04-14

    Equine periodontal disease is a common and painful condition and its severe form, periodontitis, can lead to tooth loss. Its aetiopathogenesis remains poorly understood despite recent increased awareness of this disorder amongst the veterinary profession. Bacteria have been found to be causative agents of the disease in other species, but current understanding of their role in equine periodontitis is extremely limited. The aim of this study was to use high-throughput sequencing to identify the microbiome associated with equine periodontitis and oral health. Subgingival plaque samples from 24 horses with periodontitis and gingival swabs from 24 orally healthy horses were collected. DNA was extracted from samples, the V3-V4 region of the bacterial 16S rRNA gene amplified by PCR and amplicons sequenced using Illumina MiSeq. Data processing was conducted using USEARCH and QIIME. Diversity analyses were performed with PAST v3.02. Linear discriminant analysis effect size (LEfSe) was used to determine differences between the groups. In total, 1308 OTUs were identified and classified into 356 genera or higher taxa. Microbial profiles at health differed significantly from periodontitis, both in their composition (p periodontitis group samples showed higher diversity (3.16, SD 0.98) and were dominated by the genera Prevotella and Veillonella. It is concluded that the microbiomes associated with equine oral health and periodontitis are distinct, with the latter displaying greater microbial diversity.

  8. Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing

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    Lindsay Kalan

    2016-09-01

    Full Text Available Chronic nonhealing wounds have been heralded as a silent epidemic, causing significant morbidity and mortality especially in elderly, diabetic, and obese populations. Polymicrobial biofilms in the wound bed are hypothesized to disrupt the highly coordinated and sequential events of cutaneous healing. Both culture-dependent and -independent studies of the chronic-wound microbiome have almost exclusively focused on bacteria, omitting what we hypothesize are important fungal contributions to impaired healing and the development of complications. Here we show for the first time that fungal communities (the mycobiome in chronic wounds are predictive of healing time, associated with poor outcomes, and form mixed fungal-bacterial biofilms. We longitudinally profiled 100, nonhealing diabetic-foot ulcers with high-throughput sequencing of the pan-fungal internal transcribed spacer 1 (ITS1 locus, estimating that up to 80% of wounds contain fungi, whereas cultures performed in parallel captured only 5% of colonized wounds. The “mycobiome” was highly heterogeneous over time and between subjects. Fungal diversity increased with antibiotic administration and onset of a clinical complication. The proportions of the phylum Ascomycota were significantly greater (P = 0.015 at the beginning of the study in wounds that took >8 weeks to heal. Wound necrosis was distinctly associated with pathogenic fungal species, while taxa identified as allergenic filamentous fungi were associated with low levels of systemic inflammation. Directed culturing of wounds stably colonized by pathogens revealed that interkingdom biofilms formed between yeasts and coisolated bacteria. Combined, our analyses provide enhanced resolution of the mycobiome during impaired wound healing, its role in chronic disease, and impact on clinical outcomes.

  9. Characterization of the rat oral microbiome and the effects of dietary nitrate.

    Science.gov (United States)

    Hyde, Embriette R; Luk, Berkley; Cron, Stanley; Kusic, Lenka; McCue, Tyler; Bauch, Tonya; Kaplan, Heidi; Tribble, Gena; Petrosino, Joseph F; Bryan, Nathan S

    2014-12-01

    The nitrate-nitrite-NO pathway to nitric oxide (NO) production is a symbiotic pathway in mammals that is dependent on nitrate reducing oral commensal bacteria. Studies suggest that by contributing NO to the mammalian host, the oral microbiome helps maintain cardiovascular health. To begin to understand how changes in oral microbiota affect physiological functions such as blood pressure, we have characterized the Wistar rat nitrate reducing oral microbiome. Using 16S rRNA gene sequencing and analysis we compare the native Wistar rat tongue microbiome to that of healthy humans and to that of rats with sodium nitrate and chlorhexidine mouthwash treatments. We demonstrate that the rat tongue microbiome is less diverse than the human tongue microbiome, but that the physiological activity is comparable, as sodium nitrate supplementation significantly lowered diastolic blood pressure in Wistar rats and also lowers blood pressure (diastolic and systolic) in humans. We also show for the first time that sodium nitrate supplementation alters the abundance of specific bacterial species on the tongue. Our results suggest that the changes in oral nitrate reducing bacteria may affect nitric oxide availability and physiological functions such as blood pressure. Understanding individual changes in human oral microbiome may offer novel dietary approaches to restore NO availability and blood pressure.

  10. The Denture-Associated Oral Microbiome in Health and Stomatitis.

    Science.gov (United States)

    Shi, Baochen; Wu, Tingxi; McLean, Jeffrey; Edlund, Anna; Young, Youngik; He, Xuesong; Lv, Hongyang; Zhou, Xuedong; Shi, Wenyuan; Li, Huiying; Lux, Renate

    2016-01-01

    While investigation of the microbiome on natural oral surfaces has generated a wealth of information, few studies have examined the microbial communities colonizing dentures and their relationship to oral health. To address this knowledge gap, we characterized the bacterial community associated with dentures and remaining teeth in healthy individuals and patients with denture stomatitis. The microbiome compositions of matched denture and tooth plaque samples of 10 healthy individuals and 9 stomatitis patients were determined by 16S rRNA gene pyrosequencing. The microbial communities colonizing dentures and remaining teeth in health and disease were very similar to each other. Matched denture and tooth samples from the same individuals shared a significantly higher percentage of identical phylotypes than random pairs of samples from different study participants. Despite these overall similarities, several bacterial phylotypes displayed discrete health- and stomatitis-associated denture colonization, while others were distinct in health and disease independently of the surface. Certain phylotypes exhibited differential colonization of dentures and teeth independently of denture health status. In conclusion, denture and natural tooth surfaces in health and stomatitis harbor similar bacterial communities. Individual-related rather than surface-specific factors play a significant role in the bacterial phylotype composition colonizing dentures and teeth. This individual-specific mutual influence on denture and tooth surface colonization could be an important factor in maintaining oral health in denture wearers. Discrete differences in colonization patterns for distinct genera and phylotypes warrant further studies regarding their potential involvement or utility as specific indicators of health and disease development in denture-wearing individuals. IMPORTANCE Denture stomatitis is a prevalent inflammatory condition of the mucosal tissue in denture wearers that is

  11. Uncommon opportunistic fungal infections of oral cavity: A review

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    A G Deepa

    2014-01-01

    Full Text Available The majority of opportunistic oral mucosal fungal infections are due to Candida albicans and Aspergillus fumigatus species. Mucor and Cryptococcus also have a major role in causing oral infections, whereas Geotrichum, Fusarium, Rhodotorula, Saccharomyces and Penicillium marneffei are uncommon pathogens in the oral cavity. The broad spectrum of clinical presentation includes pseudo-membranes, abscesses, ulcers, pustules and extensive tissue necrosis involving bone. This review discusses various uncommon opportunistic fungal infections affecting the oral cavity including their morphology, clinical features and diagnostic methods.

  12. Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing.

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    Changin Oh

    Full Text Available The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%, Proteobacteria (21.6%, Bacteroidetes (9.8%, Actinobacteria (7.1%, and Fusobacteria (3.9% were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%, Actinobacteria (21%, Bacteroidetes (19.7%, Firmicutes (19.3%, and Fusobacteria (12.3% were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%, Neisseria (10.3%, Haemophilus (9.6%, Prevotella (8.4%, and Veillonella (8.1%, whereas the predominant genera in the canine samples were Actinomyces (17.2%, Unknown (16.8, Porphyromonas (14.8, Fusobacterium (11.8, and Neisseria (7.2%. The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.

  13. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    DEFF Research Database (Denmark)

    Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin

    2016-01-01

    , disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow. METHODS: We used...... with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. CONCLUSION: Rapid shotgun...... and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics....

  14. Candida and other fungal species: forgotten players of healthy oral microbiota

    NARCIS (Netherlands)

    Krom, B.P.; Kidwai, S.; ten Cate, J.M.

    2014-01-01

    In the last half-decade or so, interest in the bacterial part of the human microbiome and its role in maintaining health have received considerable attention. Since 2009, over 300 publications have appeared describing the oral bacterial microbiome. Strikingly, fungi in the oral cavity have been

  15. Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

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    Bo Liu

    Full Text Available The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE and high human DNA contamination (up to ~90% we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.

  16. Fungal infections of the oral mucosa

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    P Anitha Krishnan

    2012-01-01

    This review discusses the various predisposing factors, clinical presentations, clinical differential diagnosis, diagnosis and management of oral candidiasis, as well as briefly highlights upon a few of the more exotic non-Candidal fungi that infect the oral mucosa.

  17. The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome.

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    Adam Paul Roberts

    2014-09-01

    Full Text Available The oral microbiome is composed of a multitude of different species of bacteria, each capable of occupying one or more of the many different niches found within the human oral cavity. This community exhibits many types of complex interactions which enable it to colonise and rapidly respond to changes in the environment in which they live. One of these interactions is the transfer, or acquisition, of DNA within this environment, either from co-resident bacterial species or from exogenous sources. Horizontal gene transfer in the oral cavity gives some of the resident bacteria the opportunity to sample a truly enormous metagenome affording them considerable adaptive potential which may be key to survival in such a varying environment. In this review the underlying mechanisms of HGT are discussed in relation to the oral microbiome with numerous examples described where the direct acquisition of exogenous DNA has contributed to the fitness of the bacterial host within the human oral cavity.

  18. Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals.

    Science.gov (United States)

    Davis, Eric M

    2016-06-01

    It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque. Diversity surveys utilizing this technology have demonstrated that bacterial culture techniques have vastly underestimated the richness and diversity of microorganisms in vivo, since only certain bacteria grow in vitro. Surveys using gene sequence analysis have demonstrated that the healthy oral microbiome is composed of an unexpectedly high number of diverse species, including putative pathogens. These findings support the view that coevolution microorganisms and macroscopic hosts has occurred in which certain microorganisms have adapted to survive in the oral cavity and host immune tolerance has allowed the establishment of a symbiotic relationship in which both parties receive benefits (mutualism). This review describes gene sequence analysis as an increasingly common, culture-independent tool for detecting bacteria in vivo and describes the results of recent oral microbiome diversity surveys of clinically healthy humans, dogs, and cats. Six bacterial phyla consistently dominated the healthy oral microbiome of all 3 host species. Previous hypotheses on etiology of periodontitis are reviewed in light of new scientific findings. Finally, the consideration that clinically relevant periodontal disease occurs when immune tolerance of the symbiotic oral microbiome is altered to a proinflammatory response will be discussed.

  19. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

    Science.gov (United States)

    Shakya, Migun; Gottel, Neil; Castro, Hector; Yang, Zamin K; Gunter, Lee; Labbé, Jessy; Muchero, Wellington; Bonito, Gregory; Vilgalys, Rytas; Tuskan, Gerald; Podar, Mircea; Schadt, Christopher W

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that

  20. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

    Directory of Open Access Journals (Sweden)

    Migun Shakya

    Full Text Available Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings, host plant genotype (Simple Sequence Repeat (SSR markers, season (Spring vs. Fall and geographic setting (at scales from regional watersheds to local riparian zones on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs specific to an individual trees (bacteria >90%, fungi >60%. Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal and endosphere (1 bacterial and 1 fungal microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50% while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%. While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina and seasons (Spring vs. Fall. SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities

  1. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

    Energy Technology Data Exchange (ETDEWEB)

    Shakya, Migun [ORNL; Gottel, Neil R [ORNL; Castro Gonzalez, Hector F [ORNL; Yang, Zamin [ORNL; Gunter, Lee E [ORNL; Labbe, Jessy L [ORNL; Muchero, Wellington [ORNL; Bonito, Gregory [Duke University; Vilgalys, Rytas [Duke University; Tuskan, Gerald A [ORNL; Podar, Mircea [ORNL; Schadt, Christopher Warren [ORNL

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that could be

  2. Metatranscriptomics of the human oral microbiome during health and disease.

    Science.gov (United States)

    Jorth, Peter; Turner, Keith H; Gumus, Pinar; Nizam, Nejat; Buduneli, Nurcan; Whiteley, Marvin

    2014-04-01

    The human microbiome plays important roles in health, but when disrupted, these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite interpatient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here, we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that health- and disease-associated communities exhibit defined differences in metabolism that are conserved between patients. In contrast, the metabolic gene expression of individual species was highly variable between patients. These results demonstrate that despite high interpatient variability in microbial composition, disease-associated communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes. IMPORTANCE The human microbiome project has shown that shifts in our microbiota are associated with many diseases, including obesity, Crohn's disease, diabetes, and periodontitis. While changes in microbial populations are apparent during these diseases, the species associated with each disease can vary from patient to patient. Taking into account this interpatient variability, we hypothesized that specific microbiota-associated diseases would be marked by conserved microbial community behaviors. Here, we use gene expression analyses of patient-matched healthy and diseased human periodontal plaque to show that microbial communities have highly conserved metabolic gene expression profiles, whereas individual species within the community do not. Furthermore, disease-associated communities exhibit conserved changes

  3. Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.

    Directory of Open Access Journals (Sweden)

    Jiyoung Ahn

    Full Text Available OBJECTIVES: The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. METHODS: Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp. Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM. Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. RESULTS: The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86. 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84. CONCLUSION: Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.

  4. Mouthguards: Does the indigenous microbiome play a role in maintaining oral health?

    Directory of Open Access Journals (Sweden)

    Purnima S Kumar

    2015-05-01

    Full Text Available The existence of symbiotic relationships between bacteria in different ecosystems and their host niches have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community i. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities . Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.

  5. Mouthguards: does the indigenous microbiome play a role in maintaining oral health?

    Science.gov (United States)

    Kumar, Purnima S; Mason, Matthew R

    2015-01-01

    The existence of symbiotic relationships between bacteria and their hosts in various ecosystems have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities. Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function, and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.

  6. A systematic review of oral fungal infections in patients receiving cancer therapy

    NARCIS (Netherlands)

    Lalla, Rajesh V.; Latortue, Marie C.; Hong, Catherine H.; Ariyawardana, Anura; D'Amato-Palumbo, Sandra; Fischer, Dena J.; Martof, Andrew; Nicolatou-Galitis, Ourania; Patton, Lauren L.; Elting, Linda S.; Spijkervet, Fred K. L.; Brennan, Michael T.

    The aims of this systematic review were to determine, in patients receiving cancer therapy, the prevalence of clinical oral fungal infection and fungal colonization, to determine the impact on quality of life and cost of care, and to review current management strategies for oral fungal infections.

  7. A systematic review of oral fungal infections in patients receiving cancer therapy

    NARCIS (Netherlands)

    Lalla, Rajesh V.; Latortue, Marie C.; Hong, Catherine H.; Ariyawardana, Anura; D'Amato-Palumbo, Sandra; Fischer, Dena J.; Martof, Andrew; Nicolatou-Galitis, Ourania; Patton, Lauren L.; Elting, Linda S.; Spijkervet, Fred K. L.; Brennan, Michael T.

    2010-01-01

    The aims of this systematic review were to determine, in patients receiving cancer therapy, the prevalence of clinical oral fungal infection and fungal colonization, to determine the impact on quality of life and cost of care, and to review current management strategies for oral fungal infections. T

  8. 口腔微生物组与疾病%Oral microbiome and diseases

    Institute of Scientific and Technical Information of China (English)

    李燕; 何金枝; 肖丽英; 周学东

    2014-01-01

    Human microbiome project(HMP) phase Ⅰ have been completed last year and a slew of genetic sequences have obtained from human oral microbiome project, a sub-project of HMP. This review summarized the extensive oral microbiome composition and diversity, including bacteria, fungi, virus and archae. By analyzing the microbiota of clinical samples collected from patient suffering from diseases such as caries, periodontal diseases and systematic diseases, the relationship between oral microbial shifts and human diseases was investigated.%人类微生物组计划Ⅰ期已经结束,作为该项目子项目之一的口腔微生物组项目,已经获得了海量的测序数据。本文综述了口腔微生物组(包括细菌、真菌、病毒和古细菌)的组成及多样性;通过分析患有特定疾病如龋病、牙周病、全身系统性疾病志愿者的口腔微生物组成,解析口腔微生物群落结构变化与疾病之间的相互联系。

  9. A characterization of the oral microbiome in allogeneic stem cell transplant patients.

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    Nancy J Ames

    Full Text Available BACKGROUND: The mouth is a complex biological structure inhabited by diverse bacterial communities. The purpose of this study is to describe the effects of allogeneic stem cell transplantation on the oral microbiota and to examine differences among those patients who acquired respiratory complications after transplantation. METHODOLOGY/PRINCIPAL FINDINGS: All patients were consented at the National Institutes of Health, Clinical Center. Bacterial DNA was analyzed from patients' oral specimens using the Human Oral Microbe Identification Microarray. The specimens were collected from four oral sites in 45 allogeneic transplantation patients. Specimens were collected at baseline prior to transplantation, after transplantation at the nadir of the neutrophil count and after myeloid engraftment. If respiratory signs and symptoms developed, additional specimens were obtained. Patients were followed for 100 days post transplantation. Eleven patients' specimens were subjected to further statistical analysis. Many common bacterial genera, such as Streptococcus, Veillonella, Gemella, Granulicatella and Camplyobacter were identified as being present before and after transplantation. Five of 11 patients developed respiratory complications following transplantation and there was preliminary evidence that the oral microbiome changed in their oral specimens. Cluster analysis and principal component analysis revealed this change in the oral microbiota. CONCLUSIONS/SIGNIFICANCE: After allogeneic transplantation, the oral bacterial community's response to a new immune system was not apparent and many of the most common core oral taxa remained unaffected. However, the oral microbiome was affected in patients who developed respiratory signs and symptoms after transplantation. The association related to the change in the oral microbiota and respiratory complications after transplantation will be validated by future studies using high throughput molecular methods.

  10. The Relation between Oral Candida Load and Bacterial Microbiome Profiles in Dutch Older Adults

    Science.gov (United States)

    Kraneveld, Eefje A.; Buijs, Mark J.; Bonder, Marc J.; Visser, Marjolein; Keijser, Bart J. F.; Crielaard, Wim; Zaura, Egija

    2012-01-01

    Currently there are no evidence-based ecological measures for prevention of overgrowth and subsequent infection by fungi in the oral cavity. The aim of this study was to increase our knowledge on fungal–bacterial ecological interactions. Salivary Candida abundance of 82 Dutch adults aged 58–80 years was established relative to the bacterial load by quantitative PCR analysis of the Internal Transcribed (ITS) region (Candida) and 16S rDNA gene (bacteria). The salivary microbiome was assessed using barcoded pyrosequencing of the bacterial hypervariable regions V5–V7 of 16S rDNA. Sequencing data was preprocessed by denoising and chimera removal, clustered in Operational Taxonomic Units (OTUs) and assigned to taxonomy. Both OTU-based (PCA, diversity statistics) and phylogeny-based analyses (UniFrac, PCoA) were performed. Saliva of Dutch older adults contained 0–4 × 108 CFU/mL Candida with a median Candida load of 0.06%. With increased Candida load the diversity of the salivary microbiome decreased significantly (pCandida load correlated positively with class Bacilli, and negatively with class Fusobacteria, Flavobacteria, and Bacteroidia. Microbiomes with high Candida load were less diverse and had a distinct microbial composition towards dominance by saccharolytic and acidogenic bacteria - streptococci. The control of the acidification of the oral environment may be a potential preventive measure for Candida outgrowth that should be evaluated in longitudinal clinical intervention trials. PMID:22900048

  11. Phage-bacteria interaction network in human oral microbiome.

    Science.gov (United States)

    Wang, Jinfeng; Gao, Yuan; Zhao, Fangqing

    2016-07-01

    Although increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage-bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage-bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray-Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross-infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage-bacteria interaction as networks rather than exclusively pairwise predator-prey relationships, our study provides the first insight into the participation of cross-infective phages in forming human oral microbiota.

  12. Complete Genome Sequences of Two Human Oral Microbiome Commensals, Streptococcus salivarius ATCC 25975 and S. salivarius ATCC 27945.

    Science.gov (United States)

    Butler, Robert R; Soomer-James, Jahna T A; Frenette, Michel; Pombert, Jean-François

    2017-06-15

    Streptococcus salivarius strains are significant contributors to the human oral microbiome. Some possess unique fimbriae that give them the ability to coaggregate and colonize particular oral structures. We present here the complete genomes of Streptococcus salivarius Lancefield K(-)/K(+) strains ATCC 25975 and ATCC 27945, which can and cannot, respectively, produce fimbriae. Copyright © 2017 Butler et al.

  13. Complete Genome Sequences of Two Human Oral Microbiome Commensals: Streptococcus salivarius ATCC 25975 and S. salivarius ATCC 27945

    OpenAIRE

    Butler, Robert R.; Soomer-James, Jahna T. A.; Frenette, Michel; Pombert, Jean-François

    2017-01-01

    ABSTRACT Streptococcus salivarius strains are significant contributors to the human oral microbiome. Some possess unique fimbriae that give them the ability to coaggregate and colonize particular oral structures. We present here the complete genomes of Streptococcus salivarius Lancefield K?/K+ strains ATCC 25975 and ATCC 27945, which can and cannot, respectively, produce fimbriae.

  14. Complete Genome Sequence of Lactobacillus oris J-1, a Potential Probiotic Isolated from the Human Oral Microbiome

    Science.gov (United States)

    2016-01-01

    Lactobacilli can exert health-promoting effects in the human oral microbiome through many mechanisms, including pathogen inhibition, maintenance of microbial balance, immunomodulation, and enhancement of the epithelial barrier function. Here, we present the complete genome sequence of a potential probiotic, Lactobacillus oris J-1, that was isolated from the oral cavity of a health child. PMID:27634996

  15. Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.

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    Matthew R Mason

    Full Text Available Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

  16. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

    Science.gov (United States)

    Li, Yan; He, Jinzhi; He, Zhili; Zhou, Yuan; Yuan, Mengting; Xu, Xin; Sun, Feifei; Liu, Chengcheng; Li, Jiyao; Xie, Wenbo; Deng, Ye; Qin, Yujia; VanNostrand, Joy D; Xiao, Liying; Wu, Liyou; Zhou, Jizhong; Shi, Wenyuan; Zhou, Xuedong

    2014-01-01

    Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis. PMID:24671083

  17. The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults

    NARCIS (Netherlands)

    Kraneveld, E.A.; Buijs, M.J.; Bonder, M.J.; Visser, M.; Keijser, B.J.F.; Crielaard, W.; Zaura, E.

    2012-01-01

    Currently there are no evidence-based ecological measures for prevention of overgrowth and subsequent infection by fungi in the oral cavity. The aim of this study was to increase our knowledge on fungal-bacterial ecological interactions. Salivary Candida abundance of 82 Dutch adults aged 58-80 years

  18. The relation between oral candida load and bacterial microbiome profiles in dutch older adults

    NARCIS (Netherlands)

    Kraneveld, E.A.; Buijs, M.J.; Bonder, M.J.; Visser, M.; Keijser, B.J.F.; Crielaard, W.; Zaura, E.

    2012-01-01

    Currently there are no evidence-based ecological measures for prevention of overgrowth and subsequent infection by fungi in the oral cavity. The aim of this study was to increase our knowledge on fungal-bacterial ecological interactions. Salivary Candida abundance of 82 Dutch adults aged 58-80 years

  19. Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities.

    Science.gov (United States)

    Vesty, Anna; Biswas, Kristi; Taylor, Michael W; Gear, Kim; Douglas, Richard G

    2017-01-01

    The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3-V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome.

  20. Molecular analysis of fungal populations in patients with oral candidiasis using internal transcribed spacer region.

    Science.gov (United States)

    Ieda, Shinsuke; Moriyama, Masafumi; Takeshita, Toru; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection.

  1. Fungal Root Microbiome from Healthy and Brittle Leaf Diseased Date Palm Trees (Phoenix dactylifera L.) Reveals a Hidden Untapped Arsenal of Antibacterial and Broad Spectrum Antifungal Secondary Metabolites.

    Science.gov (United States)

    Mefteh, Fedia B; Daoud, Amal; Chenari Bouket, Ali; Alenezi, Faizah N; Luptakova, Lenka; Rateb, Mostafa E; Kadri, Adel; Gharsallah, Neji; Belbahri, Lassaad

    2017-01-01

    In this study, we aimed to explore and compare the composition, metabolic diversity and antimicrobial potential of endophytic fungi colonizing internal tissues of healthy and brittle leaf diseased (BLD) date palm trees (Phoenix dactylifera L.) widely cultivated in arid zones of Tunisia. A total of 52 endophytic fungi were isolated from healthy and BLD roots of date palm trees, identified based on internal transcribed spacer-rDNA sequence analysis and shown to represent 13 species belonging to five genera. About 36.8% of isolates were shared between healthy and diseased root fungal microbiomes, whereas 18.4 and 44.7% of isolates were specific to healthy and BLD root fungal microbiomes, respectively. All isolates were able to produce at least two of the screened enzymes including amylase, cellulase, chitinase, pectinase, protease, laccase and lipase. A preliminary screening of the isolates using disk diffusion method for antibacterial activity against four Gram-positive and three Gram-negative bacteria and antifungal activities against three phytopathogenic fungi indicated that healthy and BLD root fungal microbiomes displayed interesting bioactivities against examined bacteria and broad spectrum bioactivity against fungal pathogens. Some of these endophytic fungi (17 isolates) were fermented and their extracts were evaluated for antimicrobial potential against bacterial and fungal isolates. Results revealed that fungal extracts exhibited antibacterial activities and were responsible for approximately half of antifungal activities against living fungi. These results suggest a strong link between fungal bioactivities and their secondary metabolite arsenal. EtOAc extracts of Geotrichum candidum and Thielaviopsis punctulata originating from BLD microbiome gave best results against Micrococcus luteus and Bacillus subtilis with minimum inhibitory concentration (MIC, 0.78 mg/mL) and minimum bactericidal concentration (6.25 mg/mL). G. candidum gave the best result against

  2. Fungal Root Microbiome from Healthy and Brittle Leaf Diseased Date Palm Trees (Phoenix dactylifera L.) Reveals a Hidden Untapped Arsenal of Antibacterial and Broad Spectrum Antifungal Secondary Metabolites

    Science.gov (United States)

    Mefteh, Fedia B.; Daoud, Amal; Chenari Bouket, Ali; Alenezi, Faizah N.; Luptakova, Lenka; Rateb, Mostafa E.; Kadri, Adel; Gharsallah, Neji; Belbahri, Lassaad

    2017-01-01

    In this study, we aimed to explore and compare the composition, metabolic diversity and antimicrobial potential of endophytic fungi colonizing internal tissues of healthy and brittle leaf diseased (BLD) date palm trees (Phoenix dactylifera L.) widely cultivated in arid zones of Tunisia. A total of 52 endophytic fungi were isolated from healthy and BLD roots of date palm trees, identified based on internal transcribed spacer-rDNA sequence analysis and shown to represent 13 species belonging to five genera. About 36.8% of isolates were shared between healthy and diseased root fungal microbiomes, whereas 18.4 and 44.7% of isolates were specific to healthy and BLD root fungal microbiomes, respectively. All isolates were able to produce at least two of the screened enzymes including amylase, cellulase, chitinase, pectinase, protease, laccase and lipase. A preliminary screening of the isolates using disk diffusion method for antibacterial activity against four Gram-positive and three Gram-negative bacteria and antifungal activities against three phytopathogenic fungi indicated that healthy and BLD root fungal microbiomes displayed interesting bioactivities against examined bacteria and broad spectrum bioactivity against fungal pathogens. Some of these endophytic fungi (17 isolates) were fermented and their extracts were evaluated for antimicrobial potential against bacterial and fungal isolates. Results revealed that fungal extracts exhibited antibacterial activities and were responsible for approximately half of antifungal activities against living fungi. These results suggest a strong link between fungal bioactivities and their secondary metabolite arsenal. EtOAc extracts of Geotrichum candidum and Thielaviopsis punctulata originating from BLD microbiome gave best results against Micrococcus luteus and Bacillus subtilis with minimum inhibitory concentration (MIC, 0.78 mg/mL) and minimum bactericidal concentration (6.25 mg/mL). G. candidum gave the best result against

  3. Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women

    Science.gov (United States)

    Smith, Benjamin C.; Zolnik, Christine P.; Usyk, Mykhaylo; Chen, Zigui; Kaiser, Katherine; Nucci-Sack, Anne; Peake, Ken; Diaz, Angela; Viswanathan, Shankar; Strickler, Howard D.; Schlecht, Nicolas F.; Burk, Robert D.

    2016-01-01

    Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes, oral samples with Streptococcus and Prevotella, and cervical samples with Lactobacillus. The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual. PMID:27698612

  4. The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents - A Randomized Controlled Clinical Trial.

    Directory of Open Access Journals (Sweden)

    Jessica E Koopman

    Full Text Available While the aesthetic effect of orthodontic treatment is clear, the knowledge on how it influences the oral microbiota and the consequential effects on oral health are limited. In this randomized controlled clinical trial we investigated the changes introduced in the oral ecosystem, during and after orthodontic treatment with fixed appliances in combination with or without a fluoride mouthwash, of 10-16.8 year old individuals (N = 91. We followed several clinical parameters in time, in combination with microbiome changes using next-generation sequencing of the bacterial 16S rRNA gene. During the course of our study, the oral microbial community displayed remarkable resilience towards the disturbances it was presented with. The effects of the fluoride mouthwash on the microbial composition were trivial. More pronounced microbial changes were related to gingival health status, orthodontic treatment and time. Periodontal pathogens (e.g. Selenomonas and Porphyromonas were highest in abundance during the orthodontic treatment, while the health associated Streptococcus, Rothia and Haemophilus gained abundance towards the end and after the orthodontic treatment. Only minor compositional changes remained in the oral microbiome after the end of treatment. We conclude that, provided proper oral hygiene is maintained, changes in the oral microbiome composition resulting from orthodontic treatment are minimal and do not negatively affect oral health.

  5. In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome

    Directory of Open Access Journals (Sweden)

    Emma Hernandez-Sanabria

    2017-06-01

    Full Text Available Understanding the driving forces behind the shifts in the ecological balance of the oral microbiota will become essential for the future management and treatment of periodontitis. As the use of competitive approaches for modulating bacterial outgrowth is unexplored in the oral ecosystem, our study aimed to investigate both the associations among groups of functional compounds and the impact of individual substrates on selected members of the oral microbiome. We employed the Phenotype Microarray high-throughput technology to analyse the microbial cellular phenotypes of 15 oral bacteria. Multivariate statistical analysis was used to detect respiratory activity triggers and to assess similar metabolic activities. Carbon and nitrogen were relevant for the respiration of health-associated bacteria, explaining competitive interactions when grown in biofilms. Carbon, nitrogen, and peptides tended to decrease the respiratory activity of all pathobionts, but not significantly. None of the evaluated compounds significantly increased activity of pathobionts at both 24 and 48 h. Additionally, metabolite requirements of pathobionts were dissimilar, suggesting that collective modulation of their respiratory activity may be challenging. Flow cytometry indicated that the metabolic activity detected in the Biolog plates may not be a direct result of the number of bacterial cells. In addition, damage to the cell membrane may not influence overall respiratory activity. Our methodology confirmed previously reported competitive and collaborative interactions among bacterial groups, which could be used either as marker of health status or as targets for modulation of the oral environment.

  6. In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome.

    Science.gov (United States)

    Hernandez-Sanabria, Emma; Slomka, Vera; Herrero, Esteban R; Kerckhof, Frederiek-Maarten; Zaidel, Lynette; Teughels, Wim; Boon, Nico

    2017-01-01

    Understanding the driving forces behind the shifts in the ecological balance of the oral microbiota will become essential for the future management and treatment of periodontitis. As the use of competitive approaches for modulating bacterial outgrowth is unexplored in the oral ecosystem, our study aimed to investigate both the associations among groups of functional compounds and the impact of individual substrates on selected members of the oral microbiome. We employed the Phenotype Microarray high-throughput technology to analyse the microbial cellular phenotypes of 15 oral bacteria. Multivariate statistical analysis was used to detect respiratory activity triggers and to assess similar metabolic activities. Carbon and nitrogen were relevant for the respiration of health-associated bacteria, explaining competitive interactions when grown in biofilms. Carbon, nitrogen, and peptides tended to decrease the respiratory activity of all pathobionts, but not significantly. None of the evaluated compounds significantly increased activity of pathobionts at both 24 and 48 h. Additionally, metabolite requirements of pathobionts were dissimilar, suggesting that collective modulation of their respiratory activity may be challenging. Flow cytometry indicated that the metabolic activity detected in the Biolog plates may not be a direct result of the number of bacterial cells. In addition, damage to the cell membrane may not influence overall respiratory activity. Our methodology confirmed previously reported competitive and collaborative interactions among bacterial groups, which could be used either as marker of health status or as targets for modulation of the oral environment.

  7. Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing.

    Science.gov (United States)

    Imabayashi, Yumi; Moriyama, Masafumi; Takeshita, Toru; Ieda, Shinsuke; Hayashida, Jun-Nosuke; Tanaka, Akihiko; Maehara, Takashi; Furukawa, Sachiko; Ohta, Miho; Kubota, Keigo; Yamauchi, Masaki; Ishiguro, Noriko; Yamashita, Yoshihisa; Nakamura, Seiji

    2016-01-01

    Oral candidiasis is closely associated with changes in oral fungal biodiversity and is caused primarily by Candida albicans. However, the widespread use of empiric and prophylactic antifungal drugs has caused a shift in fungal biodiversity towards other Candida or yeast species. Recently, next-generation sequencing (NGS) has provided an improvement over conventional culture techniques, allowing rapid comprehensive analysis of oral fungal biodiversity. In this study, we used NGS to examine the oral fungal biodiversity of 27 patients with pseudomembranous oral candidiasis (POC) and 66 healthy controls. The total number of fungal species in patients with POC and healthy controls was 67 and 86, respectively. The copy number of total PCR products and the proportion of non-C. albicans, especially C. dubliniensis, in patients with POC, were higher than those in healthy controls. The detection patterns in patients with POC were similar to those in controls after antifungal treatment. Interestingly, the number of fungal species and the copy number of total PCR products in healthy controls increased with aging. These results suggest that high fungal biodiversity and aging might be involved in the pathogenesis of oral candidiasis. We therefore conclude that NGS is a useful technique for investigating oral candida infections.

  8. Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis.

    Science.gov (United States)

    Slocum, C; Kramer, C; Genco, C A

    2016-07-01

    Cardiovascular disease is an inflammatory disorder characterized by the progressive formation of plaque in coronary arteries, termed atherosclerosis. It is a multifactorial disease that is one of the leading causes of death worldwide. Although a number of risk factors have been associated with disease progression, the underlying inflammatory mechanisms contributing to atherosclerosis remain to be fully delineated. Within the last decade, the potential role for infection in inflammatory plaque progression has received considerable interest. Microbial pathogens associated with periodontal disease have been of particular interest due to the high levels of bacteremia that are observed after routine dental procedures and every day oral activities, such as tooth brushing. Here, we explore the potential mechanisms that may explain how periodontal pathogens either directly or indirectly elicit immune dysregulation and consequently progressive inflammation manifested as atherosclerosis. Periodontal pathogens have been shown to contribute directly to atherosclerosis by disrupting endothelial cell function, one of the earliest indicators of cardiovascular disease. Oral infection is thought to indirectly induce elevated production of inflammatory mediators in the systemic circulation. Recently, a number of studies have been conducted focusing on how disruption of the gut microbiome influences the systemic production of proinflammatory cytokines and consequently exacerbation of inflammatory diseases such as atherosclerosis. It is clear that the immune mechanisms leading to atherosclerotic plaque progression, by oral infection, are complex. Understanding the immune pathways leading to disease progression is essential for the future development of anti-inflammatory therapies for this chronic disease.

  9. The feline oral microbiome: a provisional 16S rRNA gene based taxonomy with full-length reference sequences.

    Science.gov (United States)

    Dewhirst, Floyd E; Klein, Erin A; Bennett, Marie-Louise; Croft, Julie M; Harris, Stephen J; Marshall-Jones, Zoe V

    2015-02-25

    The human oral microbiome is known to play a significant role in human health and disease. While less well studied, the feline oral microbiome is thought to play a similarly important role. To determine roles oral bacteria play in health and disease, one first has to be able to accurately identify bacterial species present. 16S rRNA gene sequence information is widely used for molecular identification of bacteria and is also useful for establishing the taxonomy of novel species. The objective of this research was to obtain full 16S rRNA gene reference sequences for feline oral bacteria, place the sequences in species-level phylotypes, and create a curated 16S rRNA based taxonomy for common feline oral bacteria. Clone libraries were produced using "universal" and phylum-selective PCR primers and DNA from pooled subgingival plaque from healthy and periodontally diseased cats. Bacteria in subgingival samples were also cultivated to obtain isolates. Full-length 16S rDNA sequences were determined for clones and isolates that represent 171 feline oral taxa. A provisional curated taxonomy was developed based on the position of each taxon in 16S rRNA phylogenetic trees. The feline oral microbiome curated taxonomy and 16S rRNA gene reference set will allow investigators to refer to precisely defined bacterial taxa. A provisional name such as "Propionibacterium sp. feline oral taxon FOT-327" is an anchor to which clone, strain or GenBank names or accession numbers can point. Future next-generation-sequencing studies of feline oral bacteria will be able to map reads to taxonomically curated full-length 16S rRNA gene sequences.

  10. A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology

    Science.gov (United States)

    Adams, S. E.; Arnold, D.; Murphy, B.; Carroll, P.; Green, A. K.; Smith, A. M.; Marsh, P. D.; Chen, T.; Marriott, R. E.; Brading, M. G.

    2017-01-01

    The numerous species that make up the oral microbiome are now understood to play a key role in establishment and maintenance of oral health. The ability to taxonomically identify community members at the species level is important to elucidating its diversity and association to health and disease. We report the overall ecological effects of using a toothpaste containing enzymes and proteins compared to a control toothpaste on the plaque microbiome. The results reported here demonstrate that a toothpaste containing enzymes and proteins can augment natural salivary defences to promote an overall community shift resulting in an increase in bacteria associated with gum health and a concomitant decrease in those associated with periodontal disease. Statistical analysis shows significant increases in 12 taxa associated with gum health including Neisseria spp. and a significant decrease in 10 taxa associated with periodontal disease including Treponema spp. The results demonstrate that a toothpaste containing enzymes and proteins can significantly shift the ecology of the oral microbiome (at species level) resulting in a community with a stronger association to health. PMID:28240240

  11. Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae.

    Science.gov (United States)

    Kaltenpoth, Martin; Steiger, Sandra

    2014-03-01

    Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae--specifically within the Nicrophorinae--both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation

  12. The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals

    Directory of Open Access Journals (Sweden)

    Jordan E. Bisanz

    2016-06-01

    Full Text Available Background. A loss of mucosal tolerance to the resident microbiome has been postulated in the aetiopathogenesis of spondyloarthritis, thus the purpose of these studies was to investigate microbial communities that colonise the oral cavity of patients with axial spondyloarthritis (AxSpA and to compare these with microbial profiles of a matched healthy population. Methods. Thirty-nine participants, 17 patients with AxSpA and 22 age and gender-matched disease-free controls were recruited to the study. For patients with AxSpA, disease activity was assessed using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI. All participants underwent a detailed dental examination to assess oral health, including the presence of periodontal disease assessed using probing pocket depth (PPD. Plaque samples were obtained and their bacterial populations were profiled using Ion Torrent sequencing of the V6 region of the 16S rRNA gene. Results.Patients with AxSpA had active disease (BASDAI 4.1 ± 2.1 [mean ± SD], and a significantly greater prevalence of periodontitis (PPD ≥ 4 mm at ≥4 sites than controls. Bacterial communities did not differ between the two groups with multiple metrics of α and β diversity considered. Analysis of operational taxonomic units (OTUs and higher levels of taxonomic assignment did not provide strong evidence of any single taxa associated with AxSpA in the subgingival plaque. Discussion. Although 16S rRNA gene sequencing did not identify specific bacterial profiles associated with AxSpA, there remains the potential for the microbiota to exert functional and metabolic influences in the oral cavity which could be involved in the pathogenesis of AxSpA.

  13. Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry

    Science.gov (United States)

    Nallanchakravarthula, Srivathsa; Mahmood, Shahid; Alström, Sadhna; Finlay, Roger D.

    2014-01-01

    Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar. PMID:25347069

  14. Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry.

    Science.gov (United States)

    Nallanchakravarthula, Srivathsa; Mahmood, Shahid; Alström, Sadhna; Finlay, Roger D

    2014-01-01

    Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

  15. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Directory of Open Access Journals (Sweden)

    Sang Hu Kim

    2015-11-01

    Full Text Available The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1 with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from

  16. Translating the human microbiome

    NARCIS (Netherlands)

    Brown, J.; Vos, de W.M.; Distefano, P.S.; Doré, J.; Huttenhower, C.; Knight, R.; Lawley, T.D.; Raes, J.; Turnbaugh, P.

    2013-01-01

    Over the past decade, an explosion of descriptive analyses from initiatives, such as the Human Microbiome Project (HMP) and the MetaHIT project, have begun to delineate the human microbiome. Inhabitants of the intestinal tract, nasal passages, oral cavities, skin, gastrointestinal tract and urogenit

  17. Translating the human microbiome

    NARCIS (Netherlands)

    Brown, J.; Vos, de W.M.; Distefano, P.S.; Doré, J.; Huttenhower, C.; Knight, R.; Lawley, T.D.; Raes, J.; Turnbaugh, P.

    2013-01-01

    Over the past decade, an explosion of descriptive analyses from initiatives, such as the Human Microbiome Project (HMP) and the MetaHIT project, have begun to delineate the human microbiome. Inhabitants of the intestinal tract, nasal passages, oral cavities, skin, gastrointestinal tract and urogenit

  18. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J

    2015-01-19

    The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

  19. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.

    2015-01-01

    The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

  20. N-acetylglucosamine increases symptoms and fungal burden in a murine model of oral candidiasis.

    Science.gov (United States)

    Ishijima, Sanae A; Hayama, Kazumi; Takahashi, Miki; Holmes, Ann R; Cannon, Richard D; Abe, Shigeru

    2012-04-01

    The amino sugar N-acetylglucosamine (GlcNAc) is an in vitro inducer of the hyphal mode of growth of the opportunistic pathogen Candida albicans. The development of hyphae by C. albicans is considered to contribute to the pathogenesis of mucosal oral candidiasis. GlcNAc is also a commonly used nutritional supplement for the self-treatment of conditions such as arthritis. To date, no study has investigated whether ingestion of GlcNAc has an effect on the in vivo growth of C. albicans or the pathogenesis of a C. albicans infection. Using a murine model of oral candidiasis, we have found that administration of GlcNAc, but not glucose, increased oral symptoms of candidiasis and fungal burden. Groups of mice were given GlcNAc in either water or in a viscous carrier, i.e., 1% methylcellulose. There was a dose-dependent relationship between GlcNAc concentration and the severity of oral symptoms. Mice given the highest dose of GlcNAc, 45.2 mM, also showed a significant increase in fungal burden, and increased histological evidence of infection compared to controls given water alone. We propose that ingestion of GlcNAc, as a nutritional supplement, may have an impact on oral health in people susceptible to oral candidiasis.

  1. The oral microbiome of denture wearers is influenced by levels of natural dentition

    NARCIS (Netherlands)

    L.E. O'Donnell; D. Robertson; C.J. Nile; L.J. Cross; M. Riggio; A. Sherriff; D. Bradshaw; M. Lambert; J. Malcolm; M.J. Buijs; E. Zaura; W. Crielaard; B.W. Brandt; G. Ramage

    2015-01-01

    Objectives The composition of dental plaque has been well defined, whereas currently there is limited understanding of the composition of denture plaque and how it directly influences denture related stomatitis (DS). The aims of this study were to compare the microbiomes of denture wearers, and to u

  2. Structural and functional probing of PorZ, an essential bacterial surface component of the type-IX secretion system of human oral-microbiomic Porphyromonas gingivalis

    DEFF Research Database (Denmark)

    Lasica, Anna M; Goulas, Theodoros; Mizgalska, Danuta;

    2016-01-01

    Porphyromonas gingivalis is a member of the human oral microbiome abundant in dysbiosis and implicated in the pathogenesis of periodontal (gum) disease. It employs a newly described type-IX secretion system (T9SS) for secretion of virulence factors. Cargo proteins destined for secretion through T...

  3. Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome.

    Science.gov (United States)

    Brooks, J Paul; Edwards, David J; Blithe, Diana L; Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Strauss, Jerome F; Buck, Gregory A; Jefferson, Kimberly K

    2017-04-01

    Prior studies suggest that the composition of the vaginal microbiome may positively or negatively affect susceptibility to sexually transmitted infections (STIs) and bacterial vaginosis (BV). Some female hormonal contraceptive methods also appear to positively or negatively influence STI transmission and BV. Therefore, changes in the vaginal microbiome that are associated with different contraceptive methods may explain, in part, effects on STI transmission and BV. We performed a retrospective study of 16S rRNA gene survey data of vaginal samples from a subset of participants from the Human Vaginal Microbiome Project at Virginia Commonwealth University. The subset included 682 women who reported using a single form of birth control that was condoms, combined oral contraceptives (COCs), depot medroxyprogesterone acetate (DMPA) or the levonorgestrel-releasing intrauterine system (LNG-IUS). Women using COCs [adjusted odds ratio (aOR) 0.29, 95% confidence interval (CI) 0.13-0.64] and DMPA (aOR 0.34, 95% CI 0.13-0.89), but not LNG-IUS (aOR 1.55, 95% CI 0.72-3.35), were less likely to be colonized by BV-associated bacteria relative to women who used condoms. Women using COCs (aOR 1.94, 95% CI 1.25-3.02) were more likely to be colonized by beneficial H2O2-producing Lactobacillus species compared with women using condoms, while women using DMPA (aOR 1.09, 95% CI 0.63-1.86) and LNG-IUS (aOR 0.74, 95% CI 0.48-1.15) were not. Use of COCs is significantly associated with increased vaginal colonization by healthy lactobacilli and reduced BV-associated taxa. COC use may positively influence gynecologic health through an increase in healthy lactobacilli and a decrease in BV-associated bacterial taxa. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules.

    Science.gov (United States)

    Edlund, Anna; Garg, Neha; Mohimani, Hosein; Gurevich, Alexey; He, Xuesong; Shi, Wenyuan; Dorrestein, Pieter C; McLean, Jeffrey S

    2017-01-01

    Recent research indicates that the human microbiota play key roles in maintaining health by providing essential nutrients, providing immune education, and preventing pathogen expansion. Processes underlying the transition from a healthy human microbiome to a disease-associated microbiome are poorly understood, partially because of the potential influences from a wide diversity of bacterium-derived compounds that are illy defined. Here, we present the analysis of peptidic small molecules (SMs) secreted from bacteria and viewed from a temporal perspective. Through comparative analysis of mass spectral profiles from a collection of cultured oral isolates and an established in vitro multispecies oral community, we found that the production of SMs both delineates a temporal expression pattern and allows discrimination between bacterial isolates at the species level. Importantly, the majority of the identified molecules were of unknown identity, and only ~2.2% could be annotated and classified. The catalogue of bacterially produced SMs we obtained in this study reveals an undiscovered molecular world for which compound isolation and ecosystem testing will facilitate a better understanding of their roles in human health and disease. IMPORTANCE Metabolomics is the ultimate tool for studies of microbial functions under any specific set of environmental conditions (D. S. Wishart, Nat Rev Drug Discov 45:473-484, 2016, https://doi.org/10.1038/nrd.2016.32). This is a great advance over studying genes alone, which only inform about metabolic potential. Approximately 25,000 compounds have been chemically characterized thus far; however, the richness of metabolites such as SMs has been estimated to be as high as 1 × 10(30) in the biosphere (K. Garber, Nat Biotechnol 33:228-231, 2015, https://doi.org/10.1038/nbt.3161). Our classical, one-at-a-time activity-guided approach to compound identification continues to find the same known compounds and is also incredibly tedious, which

  5. Comparison of efficacy of alternative medicine with allopathy in treatment of oral fungal infection.

    Science.gov (United States)

    Maghu, Sahil; Desai, Vela D; Sharma, Rajeev

    2016-01-01

    This clinical study assessed and compared the efficacy of tea tree oil (TTO), an alternative form of medicine, with clotrimazole (i.e., allopathy) and a conservative form of management in the treatment of oral fungal infection. In this interventional, observational, and comparative study, we enrolled 36 medically fit individuals of both sexes who were aged 20-60 years old. The participants were randomly assigned to three groups. Group I was given TTO (0.25% rinse) as medicament, Group II was given clotrimazole, and Group III was managed with conservative treatment. The results were analyzed from the clinical evaluation of lesions, changes in four most common clinical parameters of lesions, and subjective symptoms on periodic follow-up. Based on the results, the percentage efficiency of the two groups were taken and compared through a bar graph on the scale of 1. No toxicity to TTO was reported. Group I (TTO) was found to be more efficient than the other two groups, as changes in four parameter indices of lesions were noted, and results for all three groups were compared on a percentage basis. The study concluded that TTO, being a natural product, is a better nontoxic modality compared to clotrimazole, in the treatment of oral fungal infection and has a promising future for its potential application in oral health products.

  6. The microbiome and the lung.

    Science.gov (United States)

    Cui, Lijia; Morris, Alison; Huang, Laurence; Beck, James M; Twigg, Homer L; von Mutius, Erika; Ghedin, Elodie

    2014-08-01

    Investigation of the human microbiome has become an important field of research facilitated by advances in sequencing technologies. The lung, which is one of the latest body sites being explored for the characterization of human-associated microbial communities, has a microbiome that is suspected to play a substantial role in health and disease. In this review, we provide an overview of the basics of microbiome studies. Challenges in the study of the lung microbiome are highlighted, and further attention is called to the optimization and standardization of methodologies to explore the role of the lung microbiome in health and disease. We also provide examples of lung microbial communities associated with disease or infection status and discuss the role of fungal species in the lung. Finally, we review studies demonstrating that the environmental microbiome can influence lung health and disease, such as the finding that the diversity of microbial exposure correlates inversely with the development of childhood asthma.

  7. Variation in fungal microbiome (mycobiome) and aflatoxins during simulated storage of in-shell peanuts and peanut kernels

    Science.gov (United States)

    Xing, Fuguo; Ding, Ning; Liu, Xiao; Selvaraj, Jonathan Nimal; Wang, Limin; Zhou, Lu; Zhao, Yueju; Wang, Yan; Liu, Yang

    2016-01-01

    Internal transcribed spacer 2 (ITS2) sequencing was used to characterize the peanut mycobiome during 90 days storage at five conditions. The fungal diversity in in-shell peanuts was higher with 110 operational taxonomic units (OTUs) and 41 genera than peanut kernels (91 OTUs and 37 genera). This means that the micro-environment in shell is more suitable for maintaining fungal diversity. At 20–30 d, Rhizopus, Eurotium and Wallemia were predominant in in-shell peanuts. In peanut kernels, Rhizopus (>30%) and Eurotium (>20%) were predominant at 10–20 d and 30 d, respectively. The relative abundances of Rhizopus, Eurotium and Wallemia were higher than Aspergillus, because they were xerophilic and grew well on substrates with low water activity (aw). During growth, they released metabolic water, thereby favoring the growth of Aspergillus. Therefore, from 30 to 90 d, the relative abundance of Aspergillus increased while that of Rhizopus, Eurotium and Wallemia decreased. Principal Coordinate Analysis (PCoA) revealed that peanuts stored for 60–90 days and for 10–30 days clustered differently from each other. Due to low aw values (0.34–0.72) and low levels of A. flavus, nine of 51 samples were contaminated with aflatoxins. PMID:27180614

  8. Evaluating the potential of cubosomal nanoparticles for oral delivery of amphotericin B in treating fungal infection

    Directory of Open Access Journals (Sweden)

    Yang Z

    2014-01-01

    Full Text Available Zhiwen Yang,1,3 Meiwan Chen,2 Muhua Yang,1 Jian Chen,1 Weijun Fang,1 Ping Xu11Department of Pharmacy, Songjiang Hospital Affiliated The First People's Hospital, Shanghai Jiao Tong University, Shanghai, 2State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 3Shanghai Songjiang Hospital Affiliated Nanjing Medical University, Nanjing, People's Republic of ChinaAbstract: The oral administration of amphotericin B (AmB has a major drawback of poor bioavailability. The aim of this study was to investigate the potential of glyceryl monoolein (GMO cubosomes as lipid nanocarriers to improve the oral efficacy of AmB. Antifungal efficacy was determined in vivo in rats after oral administration, to investigate its therapeutic use. The human colon adenocarcinoma cell line (Caco-2 was used in vitro to evaluate transport across a model of the intestinal barrier. In vivo antifungal results showed that AmB, loaded in GMO cubosomes, could significantly enhance oral efficacy, compared against Fungizone®, and that during a 2 day course of dosage 10 mg/kg the drug reached effective therapeutic concentrations in renal tissue for treating fungal infections. In the Caco-2 transport studies, GMO cubosomes resulted in a significantly larger amount of AmB being transported into Caco-2 cells, via both clathrin- and caveolae-mediated endocytosis, but not macropinocytosis. These results suggest that GMO cubosomes, as lipid nanovectors, could facilitate the oral delivery of AmB.Keywords: glyceryl monoolein cubosomes, oral delivery, amphotericin B, antifungal activity, absorption mechanism

  9. Characterisation of the human oral microbiome in patients with coronary artery disease using next-generation sequencing of 16SrRNA amplicons

    Directory of Open Access Journals (Sweden)

    Thangam Menon

    2017-01-01

    Full Text Available Introduction: Oral health is suspected to be linked to heart disease since species of bacteria that cause periodontitis and dental caries have been found in the atherosclerotic plaque in arteries in the heart. Objectives: The aim of this study was to characterize the oral microbiome in patients with coronary artery disease (CAD and in a patient with dental caries (DC without any clinical symptoms of CAD. Methods: DNA was extracted from the oral swabs collected from the patients and sequencing was performed by next generation sequencing method using Illumina (MiSeq platform. The resulting sequencing data set was analysed using QIIME. Results: A total of 31 phyla were found in all the samples. The predominant phylum found in both CAD and DC was Firmicutes (46.09% & 38.98%, Proteobacteria (17.73% & 9.79%, Fusobacteria (13.44% & 17.95%, Bacteroidetes (11.82% & 22.73%, Actinobacteria (8.33% & 7.71% and TM7 (2.25% & 2.71%. We found a similarity in the bacterial diversity in the two groups of patients. Conclusion: A comparison of the oral microbiome in patients with CAD and DC shows a similarity in the composition of the oral microbiota with variations in the proportion of a few genera.

  10. Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils.

    Science.gov (United States)

    Dai, Zhongmin; Hu, Jiajie; Xu, Xingkun; Zhang, Lujun; Brookes, Philip C; He, Yan; Xu, Jianming

    2016-11-08

    Sensitive responses among bacterial and fungal communities to pyrogenic organic matter (PyOM) (biochar) addition in rhizosphere and bulk soils are poorly understood. We conducted a pot experiment with manure and straw PyOMs added to an acidic paddy soil, and identified the sensitive "responders" whose relative abundance was significantly increased/decreased among the whole microbial community following PyOM addition. Results showed that PyOMs significantly (p rhizosphere soil was larger than in bulk soil, regardless of PyOM types and microbial domains, indicating the microbial community in rhizosphere soil was sensitive to PyOM addition than bulk soil. The significant increased root biomass and length caused by PyOM addition, associated with physiological processes, e.g. C exudates secretion, likely favored more sensitive responders in rhizosphere soil than in bulk soil. Our study identified the responders at fine taxonomic resolution in PyOM amended soils, improved the understanding of their ecological phenomena associated with PyOM addition, and examined their interactions with plant roots.

  11. Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques

    Energy Technology Data Exchange (ETDEWEB)

    McLean, Jeffrey S.; Fansler, Sarah J.; Majors, Paul D.; Mcateer, Kathleen; Allen, Lisa Z.; Shirtliff, Mark E.; Lux, Renate; Shi, Wenyuan

    2012-03-05

    Many human microbial infectious diseases including dental caries are polymicrobial in nature and how these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral microbes have been characterized in vitro, their physiology in vivo in the presence of the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these oral species remain uncultivated to date and little is known except their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated microorganisms will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a novel combination of in vivo Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for temporal monitoring of carbohydrate utilization, organic acid production and identification of metabolically active and inactive bacterial species.

  12. Variation in fungal microbiome (mycobiome and aflatoxin in stored in-shell peanuts at four different areas of China

    Directory of Open Access Journals (Sweden)

    Ning eDing

    2015-10-01

    Full Text Available The contamination of peanuts with Aspergillus sp. and subsequently aflatoxins is considered to be one of the most serious safety problems in the world. Mycobiome in peanuts is critical for aflatoxin production and food safety. To evaluate the biodiversity and ecological characteristics of whole communities in stored peanuts, the barcoded Illumina paired-end sequencing (BIPES of the internal transcribed spacer 2 (ITS2 region of rDNA was used to characterize the peanut mycobiome monthly over a period of one year at four main peanut grown areas i.e Liaoning (LN, North East, Shandong (SD, East, Hubei (HB, Central and Guangdong (GD, South provinces. The fungal diversity of peanuts stored in SD was the highest with 98 OTUs and 43 genera, followed by LN, HB and GD. In peanuts stored in SD, Rhizopus, Emericella and Clonostachys were predominant. In peanuts from LN, Penicillium, Eurotium and Clonostachys were abundant. In peanuts from HB, Penicillium, Eurotium and Aspergillus were higher. In GD peanuts, Eurotium, Aspergillus and Emericella were mainly seen. The abundances of Aspergillus in LN, SD, HB and GD were 0.53%, 6.29%, 10.86% and 25.75%, respectively. From the North of China to the South, that increased over the latitude, suggesting that the higher temperature and relative humidity might increase the risk of peanuts contaminated with Aspergillus and aflatoxins. During the storage, Aspergillus levels were higher at 7-12 months than in 0-6 months, suggesting that the risk increases over storage time. At 7-10 months, AFB1 was higher in four areas, while declined further. The reduction of AFB1 might be attributed to the inhibition and degradation of AFB1 by A. niger or to the combination with the compounds of peanuts. This is the first study that identified the mycobiome and its variation in stored peanuts using ITS2 sequencing technology, and provides the basis for a detailed characterization of whole mycobiome in peanuts.

  13. Development of SYN-004, an oral beta-lactamase treatment to protect the gut microbiome from antibiotic-mediated damage and prevent Clostridium difficile infection.

    Science.gov (United States)

    Kaleko, Michael; Bristol, J Andrew; Hubert, Steven; Parsley, Todd; Widmer, Giovanni; Tzipori, Saul; Subramanian, Poorani; Hasan, Nur; Koski, Perrti; Kokai-Kun, John; Sliman, Joseph; Jones, Annie; Connelly, Sheila

    2016-10-01

    The gut microbiome, composed of the microflora that inhabit the gastrointestinal tract and their genomes, make up a complex ecosystem that can be disrupted by antibiotic use. The ensuing dysbiosis is conducive to the emergence of opportunistic pathogens such as Clostridium difficile. A novel approach to protect the microbiome from antibiotic-mediated dysbiosis is the use of beta-lactamase enzymes to degrade residual antibiotics in the gastrointestinal tract before the microflora are harmed. Here we present the preclinical development and early clinical studies of the beta-lactamase enzymes, P3A, currently referred to as SYN-004, and its precursor, P1A. Both P1A and SYN-004 were designed as orally-delivered, non-systemically available therapeutics for use with intravenous beta-lactam antibiotics. SYN-004 was engineered from P1A, a beta-lactamase isolated from Bacillus licheniformis, to broaden its antibiotic degradation profile. SYN-004 efficiently hydrolyses penicillins and cephalosporins, the most widely used IV beta-lactam antibiotics. In animal studies, SYN-004 degraded ceftriaxone in the GI tract of dogs and protected the microbiome of pigs from ceftriaxone-induced changes. Phase I clinical studies demonstrated SYN-004 safety and tolerability. Phase 2 studies are in progress to assess the utility of SYN-004 for the prevention of antibiotic-associated diarrhea and Clostridium difficile disease.

  14. Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

    Science.gov (United States)

    Wang, Jack T H; Daly, Joshua N; Willner, Dana L; Patil, Jayee; Hall, Roy A; Schembri, Mark A; Tyson, Gene W; Hugenholtz, Philip

    2015-05-01

    Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity-the oral microbiome-by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012-2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE (p research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.

  15. Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy.

    Directory of Open Access Journals (Sweden)

    Saad S Al-Shehri

    Full Text Available Xanthine oxidase (XO is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2. Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined.Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively were ten-fold higher than in adult saliva (2.1 and 1.7 μM. Fresh breastmilk contained 27.3 ± 12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2-449 compared to adults (620 U/L, 48-1348, while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns.During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral-and hence gut-microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity.

  16. Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy.

    Science.gov (United States)

    Al-Shehri, Saad S; Knox, Christine L; Liley, Helen G; Cowley, David M; Wright, John R; Henman, Michael G; Hewavitharana, Amitha K; Charles, Bruce G; Shaw, Paul N; Sweeney, Emma L; Duley, John A

    2015-01-01

    Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined. Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3 ± 12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2-449) compared to adults (620 U/L, 48-1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns. During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral-and hence gut-microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity.

  17. Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy

    Science.gov (United States)

    Al-Shehri, Saad S.; Knox, Christine L.; Liley, Helen G.; Cowley, David M.; Wright, John R.; Henman, Michael G.; Hewavitharana, Amitha K.; Charles, Bruce G.; Shaw, Paul N.; Sweeney, Emma L.; Duley, John A.

    2015-01-01

    Introduction Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined. Results Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3±12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2–449) compared to adults (620 U/L, 48–1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns. Discussion and Conclusion During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral–and hence gut–microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity. PMID:26325665

  18. Utilization of posaconazole oral suspension or delayed-released tablet salvage treatment for invasive fungal infection.

    Science.gov (United States)

    Kim, Jong Hun; Benefield, Russell J; Ditolla, Kali

    2016-11-01

    Posaconazole may be useful for salvage treatment (ST) for invasive fungal infections (IFIs). The aim of this study was to evaluate the efficacy of posaconazole ST with either posaconazole oral suspension (SUS) or delayed-released tablet (TAB) in patients with IFI. A retrospective review of patients who received posaconazole ST for IFI at the University of Utah Health Sciences Center between December 2007 and March 2014 was conducted. A total of 14 episodes of posaconazole ST for proven (9 episodes) and probable (5 episodes) IFI were identified in 14 patients. The median age was 54 years and the majority of patients (64.3%) had underlying haematological diseases. Posaconazole SUS and TAB were used in 11 episodes and 3 episodes respectively. The duration of posaconazole ST ranged from 28 to 370 days with a median of 65 days. Posaconazole ST with TAB achieved favourable serum posaconazole trough concentrations (median 1.4 μg mL(-1) ) compared to posaconazole SUS (median 1.0 μg mL(-1) ). The overall clinical success rate with posaconazole ST was 71.4% (10 of 14 episodes). One patient died of progression of IFI. Adverse events were noted in two patients. Posaconazole SUS or TAB may be used effectively for IFI ST.

  19. Factors influencing oral health in patients during cancer treatment; with emphasis on the relationship between the oral microbiome and oral mucositis

    NARCIS (Netherlands)

    Laheij, A.M.G.A.

    2014-01-01

    The consequences of cancer therapy for oral health were studied. The effects of irradiation to the head and neck area for the protein composition of parotid saliva were mapped. It was found that irradiation to the head and neck area likely altered the gland tissues resulting in a change in the prote

  20. Factors influencing oral health in patients during cancer treatment; with emphasis on the relationship between the oral microbiome and oral mucositis

    NARCIS (Netherlands)

    Laheij, A.M.G.A.

    2014-01-01

    The consequences of cancer therapy for oral health were studied. The effects of irradiation to the head and neck area for the protein composition of parotid saliva were mapped. It was found that irradiation to the head and neck area likely altered the gland tissues resulting in a change in the

  1. Molecular phylogeny, diversity, community structure, and plant growth promoting properties of fungal endophytes associated with the corms of saffron plant: An insight into the microbiome of Crocus sativus Linn.

    Science.gov (United States)

    Wani, Zahoor Ahmed; Mirza, Dania Nazir; Arora, Palak; Riyaz-Ul-Hassan, Syed

    2016-12-01

    A total of 294 fungal endophytes were isolated from the corms of Crocus sativus at two stages of crocus life cycle collected from 14 different saffron growing sites in Jammu and Kashmir (J & K) State, India. Molecular phylogeny assigned them into 36 distinct internal transcribed spacer (ITS) genotypes which spread over 19 genera. The diversity of endophytes was higher at the dormant than at the vegetative stage. The Saffron microbiome was dominated by Phialophora mustea and Cadophora malorum, both are dark septate endophytes (DSEs). Some endophytes were found to possess antimicrobial properties that could be helpful for the host in evading the pathogens. These endophytes generally produced significant quantities of indole acetic acid (IAA) as well. However, thirteen of the endophytic taxa were found to cause corm rot in the host with different levels of severity under in vitro as well as in vivo conditions. This is the first report of community structure and biological properties of fungal endophytes associated with C. sativus, which may eventually help us to develop agro-technologies, based on plant-endophyte interactions for sustainable cultivation of saffron. The endophytes preserved ex situ, in this study, may also yield bioactive natural products for pharmacological and industrial applications.

  2. The effect of fixed orthodontic appliances and fluoride mouthwash on the oral microbiome of adolescents: a randomized controlled clinical trial

    NARCIS (Netherlands)

    Koopman, J.E.; van der Kaaij, N.C.W.; Buijs, M.J.; Elyassi, Y.; van der Veen, M.H.; Crielaard, W.; ten Cate, J.M.; Zaura, E.

    2015-01-01

    While the aesthetic effect of orthodontic treatment is clear, the knowledge on how it influences the oral microbiota and the consequential effects on oral health are limited. In this randomized controlled clinical trial we investigated the changes introduced in the oral ecosystem, during and after

  3. Microbiome in parturition and preterm birth.

    Science.gov (United States)

    Mysorekar, Indira U; Cao, Bin

    2014-01-01

    Preterm parturition is a one of the most significant global maternal-child health problem. In recent years, there has been an explosion in reports on a role for microbiomes (i.e., a microbial biomass) on a plethora of physiologic and pathologic human conditions. This review aims to describe our current understanding of the microbiome and its impact on parturition, with particular emphasis on preterm birth. We will focus on the roles of vaginal and oral mucosal microbiomes in premature parturition and describe the state-of-the-art methodologies used in microbiome studies. Next, we will present new studies on a potential microbiome in the placenta and how it may affect pregnancy outcomes. Finally, we will propose that host genetic factors can perturb the normal "pregnancy microbiome" and trigger adverse pregnancy outcomes. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  4. Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.

    Directory of Open Access Journals (Sweden)

    Jeffrey S McLean

    Full Text Available BACKGROUND: Many human microbial infectious diseases including dental caries are polymicrobial in nature. How these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS with RNA and DNA based Stable Isotope Probing (SIP to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. METHODOLOGY/PRINCIPAL FINDINGS: Supragingival plaque samples from caries-free children incubated with (13C-substrates under imposed healthy (buffered, pH 7 and diseased states (pH 5.5 and pH 4.5 produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. CONCLUSIONS/SIGNIFICANCE: Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within

  5. The role of the cutaneous microbiome in skin cancer: lessons learned from the gut.

    Science.gov (United States)

    Yu, Yang; Champer, Jackson; Beynet, David; Kim, Jenny; Friedman, Adam J

    2015-05-01

    The human microbiome has recently gained prominence as a major factor in health and disease. Here we review the literature regarding the microbiome and cancer and suggest how the microbiome may be manipulated for improved health outcomes. The gut microbiome has been relatively well studied, and the mechanisms of how it may increase or decrease the risk of certain cancers may apply to the skin microbiome. Additionally, the gut microbiome may directly impact the risk of cancer in the skin and other organs by promoting systemic inflammation. The skin microbiome itself is as diverse as the gut microbiome, but research has just begun to unravel its influence on the host. Like the gut microbiome, it affects the risk for several diseases, including cancer. By using healthpromoting strains from the microbiome in oral or topical probiotics, it may be possible to reduce the risk of skin cancer and perhaps even increase the likelihood of successful treatment.

  6. Plant and fungal food components with potential activity on the development of microbial oral diseases

    NARCIS (Netherlands)

    Daglia, M.; Papetti, A.; Mascherpa, D.; Grisoli, P.; Giusto, G.; Lingström, P.; Pratten, J.; Signoretto, C.; Spratt, D.A.; Wilson, M.; Zaura, E.; Gazzani, G.

    2011-01-01

    This paper reports the content in macronutrients, free sugars, polyphenols, and inorganic ions, known to exert any positive or negative action on microbial oral disease such as caries and gingivitis, of seven food/beverages (red chicory, mushroom, raspberry, green and black tea, cranberry juice, dar

  7. Human microbiomics

    OpenAIRE

    Rajendhran, J.; P. Gunasekaran

    2010-01-01

    The sequencing of the human genome has driven the study of human biology in a significant way and enabled the genome-wide study to elucidate the molecular basis of complex human diseases. Recently, the role of microbiota on human physiology and health has received much attention. The influence of gut microbiome (the collective genomes of the gut microbiota) in obesity has been demonstrated, which may pave the way for new prophylactic and therapeutic strategies such as bacteriotherapy. The sig...

  8. Chapter 12: Human microbiome analysis.

    Directory of Open Access Journals (Sweden)

    Xochitl C Morgan

    Full Text Available Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.

  9. Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome

    Directory of Open Access Journals (Sweden)

    Jack T.H. Wang

    2015-02-01

    Full Text Available Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE. The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity—the oral microbiome—by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012–2013 revealed significantly higher student confidence in laboratory skills following the completion of the ALURE (p < 0.05 using the Mann-Whitney U-test. Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students. Editor's Note:The ASM advocates that students must successfully demonstrate the ability to explain and practice safe laboratory techniques

  10. Plant and Fungal Food Components with Potential Activity on the Development of Microbial Oral Diseases

    Directory of Open Access Journals (Sweden)

    Maria Daglia

    2011-01-01

    Full Text Available This paper reports the content in macronutrients, free sugars, polyphenols, and inorganic ions, known to exert any positive or negative action on microbial oral disease such as caries and gingivitis, of seven food/beverages (red chicory, mushroom, raspberry, green and black tea, cranberry juice, dark beer. Tea leaves resulted the richest material in all the detected ions, anyway tea beverages resulted the richest just in fluoride. The highest content in zinc was in chicory, raspberry and mushroom. Raspberry is the richest food in strontium and boron, beer in selenium, raspberry and mushroom in copper. Beer, cranberry juice and, especially green and black tea are very rich in polyphenols, confirming these beverages as important sources of such healthy substances. The fractionation, carried out on the basis of the molecular mass (MM, of the water soluble components occurring in raspberry, chicory, and mushroom extracts (which in microbiological assays revealed the highest potential action against oral pathogens, showed that both the high and low MM fractions are active, with the low MM fractions displaying the highest potential action for all the fractionated extracts. Our findings show that more compounds that can play a different active role occur in these foods.

  11. Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study.

    Directory of Open Access Journals (Sweden)

    Philip K Frykman

    Full Text Available Development of potentially life-threatening enterocolitis is the most frequent complication in children with Hirschsprung disease (HSCR, even after definitive corrective surgery. Intestinal microbiota likely contribute to the etiology of enterocolitis, so the aim of this study was to compare the fecal bacterial and fungal communities of children who developed Hirschsprung-associated enterocolitis (HAEC with HSCR patients who had never had enterocolitis. Eighteen Hirschsprung patients who had completed definitive surgery were enrolled: 9 had a history of HAEC and 9 did not. Fecal DNA was isolated and 16S and ITS-1 regions sequenced using Next Generation Sequencing and data analysis for species identification. The HAEC group bacterial composition showed a modest reduction in Firmicutes and Verrucomicrobia with increased Bacteroidetes and Proteobacteria compared with the HSCR group. In contrast, the fecal fungi composition of the HAEC group showed marked reduction in diversity with increased Candida sp., and reduced Malassezia and Saccharomyces sp. compared with the HSCR group. The most striking finding within the HAEC group is that the Candida genus segregated into "high burden" patients with 97.8% C. albicans and 2.2% C. tropicalis compared with "low burden" patients 26.8% C. albicans and 73% C. tropicalis. Interestingly even the low burden HAEC group had altered Candida community structure with just two species compared to more diverse Candida populations in the HSCR patients. This is the first study to identify Candida sp. as potentially playing a role in HAEC either as expanded commensal species as a consequence of enterocolitis (or treatment, or possibly as pathobioants contributing to the pathogenesis of HAEC. These findings suggest a dysbiosis in the gut microbial ecosystem of HAEC patients, such that there may be dominance of fungi and bacteria predisposing patients to development of HAEC.

  12. Exploring preterm birth as a polymicrobial disease: An overview of the uterine microbiome.

    Directory of Open Access Journals (Sweden)

    Matthew S Payne

    2014-11-01

    Full Text Available Infection is the leading cause of preterm birth. A focus of many studies over the past decade has been to characterise microorganisms present in the uterine cavity and document any association with negative pregnancy outcome. A range of techniques have been used to achieve this, including microbiological culture and targeted polymerase chain reaction assays, and more recently, microbiome-level analyses involving either conserved, phylogenetically informative genes such as the bacterial 16S rRNA gene or whole shotgun metagenomic sequencing. These studies have contributed vast amounts of data towards characterisation of the uterine microbiome, specifically that present in the amniotic fluid, fetal membranes and placenta. However, an overwhelming emphasis has been placed on the bacterial microbiome, with far less data produced on the viral and fungal/yeast microbiomes. With numerous studies now referring to preterm birth as a polymicrobial condition, there is the need to investigate the role of viruses and fungi in more detail and in particular, look for associations between colonisation with these microorganisms and bacteria in the same samples. Although the major pathway by which microorganisms are believed to colonise the uterine cavity is vertical ascension from the vagina, numerous studies are now emerging suggesting haematogenous transfer of oral microbiota to the uterine cavity. Evidence of this has been produced in mouse models and although DNA-based evidence in humans appears convincing in some aspects, use of methodologies that only detect viable cells as opposed to lysed cells and extracellular DNA are needed to clarify this. Such techniques as RNA analyses and viability PCR are likely to play key roles in the clinical translation of future microbiome-based data, particularly in confined environments such as the uterus, as detection of viable cells plays a key role in diagnosis and treatment of infection.

  13. Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

    National Research Council Canada - National Science Library

    Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jørn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, Zhiheng

    2010-01-01

    .... A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species...

  14. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype

    Science.gov (United States)

    Segal, Leopoldo N.; Clemente, Jose C.; Tsay, Jun-Chieh J.; Koralov, Sergei B.; Keller, Brian C.; Wu, Benjamin G.; Li, Yonghua; Shen, Nan; Ghedin, Elodie; Morris, Alison; Diaz, Phillip; Huang, Laurence; Wikoff, William R.; Ubeda, Carles; Artacho, Alejandro; Rom, William N.; Sterman, Daniel H.; Collman, Ronald G.; Blaser, Martin J.; Weiden, Michael D.

    2016-01-01

    Microaspiration is a common phenomenon in healthy subjects, but its frequency is increased in chronic inflammatory airway diseases, and its role in inflammatory and immune phenotypes is unclear. We have previously demonstrated that acellular bronchoalveolar lavage samples from half of the healthy people examined are enriched with oral taxa (here called pneumotypeSPT) and this finding is associated with increased numbers of lymphocytes and neutrophils in bronchoalveolar lavage. Here, we have characterized the inflammatory phenotype using a multi-omic approach. By evaluating both upper airway and acellular bronchoalveolar lavage samples from 49 subjects from three cohorts without known pulmonary disease, we observed that pneumotypeSPT was associated with a distinct metabolic profile, enhanced expression of inflammatory cytokines, a pro-inflammatory phenotype characterized by elevated Th-17 lymphocytes and, conversely, a blunted alveolar macrophage TLR4 response. The cellular immune responses observed in the lower airways of humans with pneumotypeSPT indicate a role for the aspiration-derived microbiota in regulating the basal inflammatory status at the pulmonary mucosal surface. PMID:27572644

  15. Menopause and the vaginal microbiome.

    Science.gov (United States)

    Muhleisen, Alicia L; Herbst-Kralovetz, Melissa M

    2016-09-01

    For over a century it has been well documented that bacteria in the vagina maintain vaginal homeostasis, and that an imbalance or dysbiosis may be associated with poor reproductive and gynecologic health outcomes. Vaginal microbiota are of particular significance to postmenopausal women and may have a profound effect on vulvovaginal atrophy, vaginal dryness, sexual health and overall quality of life. As molecular-based techniques have evolved, our understanding of the diversity and complexity of this bacterial community has expanded. The objective of this review is to compare the changes that have been identified in the vaginal microbiota of menopausal women, outline alterations in the microbiome associated with specific menopausal symptoms, and define how hormone replacement therapy impacts the vaginal microbiome and menopausal symptoms; it concludes by considering the potential of probiotics to reinstate vaginal homeostasis following menopause. This review details the studies that support the role of Lactobacillus species in maintaining vaginal homeostasis and how the vaginal microbiome structure in postmenopausal women changes with decreasing levels of circulating estrogen. In addition, the associated transformations in the microanatomical features of the vaginal epithelium that can lead to vaginal symptoms associated with menopause are described. Furthermore, hormone replacement therapy directly influences the dominance of Lactobacillus in the microbiota and can resolve vaginal symptoms. Oral and vaginal probiotics hold great promise and initial studies complement the findings of previous research efforts concerning menopause and the vaginal microbiome; however, additional trials are required to determine the efficacy of bacterial therapeutics to modulate or restore vaginal homeostasis.

  16. Hidden fungi, emergent properties: endophytes and microbiomes.

    Science.gov (United States)

    Porras-Alfaro, Andrea; Bayman, Paul

    2011-01-01

    Endophytes are microorganisms that live within plant tissues without causing symptoms of disease. They are important components of plant microbiomes. Endophytes interact with, and overlap in function with, other core microbial groups that colonize plant tissues, e.g., mycorrhizal fungi, pathogens, epiphytes, and saprotrophs. Some fungal endophytes affect plant growth and plant responses to pathogens, herbivores, and environmental change; others produce useful or interesting secondary metabolites. Here, we focus on new techniques and approaches that can provide an integrative understanding of the role of fungal endophytes in the plant microbiome. Clavicipitaceous endophytes of grasses are not considered because they have unique properties distinct from other endophytes. Hidden from view and often overlooked, endophytes are emerging as their diversity, importance for plant growth and survival, and interactions with other organisms are revealed.

  17. COPD and the microbiome.

    Science.gov (United States)

    Mammen, Manoj J; Sethi, Sanjay

    2016-05-01

    Traditional culture techniques confirm that bacteria have an important role in Chronic Obstructive Pulmonary Disease (COPD). In individuals with COPD, acquisition of novel bacterial strains is associated with onset of acute exacerbation of COPD, which leads to further lung dysfunction and enormous health-care costs. Recent study of the human microbiome, the total composite of the bacteria on the human body, posited the microbiome as the last human organ studied, as the microbiome performs a multitude of metabolic functions absent in the human genome. The largest project to study the human microbiome was the National Institutes of Health (NIH) human microbiome project (HMP) started in 2007 to understand the 'normal' microbiome. However due to the presumption that the healthy human lung was sterile, the respiratory tract was not included in that study. The advent of next-generation sequencing technologies has allowed the investigation of the human respiratory microbiome, which revealed that the healthy lung does have a robust microbiome. Subsequent studies in individuals with COPD revealed that the microbiome composition fluctuates with severity of COPD, composition of the individual aero-digestive tract microbiomes, age, during an acute exacerbation of COPD and with the use of steroids and/or antibiotics. Understanding the impact of the microbiome on COPD progression and risk of exacerbation will lead to directed therapies for prevention of COPD progression and exacerbation.

  18. Fungal Sinusitis

    Science.gov (United States)

    ... Marketplace Find an ENT Doctor Near You Fungal Sinusitis Fungal Sinusitis Patient Health Information News media interested ... sinusitis results. There Are Four Types Of Fungal Sinusitis: Mycetoma Fungal Sinusitis produces clumps of spores, a " ...

  19. Soil microbiome transfer method affects microbiome composition, including dominant microorganisms, in a novel environment.

    Science.gov (United States)

    Howard, Mia M; Bell, Terrence H; Kao-Kniffin, Jenny

    2017-06-15

    We show that choice of soil microbiome transfer method, i.e. direct soil transfers and a common soil wash procedure, dramatically influences the microbiome that develops in a new environment, using high-throughput amplicon sequencing of 16S rRNA genes and the fungal internal transcribed spacer (ITS) region. After 3 weeks of incubation in commercial potting mix, microbiomes were most similar to the source soil when a greater volume of initial soil was transferred (5% v/v transfer), and least similar when using a soil wash. Abundant operational taxonomic units were substantially affected by transfer method, suggesting that compounds transferred from the source soil, shifts in biotic interactions, or both, play an important role in their success. © FEMS 2017.

  20. Microbiome and Anticancer Immunosurveillance

    National Research Council Canada - National Science Library

    Zitvogel, Laurence; Ayyoub, Maha; Routy, Bertrand; Kroemer, Guido

    2016-01-01

    ... microbiome affects cancer development. Oncogenic viruses (such as Papilloma virus, the agent responsible for cervical carcinoma), bacteria (exemplified by Helicobacter pylori , the agent respon...

  1. Exercise Attenuates PCB-Induced Changes in the Mouse Gut Microbiome

    OpenAIRE

    2013-01-01

    Background: The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants. Objectives: We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice. Methods: After mice exercised voluntarily for 5 weeks, they were treated by oral gav...

  2. USGS microbiome research

    Science.gov (United States)

    Kellogg, Christina A.; Hopkins, M. Camille

    2017-09-26

    Microbiomes are the communities of microorganisms (for example, bacteria, viruses, and fungi) that live on, in, and around people, plants, animals, soil, water, and the atmosphere. Microbiomes are active in the functioning of diverse ecosystems, for instance, by influencing water quality, nutrient acquisition 
and stress tolerance in plants, and stability of soil and aquatic environments. Microbiome research conducted by the U.S. Geological Survey spans many of our mission areas. Key research areas include water quality, understanding climate effects on soil and permafrost, ecosystem and wildlife health, invasive species, contaminated environments to improve bioremediation, and enhancing energy production. Microbiome research will fundamentally strengthen the ability to address the global challenges of maintaining clean water, ensuring adequate food supply, meeting energy needs, and preserving human and ecosystem health.

  3. Urban Dust Microbiome: Impact on Later Atopy and Wheezing.

    Science.gov (United States)

    Tischer, Christina; Weikl, Fabian; Probst, Alexander J; Standl, Marie; Heinrich, Joachim; Pritsch, Karin

    2016-12-01

    Investigations in urban areas have just begun to explore how the indoor dust microbiome may affect the pathogenesis of asthma and allery. We aimed to investigate the early fungal and bacterial microbiome in house dust with allergic sensitization and wheezing later in childhood. Individual dust samples from 189 homes of the LISAplus birth cohort study were collected shortly after birth from living room floors and profiled for fungal and bacterial microbiome. Fungal and bacterial diversity was assessed with terminal restriction fragment length polymorphism (tRFLP) and defined by Simpson's Diversity Index. Information on wheezing outcomes and covariates until the age of 10 years was obtained by parent questionnaires. Information on specific allergic sensitization was available at child's age 6 and 10 years. Logistic regression and general estimation equation (GEE) models were used to examine the relationship between microbial diversity and health outcomes. Adjusted logistic regression analyses revealed a significantly reduced risk of developing sensitization to aero-allergens at 6 years and ever wheezing until the age of 10 years for exposure to higher fungal diversity [adjusted odds ratio (aOR) = 0.26 (95% CI: 0.10, 0.70), and 0.42 (95% CI: 0.18, 0.96), respectively]. The associations were attenuated for the longitudinal analyses (GEE) until the age of 10 years. There was no association between higher exposure to bacterial diversity and the tested health outcomes. Higher early exposure to fungal diversity might help to prevent a child from developing sensitization to aero-allergens in early childhood, but the reasons for attenuated effects in later childhood require further prospective studies. Citation: Tischer C, Weikl F, Probst AJ, Standl M, Heinrich J, Pritsch K. 2016. Urban dust microbiome: impact on later atopy and wheezing. Environ Health Perspect 124:1919-1923; http://dx.doi.org/10.1289/EHP158.

  4. Ancient human microbiomes

    OpenAIRE

    Warinner, C.; Speller, C; Collins, M.; Lewis Jr., C.

    2015-01-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and theref...

  5. Fungal arthritis

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/000444.htm Fungal arthritis To use the sharing features on this page, please enable JavaScript. Fungal arthritis is swelling and irritation (inflammation) of a joint ...

  6. Fungal Meningitis

    Science.gov (United States)

    ... Schedules Preteen & Teen Vaccines Meningococcal Disease Sepsis Fungal Meningitis Language: English Español (Spanish) Recommend on Facebook Tweet ... the brain or spinal cord. Investigation of Fungal Meningitis, 2012 In September 2012, the Centers for Disease ...

  7. Networking in the Plant Microbiome

    NARCIS (Netherlands)

    van der Heijden, Marcel G A|info:eu-repo/dai/nl/240923901; Hartmann, Martin

    2016-01-01

    Almost all higher organisms, including plants, insects, and mammals, are colonized by complex microbial communities and harbor a microbiome. Emerging studies with plants reveal that these microbiomes are structured and form complex, interconnected microbial networks. Within these networks, different

  8. Networking in the Plant Microbiome

    NARCIS (Netherlands)

    van der Heijden, Marcel G A; Hartmann, Martin

    2016-01-01

    Almost all higher organisms, including plants, insects, and mammals, are colonized by complex microbial communities and harbor a microbiome. Emerging studies with plants reveal that these microbiomes are structured and form complex, interconnected microbial networks. Within these networks, different

  9. Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome

    Directory of Open Access Journals (Sweden)

    Justin Merritt

    2017-04-01

    Full Text Available The six Veillonella species found in the human oral cavity are among the most abundant members of the oral flora, occurring in both supra- and subgingival dental plaque as well as on the oral mucosa. Epidemiological data have also implicated these species in the development of the most common oral diseases. Despite their ubiquity, abundance, and ecological significance, surprisingly little is known about Veillonella biology, largely due to the difficulties associated with their genetic manipulation. In an effort to improve genetic analyses of Veillonella species, we isolated a collection of veillonellae from clinical plaque samples and screened for natural competence using a newly developed transformation protocol. Numerous strains of V. parvula were found to exhibit a natural competence ability that was highly influenced by growth medium composition. By exploiting this ability, we were able to utilize cloning-independent allelic exchange mutagenesis to identify the likely source of DNA uptake machinery within a locus homologous to type II secretion systems (T2SS. Interestingly, V. parvula natural competence was found to exhibit a clear hierarchy of preference for different sources of DNA (plasmid < PCR product < genomic DNA, which is unlike most naturally competent species. Genomic comparisons with other members of the Veillonellaceae family suggest that natural competence is likely to be widely distributed within this group. To the best of our knowledge, this study is the first demonstration of natural competence and targeted allelic exchange mutagenesis within the entire Veillonellaceae family and demonstrates a simple and rapid method to study Veillonella genetics.

  10. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity.

    Science.gov (United States)

    Gupta, Vinod K; Paul, Sandip; Dutta, Chitra

    2017-01-01

    One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats-Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution-a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota-the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome-nature or nurture, host genetics or his environment. Some of

  11. Insights from characterizing extinct human gut microbiomes.

    Directory of Open Access Journals (Sweden)

    Raul Y Tito

    Full Text Available In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites. To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P. in the southern United States, Caserones (1600 years B.P. in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.. Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

  12. The microbiome in asthma.

    Science.gov (United States)

    Huang, Yvonne J; Boushey, Homer A

    2015-01-01

    The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.

  13. Companion animals symposium: humanized animal models of the microbiome.

    Science.gov (United States)

    Gootenberg, D B; Turnbaugh, P J

    2011-05-01

    Humans and other mammals are colonized by trillions of microorganisms, most of which reside in the gastrointestinal tract, that provide key metabolic capabilities, such as the biosynthesis of vitamins and AA, the degradation of dietary plant polysaccharides, and the metabolism of orally administered therapeutics. Although much progress has been made by studying the human microbiome directly, comparing the human microbiome with that of other animals, and constructing in vitro models of the human gut, there remains a need to develop in vivo models where host, microbial, and environmental parameters can be manipulated. Here, we discuss some of the initial results from a promising method that enables the direct manipulation of microbial community structure, environmental exposures, host genotype, and other factors: the colonization of germ-free animals with complex microbial communities, including those from humans or other animal donors. Analyses of these resulting "humanized" gut microbiomes have begun to reveal 1) that key microbial activities can be transferred from the donor to the recipient animal (e.g., microbial reduction of cholesterol and production of equol), 2) that dietary shifts can affect the composition, gene abundance, and gene expression of the gut microbiome, 3) the succession of the microbial community in infants and ex-germ-free adult animals, and 4) the biogeography of these microbes across the length of gastrointestinal tract. Continued studies of humanized and other intentionally colonized animal models stand to provide new insight into not only the human microbiome, but also the microbiomes of our animal companions.

  14. Ancient human microbiomes.

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J; Lewis, Cecil M

    2015-02-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

  15. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

    Directory of Open Access Journals (Sweden)

    Vinod K. Gupta

    2017-06-01

    Full Text Available One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT. The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics

  16. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

    Science.gov (United States)

    Gupta, Vinod K.; Paul, Sandip; Dutta, Chitra

    2017-01-01

    One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment

  17. The gut microbiome.

    Science.gov (United States)

    Actis, Giovanni C

    2014-01-01

    Since the discovery and use of the microscope in the 17(th) century, we know that we host trillions of micro-organisms mostly in the form of bacteria indwelling the "barrier organs" skin, gut, and airways. They exert regulatory functions, are in a continuous dialogue with the intestinal epithelia, influence energy handling, produce nutrients, and may cause diabetes and obesity. The human microbiome has developed by modulating or avoiding inflammatory responses; the host senses bacterial presence through cell surface sensors (the Toll-like receptors) as well as by refining mucous barriers as passive defense mechanisms. The cell density and composition of the microbiome are variable and multifactored. The way of delivery establishes the type of initial flora; use of antibiotics is another factor; diet composition after weaning will shape the adult's microbiome composition, depending on the subject's life-style. Short-chain fatty acids participate in the favoring action exerted by microbiome in the pathogenesis of type-2 diabetes and obesity. Clinical observation has pinpointed a sharp rise of various dysimmune conditions in the last decades, including IBD and rheumatoid arthritis, changes that outweigh the input of simple heritability. It is nowadays proposed that the microbiome, incapable to keep up with the changes of our life-style and feeding sources in the past few decades might have contributed to these immune imbalances, finding itself inadequate to handle the changed gut environment. Another pathway to pathology is the rise of directly pathogenic phyla within a given microbiome: growth of adherent E. coli, of C. concisus, and of C. jejuni, might be examples of causes of local enteropathy, whereas the genus Prevotella copri is now suspected to be linked to rise of arthritic disorders. Inflammasomes are required to shape a non colitogenic flora. Treatment of IBD and infectious enteritides by the use of fecal transplant is warranted by this knowledge.

  18. [Fungal keratitis].

    Science.gov (United States)

    Bourcier, T; Sauer, A; Letscher-Bru, V; Candolfi, E

    2011-10-01

    Fungal keratitis (keratomycosis) is a rare but severe cause of infectious keratitis. Its incidence is constant, due to steroids or immunosuppressive treatments and contact lenses. Pathogens often invade corneas with chronic diseases of the ocular surface but fungal keratitis is also observed following injuries with plant foreign objects. The poor prognosis of these infections is related both to fungal virulence, decreased host defense, as well as delays in diagnosis. However, new antimycotic treatments allow better management and prognosis.

  19. Wine fermentation microbiome: a landscape from different Portuguese wine appellations

    Directory of Open Access Journals (Sweden)

    Cátia ePinto

    2015-09-01

    Full Text Available Grapes and wine musts harbour a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation – Initial Must (IM, and Start and End of alcoholic fermentation (SF and EF, respectively.The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p<0.05 were found in the fungal populations between IM, SF and EF, and in the bacterial population between MI and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the initial musts, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida and Schizosaccharomyces. Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae and acetic acid (Acetobacteriaceae were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of

  20. The fish egg microbiome

    NARCIS (Netherlands)

    Liu, Y.

    2016-01-01

    Y. Liu Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp. The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia Emerging oomycete pat

  1. The fish egg microbiome

    NARCIS (Netherlands)

    Liu, Y.

    2016-01-01

    Y. Liu Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp. The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia Emerging oomycete

  2. The minimal rhizosphere microbiome

    NARCIS (Netherlands)

    Raaijmakers, Jos; Lugtenberg, Ben

    2015-01-01

    The rhizosphere provides a home to numerous (micro)organisms that in turn may affect plant growth, development, and tolerance to abiotic and biotic stresses. How plants shape the rhizosphere microbiome has been subject of many past and present studies with the ultimate goal to identify plant genetic

  3. The minimal rhizosphere microbiome

    NARCIS (Netherlands)

    Raaijmakers, Jos; Lugtenberg, Ben

    2015-01-01

    The rhizosphere provides a home to numerous (micro)organisms that in turn may affect plant growth, development, and tolerance to abiotic and biotic stresses. How plants shape the rhizosphere microbiome has been subject of many past and present studies with the ultimate goal to identify plant genetic

  4. Microbiome and skin diseases

    NARCIS (Netherlands)

    Zeeuwen, P.L.J.M.; Kleerebezem, M.; Timmerman, H.M.; Schalkwijk, J.

    2013-01-01

    PURPOSE OF REVIEW: This article reviews recent findings on the skin microbiome. It provides an update on the current understanding of the role of microbiota in healthy skin and in inflammatory and allergic skin diseases. RECENT FINDINGS: Advances in computing and high-throughput sequencing technolog

  5. Microbiome and skin diseases

    NARCIS (Netherlands)

    Zeeuwen, P.L.; Kleerebezem, M.; Timmerman, H.M.; Schalkwijk, J.

    2013-01-01

    Purpose of review: This article reviews recent findings on the skin microbiome. It provides an update on the current understanding of the role of microbiota in healthy skin and in inflammatory and allergic skin diseases. Recent findings: Advances in computing and high-throughput sequencing technolog

  6. Microbiome and skin diseases

    NARCIS (Netherlands)

    Zeeuwen, P.L.J.M.; Kleerebezem, M.; Timmerman, H.M.; Schalkwijk, J.

    2013-01-01

    PURPOSE OF REVIEW: This article reviews recent findings on the skin microbiome. It provides an update on the current understanding of the role of microbiota in healthy skin and in inflammatory and allergic skin diseases. RECENT FINDINGS: Advances in computing and high-throughput sequencing

  7. Microbiome and skin diseases

    NARCIS (Netherlands)

    Zeeuwen, P.L.; Kleerebezem, M.; Timmerman, H.M.; Schalkwijk, J.

    2013-01-01

    Purpose of review: This article reviews recent findings on the skin microbiome. It provides an update on the current understanding of the role of microbiota in healthy skin and in inflammatory and allergic skin diseases. Recent findings: Advances in computing and high-throughput sequencing

  8. The dynamic microbiome.

    Science.gov (United States)

    Gerber, Georg K

    2014-11-17

    While our genomes are essentially static, our microbiomes are inherently dynamic. The microbial communities we harbor in our bodies change throughout our lives due to many factors, including maturation during childhood, alterations in our diets, travel, illnesses, and medical treatments. Moreover, there is mounting evidence that our microbiomes change us, by promoting health through their beneficial actions or by increasing our susceptibility to diseases through a process termed dysbiosis. Recent technological advances are enabling unprecedentedly detailed studies of the dynamics of the microbiota in animal models and human populations. This review will highlight key areas of investigation in the field, including establishment of the microbiota during early childhood, temporal variability of the microbiome in healthy adults, responses of the microbiota to intentional perturbations such as antibiotics and dietary changes, and prospective analyses linking changes in the microbiota to host disease status. Given the importance of computational methods in the field, this review will also discuss issues and pitfalls in the analysis of microbiome time-series data, and explore several promising new directions for mathematical model and algorithm development.

  9. The Minimal Rhizosphere Microbiome

    NARCIS (Netherlands)

    Raaijmakers, J.M.

    2015-01-01

    The rhizosphere provides a home to numerous (micro)organisms that in turn may affect plant growth, development, and tolerance to abiotic and biotic stresses. How plants shape the rhizosphere microbiome has been subject of many past and present studies with the ultimate goal to identify plant genetic

  10. Fluconzole in treatment of acute radiation-induced oral mucositis with fungal infection%氟康唑治疗急性放射性口腔粘膜炎继发的真菌感染

    Institute of Scientific and Technical Information of China (English)

    姚原; 吴国华; 蒋马伟; 林清; 陆冬青; 翁霞

    2001-01-01

    目的:研究头颈部肿瘤放射治疗中急性放射性口腔粘膜反应与真菌感染的关系及氟康唑治疗的有效性。方法:71例口腔粘膜受到大面积照射的肿瘤病人:男性42例,女性29例;年龄52 a± s 41 a(11~76 a),在病人的口腔粘膜反应最严重的时候,做口腔粘膜真菌学检查,32例有真菌感染的病人,用氟康唑胶囊100 mg,po, qd×5 d或氟康唑注射液150 mg,iv,gtt×3 d治疗。结果:真菌的检出率为45%,以白念珠菌感染为主。有真菌感染和无真菌感染的2组病人,在急性放射性粘膜反应上差异有显著意义(P<0.05);有真菌感染的病人用氟康唑治疗,治疗前后的粘膜反应差异有显著意义(P<0.05)。结论:严重的急性放射性粘膜反应与真菌感染有密切的关系;有真菌感染的放射性口腔粘膜反应用氟康唑治疗可以明显减轻放射性粘膜反应。%AIM: To study the relation of acute radiation-induced oral mucositis to fungal infection and evaluate the effect of fluconazole in the treatment of patients with fungal infection. METHODS: Seventy-one patients (M 42, F 29; 52 a± s 41 a,11-76 a) with large area of oral mucosas irradiated were into this study. When most serious mucositis, the patients' oral mucosas were checked, 32 patients with fungal infection were treated with fluconazole (fluconazole 100 mg, po, qd×5 d or 150 mg,iv,gtt×3 d). RESULTS: The rate of fungal infection was 45%, the most of patients were infected by candida albicans. Degrees of mucositis between the patients with fungal infection to the patients without fungal infection were significantly different (P<0.05). The patients with fungal infection were treated with fluconazole. Degree of mucositis between the pretreated patients and post-treated patients were significantly different (P<0.05). CONCLUSION: The serious acute radiation-induced oral mucositis has significantly related with fungal infection. The patients

  11. Fungal endophytes: modifiers of plant disease.

    Science.gov (United States)

    Busby, Posy E; Ridout, Mary; Newcombe, George

    2016-04-01

    Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes ("endo" = within, "phyte" = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation.

  12. Itraconazole oral solution as prophylaxis for fungal infections in neutropenic patients with hematologic malignancies: a randomized, placebo-controlled, double-blind, multicenter trial. GIMEMA Infection Program. Gruppo Italiano Malattie Ematologiche dell' Adulto.

    Science.gov (United States)

    Menichetti, F; Del Favero, A; Martino, P; Bucaneve, G; Micozzi, A; Girmenia, C; Barbabietola, G; Pagańo, L; Leoni, P; Specchia, G; Caiozzo, A; Raimondi, R; Mandelli, F

    1999-02-01

    To evaluate the efficacy and safety of itraconazole oral solution for preventing fungal infections, a randomized, placebo-controlled, double-blind, multicenter trial was conducted: 405 neutropenic patients with hematologic malignancies were randomly assigned to receive either itraconazole, 2.5 mg/kg every 12 hours (201 patients), or placebo (204 patients). Proven and suspected deep fungal infection occurred in 24% of itraconazole recipients and in 33% of placebo recipients, a difference of 9 percentage points (95% confidence interval [CI], 0.6% to 22.5%; P = .035). Fungemia due to Candida species was documented in 0.5% of itraconazole recipients and in 4% of placebo recipients, a difference of 3.5 percentage points (95% CI, 0.5% to 6%; P = .01). Deaths due to candidemia occurred in none of the itraconazole recipients compared with 4 placebo recipients, a difference of 2 percentage points (95% CI, 0.05% to 4%; P = .06). Aspergillus infection was documented in four itraconazole recipients (one death) and one placebo recipient (one death). Side effects causing drug interruption occurred in 18% of itraconazole recipients and 13% of placebo recipients. Itraconazole oral solution was well-tolerated and effectively prevented proven and suspected deep fungal infection as well as systemic infection and death due to Candida species.

  13. Microbiome Disturbances and Autism Spectrum Disorders.

    Science.gov (United States)

    Rosenfeld, Cheryl S

    2015-10-01

    Autism spectrum disorders (ASDs) are considered a heterogenous set of neurobehavioral diseases, with the rates of diagnosis dramatically increasing in the past few decades. As genetics alone does not explain the underlying cause in many cases, attention has turned to environmental factors as potential etiological agents. Gastrointestinal disorders are a common comorbidity in ASD patients. It was thus hypothesized that a gut-brain link may account for some autistic cases. With the characterization of the human microbiome, this concept has been expanded to include the microbiota-gut-brain axis. There are mounting reports in animal models and human epidemiologic studies linking disruptive alterations in the gut microbiota or dysbiosis and ASD symptomology. In this review, we will explore the current evidence that gut dysbiosis in animal models and ASD patients correlates with disease risk and severity. The studies to date have surveyed how gut microbiome changes may affect these neurobehavioral disorders. However, we harbor other microbiomes in the body that might impact brain function. We will consider microbial colonies residing in the oral cavity, vagina, and the most recently discovered one in the placenta. Based on the premise that gut microbiota alterations may be causative agents in ASD, several therapeutic options have been tested, such as diet modulations, prebiotics, probiotics, synbiotics, postbiotics, antibiotics, fecal transplantation, and activated charcoal. The potential benefits of these therapies will be considered. Finally, the possible mechanisms by which changes in the gut bacterial communities may result in ASD and related neurobehavioral disorders will be examined.

  14. Diverse CRISPRs evolving in human microbiomes.

    Directory of Open Access Journals (Sweden)

    Mina Rho

    Full Text Available CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats loci, together with cas (CRISPR-associated genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes, we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals

  15. Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology.

    Science.gov (United States)

    Verma, Mukesh

    2017-04-01

    This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

  16. Extreme Dysbiosis of the Microbiome in Critical Illness

    Science.gov (United States)

    McDonald, Daniel; Ackermann, Gail; Khailova, Ludmila; Baird, Christine; Heyland, Daren; Kozar, Rosemary; Lemieux, Margot; Derenski, Karrie; King, Judy; Vis-Kampen, Christine; Knight, Rob

    2016-01-01

    ABSTRACT Critical illness is hypothesized to associate with loss of “health-promoting” commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key “health-promoting” organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, “health-promoting” microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of

  17. Oral histoplasmosis

    Directory of Open Access Journals (Sweden)

    Patil Karthikeya

    2009-01-01

    Full Text Available Histoplasmosis is a systemic fungal disease that takes various clinical forms, among which oral lesions are rare. The disseminated form of the disease that usually occurs in association with Human Immunodeficiency Virus (HIV is one of the AIDS-defining diseases. Isolated oral histoplasmosis, without systemic involvement, with underlying immunosuppression due to AIDS is very rare. We report one such case of isolated oral histoplasmosis in a HIV-infected patient.

  18. Fungal rhinosinusitis.

    Science.gov (United States)

    Netkovski, J; Shirgoska, B

    2012-01-01

    Fungi are a major part of the ecosystem. In fact, over 250 fungal species have been reported to produce human infections. More than ever, fungal diseases have emerged as major challenges for physicians and clinical microbiologists. The aim of this study was to summarize the diagnostic procedures and endoscopic surgical treatment of patients with fungal rhinosinusitis. Eleven patients, i.e. 10% of all cases with chronic inflammation of paranasal sinuses, were diagnosed with fungal rhinosinusitis. Ten of them were patients with a noninvasive form, fungus ball, while only one patient was classified in the group of chronic invasive fungal rhinosinusitis which was accompanied with diabetes mellitus. All patients underwent nasal endoscopic examination, skin allergy test and had preoperative computed tomography (CT) scans of the sinuses in axial and coronal plane. Functional endoscopic sinus surgery was performed in 10 patients with fungus ball, while a combined approach, endoscopic and external, was done in the immunocompromised patient with the chronic invasive form of fungal rhinosinusitis. Most cases (9/11) had unilateral infection. In 9 cases infection was restricted to a single sinus, and here the maxillary sinus was most commonly affected (8/9) with infections in other patients being restricted to the sphenoid sinus (1/9). Two patients had infections affecting two or more sinuses. In patients with an invasive form of the fungal disease there was involvement of the periorbital and orbital tissues. In patients with fungus ball the mycelia masses were completely removed from the sinus cavities. Long-term outcome was positive in all the operated patients and no recurrence was detected. The most frequent fungal agent that caused rhinosinusitis was Aspergillus. Mucor was identified in the patient with the invasive form. Endoscopic examination of the nasal cavity and CT scanning of paranasal sinuses followed by endoscopic sinus surgery were represented as valuable

  19. The microbiome and probiotics in childhood.

    Science.gov (United States)

    Hsieh, Michael Harrison

    2014-01-01

    Infants, from the moment of birth, are colonized by large numbers of microbes. This colonization continues throughout childhood and from preliminary studies seems to be a highly dynamic process, even during the usual physiologic state we refer to as health. In this context, the persistence of bacterial and fungal species in and on the human body likely confers various benefits to the host. One specific approach to modulate such beneficial effects is the administration of probiotics, also known as beneficial microbes. Herein, we outline the highest level evidence in regard to the evolution of the microbiome during childhood and its manipulation by probiotics for genitourinary, enteric, and allergic and atopic disorders. Thus, probiotic approaches are promising alternatives and adjuvants to traditional vaccines and antibiotics. This may usher in a new age in which vaccine and antibiotic side effects and antibiotic resistance are minimal issues in the setting of maintaining children's health and prevention of disease.

  20. Temporal Stability of the Human Skin Microbiome.

    Science.gov (United States)

    Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

    2016-05-05

    Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states.

  1. The perinatal microbiome and pregnancy: moving beyond the vaginal microbiome.

    Science.gov (United States)

    Prince, Amanda L; Chu, Derrick M; Seferovic, Maxim D; Antony, Kathleen M; Ma, Jun; Aagaard, Kjersti M

    2015-03-16

    The human microbiome, the collective genome of the microbial community that is on and within us, has recently been mapped. The initial characterization of healthy subjects has provided investigators with a reference population for interrogating the microbiome in metabolic, intestinal, and reproductive health and disease states. Although it is known that bacteria can colonize the vagina, recent metagenomic studies have shown that the vaginal microbiome varies among reproductive age women. Similarly, the richness and diversity of intestinal microbiota also naturally fluctuate among gravidae in both human and nonhuman primates, as well as mice. Moreover, recent evidence suggests that microbiome niches in pregnancy are not limited to maternal body sites, as the placenta appears to harbor a low biomass microbiome that is presumptively established in early pregnancy and varies in association with a remote history of maternal antenatal infection as well as preterm birth. In this article, we will provide a brief overview on metagenomics science as a means to investigate the microbiome, observations pertaining to both variation and the presumptive potential role of a varied microbiome during pregnancy, and how future studies of the microbiome in pregnancy may lend to a better understanding of human biology, reproductive health, and parturition.

  2. Potential Role of the Microbiome in Barrett's Esophagus and Esophageal Adenocarcinoma.

    Science.gov (United States)

    Snider, Erik J; Freedberg, Daniel E; Abrams, Julian A

    2016-08-01

    Esophageal adenocarcinoma and its precursor Barrett's esophagus have been rapidly increasing in incidence for half a century, for reasons not adequately explained by currently identified risk factors such as gastroesophageal reflux disease and obesity. The upper gastrointestinal microbiome may represent another potential cofactor. The distal esophagus has a distinct microbiome of predominantly oral-derived flora, which is altered in Barrett's esophagus and reflux esophagitis. Chronic low-grade inflammation or direct carcinogenesis from this altered microbiome may combine with known risk factors to promote Barrett's metaplasia and progression to adenocarcinoma.

  3. Fungal allergens.

    OpenAIRE

    1995-01-01

    Airborne fungal spores occur widely and often in far greater concentrations than pollen grains. Immunoglobulin E-specific antigens (allergens) on airborne fungal spores induce type I hypersensitivity (allergic) respiratory reactions in sensitized atopic subjects, causing rhinitis and/or asthma. The prevalence of respiratory allergy to fungi is imprecisely known but is estimated at 20 to 30% of atopic (allergy-predisposed) individuals or up to 6% of the general population. Diagnosis and immuno...

  4. The microbiome systemic diseases connection

    NARCIS (Netherlands)

    van der Meulen, T.A.; Harmsen, H J M; Bootsma, H; Spijkervet, F K L; Kroese, F G M; Vissink, A

    2016-01-01

    The human microbiome consists of all microorganisms occupying the skin, mucous membranes and intestinal tract of the human body. The contact of the mucosal immune system with the human microbiome is a balanced interplay between defence mechanisms of the immune system and symbiotic or pathogenic micr

  5. Microbiome engineering: Current applications and its future.

    Science.gov (United States)

    Foo, Jee Loon; Ling, Hua; Lee, Yung Seng; Chang, Matthew Wook

    2017-03-01

    Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.

  6. Fungal nail infection

    Science.gov (United States)

    Nails - fungal infection; Onychomycosis; Infection - fungal - nails; Tinea unguium ... hair, nails, and outer skin layers. Common fungal infections include: Athlete's foot Jock itch Ringworm on the ...

  7. Omics approaches to study the oral microbiome

    OpenAIRE

    Belda Ferre, Pedro

    2015-01-01

    Introducción La visión clásica de los microorganismos como agentes infecciosos ha propiciado que se consideren como meros agentes causales de enfermedades. Sin embargo, la larga historia de coexistencia entre microorganismos y los seres humanos, ha hecho que ambos se hayan adaptado mutuamente y coevolucionen (Dubos et al. 1965, McFall-Ngai 2002)⁠. De hecho, en el cuerpo humano habitan 1014 células bacterianas, un orden de magnitud más que células humanas (Savage 1977)⁠. Entre los benefic...

  8. Omics approaches to study the oral microbiome

    OpenAIRE

    Belda Ferre, Pedro

    2015-01-01

    Introducción La visión clásica de los microorganismos como agentes infecciosos ha propiciado que se consideren como meros agentes causales de enfermedades. Sin embargo, la larga historia de coexistencia entre microorganismos y los seres humanos, ha hecho que ambos se hayan adaptado mutuamente y coevolucionen (Dubos et al. 1965, McFall-Ngai 2002)⁠. De hecho, en el cuerpo humano habitan 1014 células bacterianas, un orden de magnitud más que células humanas (Savage 1977)⁠. Entre los benefic...

  9. Microbiomes: unifying animal and plant systems through the lens of community ecology theory

    Science.gov (United States)

    Christian, Natalie; Whitaker, Briana K.; Clay, Keith

    2015-01-01

    The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant–fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant–fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant–fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research. PMID:26441846

  10. Microbiomes: unifying animal and plant systems through the lens of community ecology theory.

    Science.gov (United States)

    Christian, Natalie; Whitaker, Briana K; Clay, Keith

    2015-01-01

    The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant-fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant-fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant-fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.

  11. Microbiomes: unifying animal and plant systems through the lens of community ecology theory

    Directory of Open Access Journals (Sweden)

    Natalie eChristian

    2015-09-01

    Full Text Available The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant-fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant-fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant-fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration. The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.

  12. Fungal keratitis

    Directory of Open Access Journals (Sweden)

    Sonal S Tuli

    2011-02-01

    Full Text Available Sonal S TuliUniversity of Florida, Gainesville, FL, USA  Clinical question: What is the most appropriate management of fungal keratitis?Results: Traditionally, topical Natamycin is the most commonly used medication for filamentous fungi while Amphotericin B is most commonly used for yeast. Voriconazole is rapidly becoming the drug of choice for all fungal keratitis because of its wide spectrum of coverage and increased penetration into the cornea.Implementation: Repeated debridement of the ulcer is recommended for the penetration of topical medications. While small, peripheral ulcers may be treated in the community, larger or central ulcers, especially if associated with signs suggestive of anterior chamber penetration should be referred to a tertiary center. Prolonged therapy for approximately four weeks is usually necessary.Keywords: fungal keratitis, keratomycosis, antifungal medications, debridement

  13. Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico

    Directory of Open Access Journals (Sweden)

    Tasha M. Santiago-Rodriguez

    2017-05-01

    Full Text Available Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Methods Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Results Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Discussion Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.

  14. Captivity humanizes the primate microbiome

    Science.gov (United States)

    Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M.; Al-Ghalith, Gabriel A.; Travis, Dominic A.; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E.; Johnson, Timothy J.; Knights, Dan

    2016-01-01

    The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome. PMID:27573830

  15. Fungal prions.

    Science.gov (United States)

    Staniforth, Gemma L; Tuite, Mick F

    2012-01-01

    For both mammalian and fungal prion proteins, conformational templating drives the phenomenon of protein-only infectivity. The conformational conversion of a protein to its transmissible prion state is associated with changes to host cellular physiology. In mammals, this change is synonymous with disease, whereas in fungi no notable detrimental effect on the host is typically observed. Instead, fungal prions can serve as epigenetic regulators of inheritance in the form of partial loss-of-function phenotypes. In the presence of environmental challenges, the prion state [PRION(+)], with its resource for phenotypic plasticity, can be associated with a growth advantage. The growing number of yeast proteins that can switch to a heritable [PRION(+)] form represents diverse and metabolically penetrating cellular functions, suggesting that the [PRION(+)] state in yeast is a functional one, albeit rarely found in nature. In this chapter, we introduce the biochemical and genetic properties of fungal prions, many of which are shared by the mammalian prion protein PrP, and then outline the major contributions that studies on fungal prions have made to prion biology.

  16. Fungal Entomopathogens

    Science.gov (United States)

    Fungal entomopathogens are important biological control agents worldwide and have been the subject of intense research for more than100 years. They exhibit both sexual and asexual reproduction and produce different types of infective propagules. Their mode of action against insects involves attachme...

  17. The lung microbiome in moderate and severe chronic obstructive pulmonary disease.

    Directory of Open Access Journals (Sweden)

    Alexa A Pragman

    Full Text Available Chronic obstructive pulmonary disease (COPD is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples.

  18. Variation in koala microbiomes within and between individuals: effect of body region and captivity status

    Science.gov (United States)

    Alfano, Niccoló; Courtiol, Alexandre; Vielgrader, Hanna; Timms, Peter; Roca, Alfred L.; Greenwood, Alex D.

    2015-01-01

    Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae. PMID:25960327

  19. 肝移植术后早期口腔并发症及深部真菌感染的预防%Clinical Research of Prevention on Prophase Oral Cavity Infection and Deep Fungal Infection after Liver Transplantation

    Institute of Scientific and Technical Information of China (English)

    李萌萌; 李荣华; 殷恺; 曹晓丽

    2011-01-01

    目的:观察研究口腔内局部联合用药预防肝移植术后早期口腔感染及深部真菌感染的临床效果.方法:将162例肝移植术后患者随机分为观察组A(57例)、观察组B(62例)和对照组(43例),观察组A采用3%碳酸氢钠溶液和0.1%西吡氯铵含漱液局部联合进行口腔干预,观察组B采用5×104 U/mL制霉菌素水混悬液和0.1%西吡氯铵含漱液局部联合进行口腔干预,对照组常规采用生理盐水进行口腔干预.观察并记录患者术后口腔并发症,并进行血浆(1-3)-β-D葡聚糖水平检测.结果:3组口腔并发症和(1-3)-β-D葡聚糖水平差异均有统计学意义(P0.05).结论:采用0.1%西吡氯铵含漱液分别与3%碳酸氢钠溶液或5×104 U/mL制霉菌素水混悬液联合应用进行口腔干预对预防肝移植术后早期口腔并发症及深部真菌感染有临床意义.%Objective :To observe the clinical effect of drug combination using in oral cavity on prevention of prophase oral infection and deep fungal infection after liver transplantation. Methods: One hundred and sixty-two patients with liver transplantation were randomly divided into observation group A (n=57), observation group B (n=62) and control group(n=43).For the group A, 3% sodium bicarbonate gargle and 0.1% cetylpyridinium chloride gargle were combinedly used to cavity nursing. For patients of group B, 5 × 104 U/mL nystatin aqueous suspension combinedly with 0.1% cetylpyridinium chloride gargle were used to oral nursing. For patients of control group only normal saline was used in nursing oral cavity. The oral complications were observed in patients of groups. The level of plasma (l-3)-β-D-glucan was detected. Results: There were significant differences in oral complications and (1-3)-β-D-glucan level between three groups (P < 0.05 or P < 0.01). There was a significant difference in gingivitis between group A and control group(P < 0.05). There were also significant differences in oral

  20. Bioprospecting plant-associated microbiomes.

    Science.gov (United States)

    Müller, Christina A; Obermeier, Melanie M; Berg, Gabriele

    2016-10-10

    There is growing demand for new bioactive compounds and biologicals for the pharmaceutical, agro- and food industries. Plant-associated microbes present an attractive and promising source to this end, but are nearly unexploited. Therefore, bioprospecting of plant microbiomes is gaining more and more attention. Due to their highly specialized and co-evolved genetic pool, plant microbiomes host a rich secondary metabolism. This article highlights the potential detection and use of secondary metabolites and enzymes derived from plant-associated microorganisms in biotechnology. As an example we summarize the findings from the moss microbiome with special focus on the genus Sphagnum and its biotechnological potential for the discovery of novel microorganisms and bioactive molecules. The selected examples illustrate unique and yet untapped properties of plant-associated microbiomes, which are an immense treasure box for future research.

  1. The rhizosphere revisited: root microbiomics

    Directory of Open Access Journals (Sweden)

    Peter A.H.M. Bakker

    2013-05-01

    Full Text Available The rhizosphere was defined over 100 years ago as the zone around the root where microorganisms and processes important for plant growth and health are located. Recent studies show that the diversity of microorganisms associated with the root system is enormous. This rhizosphere microbiome extends the functional repertoire of the plant beyond imagination. The rhizosphere microbiome of Arabidopsis thaliana is currently being studied for the obvious reason that it allows the use of the extensive toolbox that comes with this model plant. Deciphering plant traits that drive selection and activities of the microbiome is now a major challenge in which Arabidopsis will undoubtedly be a major research object. Here we review recent microbiome studies and discuss future research directions and applicability of the generated knowledge

  2. Maternal microbiome and pregnancy outcomes.

    Science.gov (United States)

    Fox, Chelsea; Eichelberger, Kacey

    2015-12-01

    Alterations of the human microbiome are a known characteristic of various inflammatory disease states and have been linked to spontaneous preterm birth and other adverse pregnancy outcomes. Recent advances in metagenomic research have proven that the placenta harbors its own rich diverse microbiome, even in clinically healthy pregnancies, and preterm birth may be a result of hematogenous infection rather than exclusively ascending infection as previously hypothesized. In this review, we describe the microbiome in healthy nongravid and gravid women to contrast it with the alterations of the microbiome associated with spontaneous preterm birth. We also discuss the importance of host gene-environment interactions and the potential for microbiota-specific targeted therapies to reduce the risk of adverse pregnancy outcomes.

  3. Captivity humanizes the primate microbiome

    National Research Council Canada - National Science Library

    Clayton, Jonathan B; Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M; Al-Ghalith, Gabriel A; Travis, Dominic A; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E; Johnson, Timothy J; Knights, Dan

    2016-01-01

    .... Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study...

  4. The Airway Microbiome at Birth

    National Research Council Canada - National Science Library

    Lal, Charitharth Vivek; Travers, Colm; Aghai, Zubair H; Eipers, Peter; Jilling, Tamas; Halloran, Brian; Carlo, Waldemar A; Keeley, Jordan; Rezonzew, Gabriel; Kumar, Ranjit; Morrow, Casey; Bhandari, Vineet; Ambalavanan, Namasivayam

    2016-01-01

    .... We found an established diverse and similar airway microbiome at birth in both preterm and term infants, which was more diverse and different from that of older preterm infants with established chronic lung disease...

  5. Exploring interactions of plant microbiomes

    Directory of Open Access Journals (Sweden)

    Fernando Dini Andreote

    2014-12-01

    Full Text Available A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. In this review, we first summarize features of microbial communities that compose the plant microbiome and further present a series of studies describing the underpinning factors that shape the phylogenetic and functional plant-associated communities. We advocate the idea that understanding the mechanisms by which plants select and interact with their microbiomes may have a direct effect on plant development and health, and further lead to the establishment of novel microbiome-driven strategies, that can cope with the development of a more sustainable agriculture.

  6. Changes in abundance of oral microbiota associated with oral cancer.

    Directory of Open Access Journals (Sweden)

    Brian L Schmidt

    Full Text Available Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus and Actinobacteria (especially Rothia was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.

  7. Effects of host species and environment on the skin microbiome of Plethodontid salamanders.

    Science.gov (United States)

    Muletz Wolz, Carly R; Yarwood, Stephanie A; Campbell Grant, Evan H; Fleischer, Robert C; Lips, Karen R

    2017-07-06

    The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus, 17 Plethodon glutinosus, 10 Plethodon cylindraceus) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700-1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% (SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that

  8. Fungal laryngitis in immunocompetent patients.

    Science.gov (United States)

    Ravikumar, A; Prasanna Kumar, S; Somu, L; Sudhir, B

    2014-01-01

    The diagnosis of fungal laryngitis is often overlooked in immunocompetent patients because it is commonly considered a disease of the immunocompromised. Further confusion is caused by clinical and histological similarity to more common conditions like Leukoplakia. Demonstration of hyperkeratosis particularly if associated with intraepithelial neutrophils on biopsy should trigger a search for fungus using specialized stains. These patients usually present with hoarseness of voice. Pain is present inconsistently along with dysphagia and odynophagia. We present three cases of fungal laryngitis in immunocompetent patients out of which one underwent microlaryngeal surgery with excision biopsy. All these patients responded well with oral antifungal therapy.

  9. The microbiome of New World vultures.

    Science.gov (United States)

    Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Pontén, Thomas Sicheritz; Sørensen, Søren Johannes; Gilbert, M Thomas P; Graves, Gary R; Hansen, Lars H

    2014-11-25

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

  10. Oral Histoplasmosis.

    Science.gov (United States)

    Folk, Gillian A; Nelson, Brenda L

    2017-02-20

    A 44-year-old female presented to her general dentist with the chief complaint of a painful mouth sore of 2 weeks duration. Clinical examination revealed an irregularly shaped ulcer of the buccal and lingual attached gingiva of the anterior mandible. A biopsy was performed and microscopic evaluation revealed histoplasmosis. Histoplasmosis, caused by Histoplasma capsulate, is the most common fungal infection in the United States. Oral lesions of histoplasmosis are generally associated with the disseminated form of histoplasmosis and may present as a fungating or ulcerative lesion of the oral mucosa. The histologic findings and differential diagnosis for oral histoplasmosis are discussed.

  11. Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

    Institute of Scientific and Technical Information of China (English)

    Carlos; W; Nossa; William; E; Oberdorf; Jφrn; A; Aas; Bruce; J; Paster; Todd; Z; DeSantis; Eoin; L; Brodie; Daniel; Malamud; Michael; A; Poles

    2010-01-01

    AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classifica...

  12. Improved Glucose Homeostasis in Obese Mice Treated With Resveratrol Is Associated With Alterations in the Gut Microbiome.

    Science.gov (United States)

    Sung, Miranda M; Kim, Ty T; Denou, Emmanuel; Soltys, Carrie-Lynn M; Hamza, Shereen M; Byrne, Nikole J; Masson, Grant; Park, Heekuk; Wishart, David S; Madsen, Karen L; Schertzer, Jonathan D; Dyck, Jason R B

    2017-02-01

    Oral administration of resveratrol is able to improve glucose homeostasis in obese individuals. Herein we show that resveratrol ingestion produces taxonomic and predicted functional changes in the gut microbiome of obese mice. In particular, changes in the gut microbiome were characterized by a decreased relative abundance of Turicibacteraceae, Moryella, Lachnospiraceae, and Akkermansia and an increased relative abundance of Bacteroides and Parabacteroides Moreover, fecal transplantation from healthy resveratrol-fed donor mice is sufficient to improve glucose homeostasis in obese mice, suggesting that the resveratrol-mediated changes in the gut microbiome may play an important role in the mechanism of action of resveratrol. © 2017 by the American Diabetes Association.

  13. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds enorm

  14. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2016-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds enorm

  15. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds

  16. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.

    Science.gov (United States)

    Shi, Baochen; Chang, Michaela; Martin, John; Mitreva, Makedonka; Lux, Renate; Klokkevold, Perry; Sodergren, Erica; Weinstock, George M; Haake, Susan K; Li, Huiying

    2015-02-17

    The human microbiome influences and reflects the health or disease state of the host. Periodontitis, a disease affecting about half of American adults, is associated with alterations in the subgingival microbiome of individual tooth sites. Although it can be treated, the disease can reoccur and may progress without symptoms. Without prognostic markers, follow-up examinations are required to assess reoccurrence and disease progression and to determine the need for additional treatments. To better identify and predict the disease progression, we aim to determine whether the subgingival microbiome can serve as a diagnosis and prognosis indicator. Using metagenomic shotgun sequencing, we characterized the dynamic changes in the subgingival microbiome in periodontitis patients before and after treatment at the same tooth sites. At the taxonomic composition level, the periodontitis-associated microorganisms were significantly shifted from highly correlated in the diseased state to poorly correlated after treatment, suggesting that coordinated interactions among the pathogenic microorganisms are essential to disease pathogenesis. At the functional level, we identified disease-associated pathways that were significantly altered in relative abundance in the two states. Furthermore, using the subgingival microbiome profile, we were able to classify the samples to their clinical states with an accuracy of 81.1%. Follow-up clinical examination of the sampled sites supported the predictive power of the microbiome profile on disease progression. Our study revealed the dynamic changes in the subgingival microbiome contributing to periodontitis and suggested potential clinical applications of monitoring the subgingival microbiome as an indicator in disease diagnosis and prognosis. Periodontitis is a common oral disease. Although it can be treated, the disease may reoccur without obvious symptoms. Current clinical examination parameters are useful in disease diagnosis but cannot

  17. Microbiomes associated with infective stages of root-knot and lesion nematodes in soil.

    Science.gov (United States)

    Elhady, Ahmed; Giné, Ariadna; Topalovic, Olivera; Jacquiod, Samuel; Sørensen, Søren J; Sorribas, Francisco Javier; Heuer, Holger

    2017-01-01

    Endoparasitic root-knot (Meloidogyne spp.) and lesion (Pratylenchus spp.) nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of phytonematodes in

  18. Microbiome interplay: plants alter microbial abundance and diversity within the built environment.

    Science.gov (United States)

    Mahnert, Alexander; Moissl-Eichinger, Christine; Berg, Gabriele

    2015-01-01

    The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria, and Eukaryota (fungi) increased on surrounding floor and wall surfaces within 6 months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g., Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  19. Microbiome interplay: plants alter microbial abundance and diversity within the built environment

    Directory of Open Access Journals (Sweden)

    Alexander eMahnert

    2015-08-01

    Full Text Available The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria and Eukaryota (fungi increased on surrounding floor and wall surfaces within six months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g. Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  20. Review of human hand microbiome research.

    Science.gov (United States)

    Edmonds-Wilson, Sarah L; Nurinova, Nilufar I; Zapka, Carrie A; Fierer, Noah; Wilson, Michael

    2015-10-01

    Recent advances have increased our understanding of the human microbiome, including the skin microbiome. Despite the importance of the hands as a vector for infection transmission, there have been no comprehensive reviews of recent advances in hand microbiome research or overviews of the factors that influence the composition of the hand microbiome. A comprehensive and systematic database search was conducted for skin microbiome-related articles published from January 1, 2008 to April 1, 2015. Only primary research articles that used culture-independent, whole community analysis methods to study the healthy hand skin microbiome were included. Eighteen articles were identified containing hand microbiome data. Most focused on bacteria, with relatively little reported on fungi, viruses, and protozoa. Bacteria from four phyla were found across all studies of the hand microbiome (most to least relative abundance): Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes. Key factors that impacted the hand microbiome composition included temporal and biogeographical dynamics, as well as intrinsic (age, gender) and extrinsic (product use, cohabitants, pet-ownership) variables. There was more temporal variability in the composition of the hand microbiome than in other body sites, making identification of the "normal" microbiome of the hands challenging. The microbiome of the hands is in constant flux as the hands are a critical vector for transmitting microorganisms between people, pets, inanimate objects and our environments. Future studies need to resolve methodological influences on results, and further investigate factors which alter the hand microbiome including the impact of products applied to hands. Increased understanding of the hand microbiome and the skin microbiome in general, will open the door to product development for disease prevention and treatment, and may lead to other applications, including novel diagnostic and forensic approaches.

  1. Microbiome and Gluten.

    Science.gov (United States)

    Sanz, Yolanda

    2015-01-01

    Celiac disease (CD) is a frequent chronic inflammatory enteropathy caused by gluten in genetically predisposed individuals that carry disease susceptibility genes (HLA-DQ2/8). These genes are present in about 30-40% of the general population, but only a small percentage of carriers develops CD. Gluten is the key environmental trigger of CD, but its intake does not fully explain disease onset; indeed, an increased number of cases experience gluten intolerance in late adulthood after many years of gluten exposure. Consequently, additional environmental factors seem to be involved in CD. Epidemiological studies indicate that common perinatal and early postnatal factors influence both CD risk and intestinal microbiota structure. Prospective studies in healthy infants at risk of developing CD also reveal that the HLA-DQ genotype, in conjunction with other environmental factors, influences the microbiota composition. Furthermore, CD patients have imbalances in the intestinal microbiota (dysbiosis), which are not fully normalized despite their adherence to a gluten-free diet. Therefore, it is hypothesized that the disease can promote dysbiosis that aggravates CD pathogenesis, and dysbiosis, in turn, can initiate and sustain inflammation through the expansion of proinflammatory pathobionts and decline of anti-inflammatory mutualistic bacteria. Studies in experimental models are also contributing to understand the role of intestinal bacteria and its interactions with a predisposed genotype in promoting CD. Advances in this area could aid in the development of microbiome-informed intervention strategies that optimize the partnership between the gut microbiota and host immunity for improving CD management.

  2. Gaia and her microbiome.

    Science.gov (United States)

    Stolz, John F

    2017-02-01

    The Gaia hypothesis, proposed 50 years ago, posits that the Earth's biosphere, atmosphere, hydrosphere and lithosphere interact as a cybernetic system, maintaining the long-term habitability of the planet. The resulting chemical composition of the atmosphere, oceans and crust is unique as compared to the other planets of our solar system, and due to the presence of life. Together these components comprise the biosphere, the life support system of the planet, with most of the essential processes carried out by microbes. Over a half of the elements in the periodic table are now known to have some biological role with many having complex biogeochemical cycles. The global microbiome inhabits a wide range of environments including deep into the Earth's crust, with a population of ∼10(30) cells and more than a trillion species. Deep sequencing projects have revealed hitherto unknown phyla and 'microbial dark matter'. The discoveries of conductive pili and cable bacteria have demonstrated that microbes transfer electrons to and from external sources, sometimes over significant distances, while research on quorum sensing and the plethora of microbial volatile organic substances have provided new insights into how microbes communicate. These advances in microbiology have expanded our understanding how Gaia could actually work. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Hypothesis testing and statistical analysis of microbiome

    Directory of Open Access Journals (Sweden)

    Yinglin Xia

    2017-09-01

    Full Text Available After the initiation of Human Microbiome Project in 2008, various biostatistic and bioinformatic tools for data analysis and computational methods have been developed and applied to microbiome studies. In this review and perspective, we discuss the research and statistical hypotheses in gut microbiome studies, focusing on mechanistic concepts that underlie the complex relationships among host, microbiome, and environment. We review the current available statistic tools and highlight recent progress of newly developed statistical methods and models. Given the current challenges and limitations in biostatistic approaches and tools, we discuss the future direction in developing statistical methods and models for the microbiome studies.

  4. Antibiotics and the resistant microbiome

    DEFF Research Database (Denmark)

    Sommer, Morten; Dantas, Gautam

    2011-01-01

    . Less appreciated are the concomitant changes in the human microbiome in response to these assaults and their contribution to clinical resistance problems. Studies have shown that pervasive changes to the human microbiota result from antibiotic treatment and that resistant strains can persist for years......Since the discovery and clinical application of antibiotics, pathogens and the human microbiota have faced a near continuous exposure to these selective agents. A well-established consequence of this exposure is the evolution of multidrug-resistant pathogens, which can become virtually untreatable....... Additionally, culture-independent functional characterization of the resistance genes from the microbiome has demonstrated a close evolutionary relationship between resistance genes in the microbiome and in pathogens. Application of these techniques and novel cultivation methods are expected to significantly...

  5. The Gut Microbiome and Obesity.

    Science.gov (United States)

    John, George Kunnackal; Mullin, Gerard E

    2016-07-01

    The gut microbiome consists of trillions of bacteria which play an important role in human metabolism. Animal and human studies have implicated distortion of the normal microbial balance in obesity and metabolic syndrome. Bacteria causing weight gain are thought to induce the expression of genes related to lipid and carbohydrate metabolism thereby leading to greater energy harvest from the diet. There is a large body of evidence demonstrating that alteration in the proportion of Bacteroidetes and Firmicutes leads to the development of obesity, but this has been recently challenged. It is likely that the influence of gut microbiome on obesity is much more complex than simply an imbalance in the proportion of these phyla of bacteria. Modulation of the gut microbiome through diet, pre- and probiotics, antibiotics, surgery, and fecal transplantation has the potential to majorly impact the obesity epidemic.

  6. Fungal Eye Infections

    Science.gov (United States)

    ... Treatment & Outcomes Statistics More Resources Fungal Nail Infections Histoplasmosis Definition Symptoms People at Risk & Prevention Sources Diagnosis & ... CDC at Work Global Fungal Diseases Cryptococcal Meningitis Histoplasmosis ... Resistance Resources Laboratory Submission Information Reportable Fungal ...

  7. The successful use of amphotericin B followed by oral posaconazole in a rare case of invasive fungal sinusitis caused by co-infection with mucormycosis and aspergillus

    Directory of Open Access Journals (Sweden)

    Sharana Mahomed

    2015-01-01

    Full Text Available We report on an unusual case of oro-rhinocerebral disease caused by mucormycosis and aspergillus co-infection in a 54-year-old insulin dependent diabetic patient. Although she was successfully treated with parenteral amphotericin B followed by oral posaconazole, she was left with irreversible blindness of the right eye and multiple cranial nerve palsies.

  8. Persistence of the Oral Probiotic Streptococcus salivarius M18 Is Dose Dependent and Megaplasmid Transfer Can Augment Their Bacteriocin Production and Adhesion Characteristics: e65991

    National Research Council Canada - National Science Library

    Jeremy P Burton; Philip A Wescombe; Jean M Macklaim; Melissa H C Chai; Kyle MacDonald; John D F Hale; John Tagg; Gregor Reid; Gregory B Gloor; Peter A Cadieux

    2013-01-01

      Bacteriocin-producing probiotic Streptococcus salivarius M18 offers beneficial modulatory capabilities within the oral microbiome, apparently through potent inhibitory activity against potentially...

  9. Metagenomic Analysis of the Human Gut Microbiome

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha

    Understanding the link between the human gut microbiome and human health is one of the biggest scientific challenges in our decade. Because 90% of our cells are bacteria, and the microbial genome contains 200 times more genes than the human genome, the study of the human microbiome has...... the potential to impact many areas of our health. This PhD thesis is the first study to generate a large amount of experimental data on the DNA and RNA of the human gut microbiome. This was made possible by our development of a human gut microbiome array capable of profiling any human gut microbiome. Analysis...... of our results changes the way we link the gut microbiome with diseases. Our results indicate that inflammatory diseases will affect the ecological system of the human gut microbiome, reducing its diversity. Classification analysis of healthy and unhealthy individuals demonstrates that unhealthy...

  10. Phylogenetics and the human microbiome.

    Science.gov (United States)

    Matsen, Frederick A

    2015-01-01

    The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.

  11. Where next for microbiome research?

    Directory of Open Access Journals (Sweden)

    Matthew K Waldor

    2015-01-01

    Full Text Available The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of "van Leeuwenhoek"-like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what's next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.

  12. Childhood Malnutrition and the Intestinal Microbiome Malnutrition and the microbiome

    Science.gov (United States)

    Kane, Anne V.; Dinh, Duy M.; Ward, Honorine D.

    2015-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 years, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it towards an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition. PMID:25356748

  13. The Serpentinite Subsurface Microbiome

    Science.gov (United States)

    Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

    2011-12-01

    Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

  14. 制霉菌素与氟康唑外用对口腔真菌感染治疗的效果分析%Efficacy analysis of external application of nystatin and fluconazole treatment of oral fungal infection

    Institute of Scientific and Technical Information of China (English)

    黄菊; 赵蔚萍; 雷先会

    2015-01-01

    目的:探讨制霉菌素与氟康唑外用两种治疗方案对于口腔真菌感染的临床治疗疗效,以指导临床更加规范化的治疗。方法将2011年8月-2013年8月间质性肺炎并发口腔真菌感染的64例患者随机分为制霉菌素组及氟康唑组,每组各32例,制霉菌素组给予制霉菌素药膏治疗,而氟康唑组给予氟康唑外用治疗,治疗结束后判断两组患者临床治疗疗效。结果两组患者感染真菌类别比较,差异无统计学意义;患者治疗后总有效率制霉菌素组为93.8%、氟康唑组为68.8%,制霉菌素组患者治疗总有效率明显高于氟康唑组,差异有统计学意义( P<0.05)。结论制霉菌素治疗间质性的肺炎所致口腔真菌感染患者的临床疗效,明显优于氟康唑外用的治疗有效率,同时治疗方法简单、安全。%OBJECTIVE To investigate clinical efficacy of nystatin vs .fluconazole for the treatment of oral fungal infection ,so as to guide more standardized clinical treatment . METHODS The 64 patients with interstitial pneumonia complicated by oral fungal infection during Aug .2011 to Aug .2013 were divided into the nystatin group and the fluconazole group with 32 patients in each group .The nystatin group was given nystatin ointment and the fluconazole group was given external fluconazole .The clinical efficacy was determined according to the clinical condition of the two groups of patients .RESULTS There was no significant difference in types of fungi between the two groups .The total effective rate was 93 .8% in the nystatin group and 68 .8% in the fluconazole group ,indicating the total efficiency in the nystatin group was significantly higher than in the fluconazole group (P<0 .05) .CONCLUSION The clinical efficacy of nystatin for the treatment of oral fungal infection caused by interstitial pneumonia was significantly superior to that of fluconazole and the treatment was simple ,safe and worthy

  15. Fungal distribution and drug sensitivity analysis of cancer patients with oral infection%肿瘤患者口腔感染真菌分布与药敏分析

    Institute of Scientific and Technical Information of China (English)

    李玲; 徐峰; 鞠博; 高振; 李伟

    2016-01-01

    目的:研究肿瘤患者口腔感染真菌分布及敏感性,为临床抗真菌药物的选择提供依据。方法选取2014年12月-2015年12月医院口腔科诊治82例肿瘤真菌感染患者临床资料,采集患者标本,分析肿瘤患者口腔感染真菌分布及其对抗真菌药物的敏感性,数据采用SPSS 18.0软件进行统计分析。结果82例口腔真菌感染肿瘤患者的科室分布相对较广,排前3位的科室分别为老年科、IC U 及内分泌科,分别占31.71%、28.05%及12.20%;肿瘤口腔感染患者中共分离出真菌103株,排在前3位的分别为白色假丝酵母菌、热带假丝酵母菌以及光滑假丝酵母菌,分别占50.49%、20.39%以及12.62%;白色假丝酵母菌、热带假丝酵母菌及光滑假丝酵母菌对两性霉素B敏感率均为100.00%。结论肿瘤患者口腔感染的真菌相对复杂,应加强真菌的分离、鉴定,并根据真菌类型进行药敏试验,选择敏感抗菌药物。%OBJECTIVE To study fungal distribution and sensitivity to drugs of cancer patients with oral infection , so as to provide reference about how to choose antifungal drugs in clinic .METHODS A total of 82 cases of cancer patients with fungal infections got treatment from department of stomatology in our hospital during Dec .2014 to Dec .2015 were selected and samples of these patients were collected to analyze fungal distribution and sensitivity to antifungal drugs by using SPSS 18 .0 to give statistic analysis .RESULTS The departments of 82 cancer patients with oral infection were distributed widely ,and the top three were department of geriatrics ,ICU and endocrinolo‐gy ,accounting for 31 .71% ,28 .05 and 12 .20% respectively .A total of 103 strains of fungi were isolated from the cancer patients with oral infection ,and the top three were Candida ,Candida tropicalis and Candida glabrata , accounting for 50 .49% ,20 .39% and 12 .62% ,respectively .Drug

  16. Control of the gut microbiome by fecal microRNA

    Directory of Open Access Journals (Sweden)

    Shirong Liu

    2016-03-01

    Full Text Available Since their discovery in the early 90s, microRNAs (miRNAs, small non-coding RNAs, have mainly been associated with posttranscriptional regulation of gene expression on a cell-autonomous level. Recent evidence has extended this role by adding inter-species communication to the manifold functional range. In our latest study [Liu S, et al., 2016, Cell Host & Microbe], we identified miRNAs in gut lumen and feces of both mice and humans. We found that intestinal epithelial cells (IEC and Hopx+ cells were the two main sources of fecal miRNA. Deficiency of IEC-miRNA resulted in gut dysbiosis and WT fecal miRNA transplantation restored the gut microbiota. We investigated potential mechanisms for this effect and found that miRNAs were able to regulate the gut microbiome. By culturing bacteria with miRNAs, we found that host miRNAs were able to enter bacteria, specifically regulate bacterial gene transcripts and affect bacterial growth. Oral administration of synthetic miRNA mimics affected specific bacteria in the gut. Our findings describe a previously unknown pathway by which the gut microbiome is regulated by the host and raises the possibility that miRNAs may be used therapeutically to manipulate the microbiome for the treatment of disease.

  17. Honey bee gut microbiome is altered by in-hive pesticide exposures

    Directory of Open Access Journals (Sweden)

    Madhavi Kakumanu

    2016-08-01

    Full Text Available Honey bees (Apis mellifera are the primary pollinators of major horticultural crops. Over the last few decades, a substantial decline in honey bees and their colonies have been reported. While a plethora of factors could contribute to the putative decline, pathogens and pesticides are common concerns that draw attention. In addition to potential direct effects on honey bees, indirect pesticide effects could include alteration of essential gut microbial communities and symbionts that are important to honey bee health (e.g. immune system. The primary objective of this study was to determine the microbiome associated with honey bees exposed to commonly used in-hive pesticides: coumaphos, tau-fluvalinate and chlorothalonil. Treatments were replicated at three independent locations near Blacksburg Virginia, and included a no-pesticide amended control at each location. The microbiome was characterized through pyrosequencing of V2-V3 regions of the bacterial 16S rRNA gene and fungal ITS region. Pesticide exposure significantly affected the structure of bacterial but not fungal communities. The bee bacteriome, similar to other studies, was dominated by sequences derived from Bacilli, Actinobacteria, α-, β-, γ-proteobacteria. The fungal community sequences were dominated by Ascomycetes and Basidiomycetes. The Multi-response permutation procedures (MRPP and subsequent Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt analysis indicated that chlorothalonil caused significant change to the structure and functional potential of the honey bee gut bacterial community relative to control. Putative genes for oxidative phosphorylation, for example, increased while sugar metabolism and peptidase potential declined in the microbiome of chlorothalonil exposed bees. The results of this field-based study suggest the potential for pesticide induced changes to the honey bee gut microbiome that warrant further investigation.

  18. Honey Bee Gut Microbiome Is Altered by In-Hive Pesticide Exposures.

    Science.gov (United States)

    Kakumanu, Madhavi L; Reeves, Alison M; Anderson, Troy D; Rodrigues, Richard R; Williams, Mark A

    2016-01-01

    Honey bees (Apis mellifera) are the primary pollinators of major horticultural crops. Over the last few decades, a substantial decline in honey bees and their colonies have been reported. While a plethora of factors could contribute to the putative decline, pathogens, and pesticides are common concerns that draw attention. In addition to potential direct effects on honey bees, indirect pesticide effects could include alteration of essential gut microbial communities and symbionts that are important to honey bee health (e.g., immune system). The primary objective of this study was to determine the microbiome associated with honey bees exposed to commonly used in-hive pesticides: coumaphos, tau-fluvalinate, and chlorothalonil. Treatments were replicated at three independent locations near Blacksburg Virginia, and included a no-pesticide amended control at each location. The microbiome was characterized through pyrosequencing of V2-V3 regions of the bacterial 16S rRNA gene and fungal ITS region. Pesticide exposure significantly affected the structure of bacterial but not fungal communities. The bee bacteriome, similar to other studies, was dominated by sequences derived from Bacilli, Actinobacteria, α-, β-, γ-proteobacteria. The fungal community sequences were dominated by Ascomycetes and Basidiomycetes. The Multi-response permutation procedures (MRPP) and subsequent Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated that chlorothalonil caused significant change to the structure and functional potential of the honey bee gut bacterial community relative to control. Putative genes for oxidative phosphorylation, for example, increased while sugar metabolism and peptidase potential declined in the microbiome of chlorothalonil exposed bees. The results of this field-based study suggest the potential for pesticide induced changes to the honey bee gut microbiome that warrant further investigation.

  19. Microbiome change by symbiotic invasion in lichens

    Science.gov (United States)

    Maier, Stefanie; Wedin, Mats; Fernandez-Brime, Samantha; Cronholm, Bodil; Westberg, Martin; Weber, Bettina; Grube, Martin

    2016-04-01

    Biological soil crusts (BSC) seal the soil surface from erosive forces in many habitats where plants cannot compete. Lichens symbioses of fungi and algae often form significant fraction of these microbial assemblages. In addition to the fungal symbiont, many species of other fungi can inhabit the lichenic structures and interact with their hosts in different ways, ranging from commensalism to parasitism. More than 1800 species of lichenicolous (lichen-inhabiting) fungi are known to science. One example is Diploschistes muscorum, a common species in lichen-dominated BSC that infects lichens of the genus Cladonia. D. muscorum starts as a lichenicolous fungus, invading the lichen Cladonia symphycarpa and gradually develops an independent Diploschistes lichen thallus. Furthermore, bacterial groups, such as Alphaproteobacteria and Acidobacteria, have been consistently recovered from lichen thalli and evidence is rapidly accumulating that these microbes may generally play integral roles in the lichen symbiosis. Here we describe lichen microbiome dynamics as the parasitic lichen D. muscorum takes over C. symphycarpa. We used high-throughput 16S rRNA gene and photobiont-specific ITS rDNA sequencing to track bacterial and algal transitions during the infection process, and employed fluorescence in situ hybridization to localize bacteria in the Cladonia and Diploschistes lichen thalli. We sampled four transitional stages, at sites in Sweden and Germany: A) Cladonia with no visible infection, B) early infection stage defined by the first visible Diploschistes thallus, C) late-stage infection with parts of the Cladonia thallus still identifiable, and D) final stage with a fully developed Diploschistes thallus, A gradual microbiome shift occurred during the transition, but fractions of Cladonia-associated bacteria were retained during the process of symbiotic reorganization. Consistent changes observed across sites included a notable decrease in the relative abundance of

  20. Xerostomia and the oral microflora

    NARCIS (Netherlands)

    Ligtenberg, A.J.M.; Almståhl, A.; Carpenter, G.

    2015-01-01

    Xerostomia is the feeling of a dry mouth usually caused by hyposalivation. It may occur after radiation therapy of the head and neck, in systemic diseases such as Sjögren’s syndrome, or as a side effect of medication. Hyposalivation changes the oral microbiome with the most dramatic changes after ra

  1. Oral candidiasis.

    Science.gov (United States)

    Millsop, Jillian W; Fazel, Nasim

    2016-01-01

    Oral candidiasis (OC) is a common fungal disease encountered in dermatology, most commonly caused by an overgrowth of Candida albicans in the mouth. Although thrush is a well-recognized presentation of OC, it behooves clinicians to be aware of the many other presentations of this disease and how to accurately diagnose and manage these cases. The clinical presentations of OC can be broadly classified as white or erythematous candidiasis, with various subtypes in each category. The treatments include appropriate oral hygiene, topical agents, and systemic medications. This review focuses on the various clinical presentations of OC and treatment options.

  2. Mucosal microbiome in patients with recurrent aphthous stomatitis.

    Science.gov (United States)

    Hijazi, K; Lowe, T; Meharg, C; Berry, S H; Foley, J; Hold, G L

    2015-03-01

    Recurrent aphthous stomatitis (RAS) is the most common disease affecting oral mucosae. Etiology is unknown, but several factors have been implicated, all of which influence the composition of microbiota residing on oral mucosae, which in turn modulates immunity and thereby affects disease progression. Although no individual pathogens have been conclusively shown to be causative agents of RAS, imbalanced composition of the oral microbiota may play a key role. In this study, we sought to determine composition profiles of bacterial microbiota in the oral mucosa associated with RAS. Using high-throughput 16S rRNA gene sequencing, we characterized the most abundant bacterial populations residing on healthy and ulcerated mucosae in patients with RAS (recruited using highly stringent criteria) and no associated medical conditions; we also compared these to the bacterial microbiota of healthy controls (HCs). Phylum-level diversity comparisons revealed decreased Firmicutes and increased Proteobacteria in ulcerated sites, as compared with healthy sites in RAS patients, and no differences between RAS patients with healthy sites and HCs. Genus-level analysis demonstrated higher abundance of total Bacteroidales in RAS patients with healthy sites over HCs. Porphyromonadaceae comprising species associated with periodontal disease and Veillonellaceae predominated in ulcerated sites over HCs, while no quantitative differences of these families were observed between healthy sites in RAS patients and HCs. Streptococcaceae comprising species associated with oral health predominated in HCs over ulcerated sites but not in HCs over healthy sites in RAS patients. This study demonstrates that mucosal microbiome changes in patients with idiopathic RAS--namely, increased Bacteroidales species in mucosae of RAS patients not affected by active ulceration. While these changes suggest a microbial role in initiation of RAS, this study does not provide data on causality. Within this limitation

  3. A Framework for Human Microbiome Research

    Science.gov (United States)

    2012-06-14

    microbiome ) exist throughout the human body, with fundamental roles in human health and disease . The National Institutes of Health (NIH)-funded Human...roles in human health and disease . The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population...human health and disease . The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale

  4. Childhood Malnutrition and the Intestinal Microbiome Malnutrition and the microbiome

    OpenAIRE

    2014-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 years, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has be...

  5. Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection

    Science.gov (United States)

    De Tender, Caroline; Haegeman, Annelies; Vandecasteele, Bart; Clement, Lieven; Cremelie, Pieter; Dawyndt, Peter; Maes, Martine; Debode, Jane

    2016-01-01

    Adding biochar, the solid coproduct of biofuel production, to peat can enhance strawberry growth, and disease resistance against the airborne fungal pathogen Botrytis cinerea. Additionally, biochar can induce shifts in the strawberry rhizosphere microbiome. However, the moment that this biochar-mediated shift occurs in the rhizosphere is not known. Further, the effect of an above-ground infection on the strawberry rhizosphere microbiome is unknown. In the present study we established two experiments in which strawberry transplants (cv. Elsanta) were planted either in peat or in peat amended with 3% biochar. First, we established a time course experiment to measure the effect of biochar on the rhizosphere bacterial and fungal communities over time. In a second experiment, we inoculated the strawberry leaves with B. cinerea, and studied the impact of the infection on the rhizosphere bacterial community. The fungal rhizosphere community was stabilized after 1 week, except for the upcoming Auriculariales, whereas the bacterial community shifted till 6 weeks. An effect of the addition of biochar to the peat on the rhizosphere microbiome was solely measured for the bacterial community from week 6 of plant growth onwards. When scoring the plant development, biochar addition was associated with enhanced root formation, fruit production, and postharvest resistance of the fruits against B. cinerea. We hypothesize that the bacterial rhizosphere microbiome, but also biochar-mediated changes in chemical substrate composition could be involved in these events. Infection of the strawberry leaves with B. cinerea induced shifts in the bacterial rhizosphere community, with an increased bacterial richness. This disease-induced effect was not observed in the rhizospheres of the B. cinerea-infected plants grown in the biochar-amended peat. The results show that an above-ground infection has its effect on the strawberry rhizosphere microbiome, changing the bacterial interactions in the

  6. Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice.

    Science.gov (United States)

    Brown, Kirsty; Godovannyi, Artem; Ma, Caixia; Zhang, YiQun; Ahmadi-Vand, Zahra; Dai, Chaunbin; Gorzelak, Monika A; Chan, YeeKwan; Chan, Justin M; Lochner, Arion; Dutz, Jan P; Vallance, Bruce A; Gibson, Deanna L

    2016-02-01

    Accumulating evidence supports that the intestinal microbiome is involved in Type 1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse model played a role in T1D through the gut. To examine the effect of the intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2) the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes onset, quantified CD4+T cells in the Peyer's patches, profiled the microbiome and measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice harbored more pathobionts and fewer beneficial microbes in comparison with NOR mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1 (Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic microbiome was characterized by a metagenome altered in several metabolic gene clusters. Furthermore, diabetes susceptibility correlated with reduced fecal SCFAs. In an attempt to correct the diabetogenic microbiome, we administered VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly and did not delay diabetes. We conclude that NOD mice harbor gut microbes that induce diabetes and that their diabetogenic microbiome can be amplified early in life through antibiotic exposure. Protective microbes like VSL#3 are insufficient to overcome the effects of a diabetogenic microbiome.

  7. Oral candidiasis: pathogenesis, clinical presentation, diagnosis and treatment strategies.

    Science.gov (United States)

    Lalla, Rajesh V; Patton, Lauren L; Dongari-Bagtzoglou, Anna

    2013-04-01

    Oral candidiasis is a clinical fungal infection that is the most common opportunistic infection affecting the human oral cavity. This article reviews the pathogenesis, clinical presentations, diagnosis and treatmentstrategies for oral candidiasis.

  8. Burden of fungal infections in Senegal.

    Science.gov (United States)

    Badiane, Aida S; Ndiaye, Daouda; Denning, David W

    2015-10-01

    Senegal has a high rate of tuberculosis and a low HIV seropositivity rate and aspergilloma, life-threatening fungal infections, dermatophytosis and mycetoma have been reported in this study. All published epidemiology papers reporting fungal infection rates from Senegal were identified. Where no data existed, we used specific populations at risk and fungal infection frequencies in each to estimate national incidence or prevalence. The results show that tinea capitis is common being found in 25% of children, ~1.5 million. About 191,000 Senegalese women get recurrent vaginal thrush, ≥4 times annually. We estimate 685 incident cases of chronic pulmonary aspergillosis (CPA) following TB and prevalence of 2160 cases. Asthma prevalence in adults varies from 3.2% to 8.2% (mean 5%); 9976 adults have allergic bronchopulmonary aspergillosis (ABPA) and 13,168 have severe asthma with fungal sensitisation (SAFS). Of the 59,000 estimated HIV-positive patients, 366 develop cryptococcal meningitis; 1149 develop Pneumocystis pneumonia and 1946 develop oesophageal candidiasis, in which oral candidiasis (53%) and dermatophytosis (16%) are common. Since 2008-2010, 113 cases of mycetoma were diagnosed. In conclusion, we estimate that 1,743,507 (12.5%) people in Senegal suffer from a fungal infection, excluding oral candidiasis, fungal keratitis, invasive candidiasis or aspergillosis. Diagnostic and treatment deficiencies should be rectified to allow epidemiological studies.

  9. Diagnosis and management of oral candidiasis.

    Science.gov (United States)

    Giannini, Peter J; Shetty, Kishore V

    2011-02-01

    Oral candidiasis is the most common fungal infection in both the immunocompetent and the immunocompromised populations. This article reviews the clinical presentations of the different forms of oral candidiasis, as well as the diagnosis and management.

  10. Context and the human microbiome.

    Science.gov (United States)

    McDonald, Daniel; Birmingham, Amanda; Knight, Rob

    2015-11-04

    Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study design considerations such as sample size decisions. We discuss the importance of reference sets in human microbiome research, limitations of existing resources, technical challenges to employing reference sets, examples of their usage, and contributions of the American Gut Project to the development of a comprehensive reference set. Through engaging the general public, the American Gut Project aims to address many of the issues present in existing reference resources, characterizing health and disease, lifestyle, and dietary choices of the participants while extending its efforts globally through international collaborations.

  11. Microbiome Tools for Forensic Science.

    Science.gov (United States)

    Metcalf, Jessica L; Xu, Zhenjiang Z; Bouslimani, Amina; Dorrestein, Pieter; Carter, David O; Knight, Rob

    2017-09-01

    Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics. Copyright © 2017. Published by Elsevier Ltd.

  12. Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria.

    Science.gov (United States)

    Sukumar, S; Roberts, A P; Martin, F E; Adler, C J

    2016-08-01

    Antibiotic resistance is considered one of the greatest threats to global public health. Resistance is often conferred by the presence of antibiotic resistance genes (ARGs), which are readily found in the oral microbiome. In-depth genetic analyses of the oral microbiome through metagenomic techniques reveal a broad distribution of ARGs (including novel ARGs) in individuals not recently exposed to antibiotics, including humans in isolated indigenous populations. This has resulted in a paradigm shift from focusing on the carriage of antibiotic resistance in pathogenic bacteria to a broader concept of an oral resistome, which includes all resistance genes in the microbiome. Metagenomics is beginning to demonstrate the role of the oral resistome and horizontal gene transfer within and between commensals in the absence of selective pressure, such as an antibiotic. At the chairside, metagenomic data reinforce our need to adhere to current antibiotic guidelines to minimize the spread of resistance, as such data reveal the extent of ARGs without exposure to antimicrobials and the ecologic changes created in the oral microbiome by even a single dose of antibiotics. The aim of this review is to discuss the role of metagenomics in the investigation of the oral resistome, including the transmission of antibiotic resistance in the oral microbiome. Future perspectives, including clinical implications of the findings from metagenomic investigations of oral ARGs, are also considered. © International & American Associations for Dental Research 2016.

  13. Short Course in the Microbiome

    Directory of Open Access Journals (Sweden)

    Kimberly Falana

    2015-07-01

    provides us with ideas as to how we can manipulate our microbiome to prevent certain diseases. However, given the variety of applications, there are scientific challenges, though there are very promising areas in reference to the clinical benefits of understanding more about our micro‐ biome, whether in our gut or on our skin: the outlook is bright. A summary of the short course is presented as a meeting dispatch.

  14. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

    Science.gov (United States)

    Turner, Thomas R; Ramakrishnan, Karunakaran; Walshaw, John; Heavens, Darren; Alston, Mark; Swarbreck, David; Osbourn, Anne; Grant, Alastair; Poole, Philip S

    2013-01-01

    Plant–microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants. PMID:23864127

  15. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants.

    Science.gov (United States)

    Turner, Thomas R; Ramakrishnan, Karunakaran; Walshaw, John; Heavens, Darren; Alston, Mark; Swarbreck, David; Osbourn, Anne; Grant, Alastair; Poole, Philip S

    2013-12-01

    Plant-microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.

  16. Novel device to sample the esophageal microbiome--the esophageal string test.

    Directory of Open Access Journals (Sweden)

    Sophie A Fillon

    Full Text Available A growing number of studies implicate the microbiome in the pathogenesis of intestinal inflammation. Previous work has shown that adults with esophagitis related to gastroesophageal reflux disease have altered esophageal microbiota compared to those who do not have esophagitis. In these studies, sampling of the esophageal microbiome was accomplished by isolating DNA from esophageal biopsies obtained at the time of upper endoscopy. The aim of the current study was to identify the esophageal microbiome in pediatric individuals with normal esophageal mucosa using a minimally invasive, capsule-based string technology, the Enterotest™. We used the proximal segment of the Enterotest string to sample the esophagus, and term this the "Esophageal String Test" (EST. We hypothesized that the less invasive EST would capture mucosal adherent bacteria present in the esophagus in a similar fashion as mucosal biopsy. EST samples and mucosal biopsies were collected from children with no esophageal inflammation (n = 15 and their microbiome composition determined by 16S rRNA gene sequencing. Microbiota from esophageal biopsies and ESTs produced nearly identical profiles of bacterial genera and were different from the bacterial contents of samples collected from the nasal and oral cavity. We conclude that the minimally invasive EST can serve as a useful device for study of the esophageal microbiome.

  17. Furcation Therapy With Enamel Matrix Derivative: Effects on the Subgingival Microbiome.

    Science.gov (United States)

    Queiroz, Lucas A; Casarin, Renato C V; Dabdoub, Shareef M; Tatakis, Dimitris N; Sallum, Enilson A; Kumar, Purnima S

    2017-07-01

    Although enamel matrix derivative (EMD) has been used to promote periodontal regeneration, little is known of its effect on the microbiome. Therefore, this investigation aims to identify changes in periodontal microbiome after treatment with EMD using a deep-sequencing approach. Thirty-nine patients with mandibular Class II buccal furcation defects were randomized to beta-tricalcium-phosphate/hydroxyapatite graft (BONE group), EMD+BONE, or EMD alone. Plaque was collected from furcation defects at baseline and 3 and 6 months post-treatment. Bacterial DNA was analyzed using terminal restriction fragment length polymorphism and 16S pyrotag sequencing, resulting in 169,000 classifiable sequences being compared with the Human Oral Microbiome Database. Statistical comparisons were made using parametric tests. At baseline, a total of 422 species were identified from the 39 defects, belonging to Fusobacterium, Pseudomonas, Streptococcus, Filifactor, and Parvimonas. All three regenerative procedures predictably altered the disease-associated microbiome, with a restitution of health-compatible species. However, EMD and BONE+EMD groups demonstrated more long-term reductions in a higher number of species than the BONE group (P <0.05), especially disease-associated species, e.g., Selenomonas noxia, F. alocis, and Fusobacterium. EMD treatment predictably alters a dysbiotic subgingival microbiome, decreasing pathogen richness and increasing commensal abundance. Further investigations are needed to investigate how this impacts regenerative outcomes.

  18. Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces.

    Science.gov (United States)

    Zaura, Egija; Brandt, Bernd W; Teixeira de Mattos, M Joost; Buijs, Mark J; Caspers, Martien P M; Rashid, Mamun-Ur; Weintraub, Andrej; Nord, Carl Erik; Savell, Ann; Hu, Yanmin; Coates, Antony R; Hubank, Mike; Spratt, David A; Wilson, Michael; Keijser, Bart J F; Crielaard, Wim

    2015-11-10

    Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body. Many health care professionals use antibiotic prophylaxis strategies to prevent

  19. Microbial cargo: do bacteria on symbiotic propagules reinforce the microbiome of lichens?

    Science.gov (United States)

    Aschenbrenner, Ines Aline; Cardinale, Massimiliano; Berg, Gabriele; Grube, Martin

    2014-12-01

    According to recent research, bacteria contribute as recurrent associates to the lichen symbiosis. Yet, the variation of the microbiomes within species and across geographically separated populations remained largely elusive. As a quite common dispersal mode, lichens evolved vertical transmission of both fungal and algal partners in specifically designed mitotic propagules. Bacteria, if co-transmitted with these symbiotic propagules, could contribute to a geographical structure of lichen-associated microbiomes. The lung lichen was sampled from three localities in eastern Austria to analyse their associated bacterial communities by bar-coded pyrosequencing, network analysis and fluorescence in situ hybridization. For the first time, bacteria were documented to colonize symbiotic propagules of lichens developed for short-distance transmission of the symbionts. The propagules share the overall bacterial community structure with the thalli at class level, except for filamentous Cyanobacteria (Nostocophycideae), and with Alphaproteobacteria as predominant group. All three sampling sites share a core fraction of the microbiome. Bacterial communities of lichen thalli from the same sampling site showed higher similarity than those of distant populations. This variation and the potential co-dispersal of a microbiome fraction with structures of the host organism contribute new aspects to the 'everything is everywhere' hypothesis. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Introduction: Microbiome in human reproduction.

    Science.gov (United States)

    Franasiak, Jason M; Scott, Richard T

    2015-12-01

    The human microbiome has been termed the "second human genome" and data that has come about of late certainly makes it appear every bit as complex. The human body contains 10-fold more microbial cells than the human cells and accounts for 1%-3% of our total body mass. As we learn more about this symbiotic relationship, it appears this complex interaction occurs in nearly every part of the body, even those areas at one time considered to be sterile. Indeed, the microbiome in human reproduction has been investigated in terms of both the lower and upper reproductive tract and includes interactions even at the point of gametogenesis. What is all the more fascinating is that we have known about the importance of microbes for over 150 years, even before they existed in name. And now, with the assistance of an exciting technologic revolution which has pushed forward our understanding of the microbiome, we appear to stand on the precipice of a higher level of understanding of microbes, the biofilms they create, and their impact of health and disease in human reproduction.

  1. Microbiome/microbiota and allergies.

    Science.gov (United States)

    Inoue, Yuzaburo; Shimojo, Naoki

    2015-01-01

    Allergies are characterized by a hypersensitive immune reaction to originally harmless antigens. In recent decades, the incidence of allergic diseases has markedly increased, especially in developed countries. The increase in the frequency of allergic diseases is thought to be primarily due to environmental changes related to a westernized lifestyle, which affects the commensal microbes in the human body. The human gut is the largest organ colonized by bacteria and contains more than 1000 bacterial species, called the "gut microbiota." The recent development of sequencing technology has enabled researchers to genetically investigate and clarify the diversity of all species of commensal microbes. The collective genomes of commensal microbes are together called the "microbiome." Although the detailed mechanisms remain unclear, it has been proposed that the microbiota/microbiome, especially that in the gut, impacts the systemic immunity and metabolism, thus affecting the development of various immunological diseases, including allergies. In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.

  2. Xenobiotic Metabolism and Gut Microbiomes

    Science.gov (United States)

    Das, Anubhav; Srinivasan, Meenakshi; Ghosh, Tarini Shankar; Mande, Sharmila S.

    2016-01-01

    Humans are exposed to numerous xenobiotics, a majority of which are in the form of pharmaceuticals. Apart from human enzymes, recent studies have indicated the role of the gut bacterial community (microbiome) in metabolizing xenobiotics. However, little is known about the contribution of the plethora of gut microbiome in xenobiotic metabolism. The present study reports the results of analyses on xenobiotic metabolizing enzymes in various human gut microbiomes. A total of 397 available gut metagenomes from individuals of varying age groups from 8 nationalities were analyzed. Based on the diversities and abundances of the xenobiotic metabolizing enzymes, various bacterial taxa were classified into three groups, namely, least versatile, intermediately versatile and highly versatile xenobiotic metabolizers. Most interestingly, specific relationships were observed between the overall drug consumption profile and the abundance and diversity of the xenobiotic metabolizing repertoire in various geographies. The obtained differential abundance patterns of xenobiotic metabolizing enzymes and bacterial genera harboring them, suggest their links to pharmacokinetic variations among individuals. Additional analyses of a few well studied classes of drug modifying enzymes (DMEs) also indicate geographic as well as age specific trends. PMID:27695034

  3. Gut microbiome and metabolic syndrome.

    Science.gov (United States)

    Mazidi, Mohsen; Rezaie, Peyman; Kengne, Andre Pascal; Mobarhan, Majid Ghayour; Ferns, Gordon A

    2016-01-01

    The gut microbiome contributes approximately 2kg of the whole body weight, and recent studies suggest that gut microbiota has a profound effect on human metabolism, potentially contributing to several features of the metabolic syndrome. Metabolic syndrome is defined by a clustering of metabolic disorders that include central adiposity with visceral fat accumulation, dyslipidemia, insulin resistance, dysglycemia and non-optimal blood pressure levels. Metabolic syndrome is associated with an increased risk of cardiovascular diseases and type 2 diabetes. It is estimated that around 20-25 percent of the world's adult population has metabolic syndrome. In this manuscript, we have reviewed the existing data linking gut microbiome with metabolic syndrome. Existing evidence from studies both in animals and humans support a link between gut microbiome and various components of metabolic syndrome. Possible pathways include involvement with energy homeostasis and metabolic processes, modulation of inflammatory signaling pathways, interferences with the immune system, and interference with the renin-angiotensin system. Modification of gut microbiota via prebiotics, probiotics or other dietary interventions has provided evidence to support a possible beneficial effect of interventions targeting gut microbiota modulation to treat components or complications of metabolic syndrome.

  4. Immunological Consequences of Intestinal Fungal Dysbiosis.

    Science.gov (United States)

    Wheeler, Matthew L; Limon, Jose J; Bar, Agnieszka S; Leal, Christian A; Gargus, Matthew; Tang, Jie; Brown, Jordan; Funari, Vincent A; Wang, Hanlin L; Crother, Timothy R; Arditi, Moshe; Underhill, David M; Iliev, Iliyan D

    2016-06-08

    Compared to bacteria, the role of fungi within the intestinal microbiota is poorly understood. In this study we investigated whether the presence of a "healthy" fungal community in the gut is important for modulating immune function. Prolonged oral treatment of mice with antifungal drugs resulted in increased disease severity in acute and chronic models of colitis, and also exacerbated the development of allergic airway disease. Microbiota profiling revealed restructuring of fungal and bacterial communities. Specifically, representation of Candida spp. was reduced, while Aspergillus, Wallemia, and Epicoccum spp. were increased. Oral supplementation with a mixture of three fungi found to expand during antifungal treatment (Aspergillus amstelodami, Epicoccum nigrum, and Wallemia sebi) was sufficient to recapitulate the exacerbating effects of antifungal drugs on allergic airway disease. Taken together, these results indicate that disruption of commensal fungal populations can influence local and peripheral immune responses and enhance relevant disease states.

  5. The Willow Microbiome is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects

    Directory of Open Access Journals (Sweden)

    Stacie Tardif

    2016-09-01

    Full Text Available The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and, after two growing seasons, bulk soil, rhizosphere soil, roots and stems samples of two willow cultivars (Salix purpurea cv. FishCreek and Salix miyabeana cv. SX67 growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS regions were amplified and sequenced using an Ion Torrent Personal Genome Machine. Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment and thus protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.

  6. Analyses of the microbial diversity across the human microbiome.

    Directory of Open Access Journals (Sweden)

    Kelvin Li

    Full Text Available Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ", based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for

  7. Bespoke microbiome therapy to manage plant diseases

    Directory of Open Access Journals (Sweden)

    Murali eGopal

    2013-12-01

    Full Text Available Advanced biological technologies are revealing that the microbiome, located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a ‘core-microbiome’ exists that plays the pivotal role. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can become a viable strategy for management of plant diseases in future.

  8. The microbiome-systemic diseases connection

    NARCIS (Netherlands)

    van der Meulen, T. A.; Harmsen, H. J. M.; Bootsma, H.; Spijkervet, F. K. L.; Kroese, F. G. M.; Vissink, A.

    2016-01-01

    The human microbiome consists of all microorganisms occupying the skin, mucous membranes and intestinal tract of the human body. The contact of the mucosal immune system with the human microbiome is a balanced interplay between defence mechanisms of the immune system and symbiotic or pathogenic micr

  9. Different types of fungal sinusitis occurring concurrently: implications for therapy.

    Science.gov (United States)

    Rupa, V; Thomas, Meera

    2013-02-01

    The purpose of this study is to describe the clinical and histopathological features, management and outcome of a series of patients with simultaneous occurrence of invasive and non-invasive fungal sinusitis (mixed fungal sinusitis). The histopathological records of patients with fungal sinusitis seen over the last 6 years were reviewed. The clinical, histopathological, treatment and follow up details of all cases with mixed fungal sinusitis were noted. Six cases of mixed fungal sinusitis with concurrent occurrence of chronic granulomatous fungal sinusitis and allergic fungal sinusitis (AFS) were seen during the study period. Most (83.3 %) had bilateral disease. All patients had undergone prior endoscopic sinus surgery at least once within the previous 2 years. Histopathological features showed predominance of invasive disease in half the patients. Except for one patient who did not report for follow up, all patients with predominant chronic granulomatous fungal sinusitis received systemic antifungal therapy and inhaled steroids. Those with predominant features of AFS received oral and inhaled steroids. Five patients with mixed fungal sinusitis who had follow up ranging from 6 months to 5 years were disease free following treatment. Mixed fungal sinusitis should be recognized by the surgeon and pathologist as a separate category of fungal sinusitis whose treatment depends on accurate histological diagnosis. A good outcome may be expected with appropriate therapy.

  10. Application of metagenomics in understanding oral health and disease.

    Science.gov (United States)

    Xu, Ping; Gunsolley, John

    2014-04-01

    Oral diseases including periodontal disease and caries are some of the most prevalent infectious diseases in humans. Different microbial species cohabitate and form a polymicrobial biofilm called dental plaque in the oral cavity. Metagenomics using next generation sequencing technologies has produced bacterial profiles and genomic profiles to study the relationships between microbial diversity, genetic variation, and oral diseases. Several oral metagenomic studies have examined the oral microbiome of periodontal disease and caries. Gene annotations in these studies support the association of specific genes or metabolic pathways with oral health and with specific diseases. The roles of pathogenic species and functions of specific genes in oral disease development have been recognized by metagenomic analysis. A model is proposed in which three levels of interactions occur in the oral microbiome that determines oral health or disease.

  11. Entomopathogenic fungal endophytes

    Science.gov (United States)

    Fungal endophytes are quite common in nature and some of them have been shown to have adverse effects against insects, nematodes, and plant pathogens. An introduction to fungal endophytes will be presented, followed by a discussion of research aimed at introducing Beauveria bassiana as a fungal endo...

  12. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.

    Science.gov (United States)

    Bikel, Shirley; Valdez-Lara, Alejandra; Cornejo-Granados, Fernanda; Rico, Karina; Canizales-Quinteros, Samuel; Soberón, Xavier; Del Pozo-Yauner, Luis; Ochoa-Leyva, Adrián

    2015-01-01

    The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.

  13. Antenatal Microbiome: Potential Contributor to Fetal Programming and Establishment of the Microbiome in Offspring.

    Science.gov (United States)

    Wright, Michelle L; Starkweather, Angela R

    2015-01-01

    Endogenous and exogenous exposures during fetal development have potential to impact birth and health outcomes of offspring. Accumulating evidence suggests exposures may alter the antenatal microbiome and subsequently alter the microbiome and health of offspring. The purpose of this integrative review is to summarize and critically evaluate the current state of knowledge regarding the assessment of the antenatal microbiome on the health of human offspring. The article provides a brief summary of the known factors affecting the human microbiome and studies that assessed relationships between the antenatal microbiome and health outcomes of the offspring. An integrative review was conducted to examine human research studies that focused on the antenatal microbiome and the health of the offspring using the electronic databases PubMed/MEDLINE and CINAHL from 2004 to the present. In addition to the known individual factors that are associated with establishment of the microbiome, the results of the integrative review suggest that medications (including antibiotics) and comorbidities (including infectious diseases, diet, socioeconomic status, and exposure to pollutants) should also be measured. The composition of the antenatal microbiome at various time points and body sites may be important mediators of short- and long-term health outcomes in offspring. In order to advance our understanding of the role of the antenatal microbiome on health and disease risk of the offspring, it will be important to further elucidate the composition of a healthy microbiome and specific mechanisms that contribute to altered health in later life.

  14. Oral candidosis in lichen planus

    DEFF Research Database (Denmark)

    Kragelund, Camilla; Kieffer-Kristensen, L; Reibel, J;

    2012-01-01

    OBJECTIVES: Candida albicans is the most common fungal pathogen in humans, but other Candida species cause candidosis. Candida species display significant differences in their susceptibility to antimycotic drugs. Patients with symptomatic or erythematous oral lichen planus (OLP) commonly have...

  15. Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii.

    Directory of Open Access Journals (Sweden)

    Mary E Lucero

    Full Text Available Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.

  16. Modeling the Dynamic Digestive System Microbiome

    Directory of Open Access Journals (Sweden)

    Anne M. Estes

    2015-08-01

    Full Text Available “Modeling the Dynamic Digestive System Microbiome” is a hands-on activity designed to demonstrate the dynamics of microbiome ecology using dried pasta and beans to model disturbance events in the human digestive system microbiome. This exercise demonstrates how microbiome diversity is influenced by: 1 niche availability and habitat space and 2 a major disturbance event, such as antibiotic use. Students use a pictorial key to examine prepared models of digestive system microbiomes to determine what the person with the microbiome “ate.” Students then model the effect of taking antibiotics by removing certain “antibiotic sensitive” pasta. Finally, they add in “environmental microbes” or “native microbes” to recolonize the digestive system, determine how resilient their model microbome community is to disturbance, and discuss the implications. Throughout the exercise, students discuss differences in the habitat space available and microbiome community diversity. This exercise can be modified to discuss changes in the microbiome due to diet shifts and the emergence of antibiotic resistance in more depth.

  17. The human microbiome and juvenile idiopathic arthritis.

    Science.gov (United States)

    Verwoerd, Anouk; Ter Haar, Nienke M; de Roock, Sytze; Vastert, Sebastiaan J; Bogaert, Debby

    2016-09-20

    Juvenile idiopathic arthritis (JIA) is the most common rheumatic disease in childhood. The pathogenesis of JIA is thought to be the result of a combination of host genetic and environmental triggers. However, the precise factors that determine one's susceptibility to JIA remain to be unravelled. The microbiome has received increasing attention as a potential contributing factor to the development of a wide array of immune-mediated diseases, including inflammatory bowel disease, type 1 diabetes and rheumatoid arthritis. Also in JIA, there is accumulating evidence that the composition of the microbiome is different from healthy individuals. A growing body of evidence indeed suggests that, among others, the microbiome may influence the development of the immune system, the integrity of the intestinal mucosal barrier, and the differentiation of T cell subsets. In turn, this might lead to dysregulation of the immune system, thereby possibly playing a role in the development of JIA. The potential to manipulate the microbiome, for example by faecal microbial transplantation, might then offer perspectives for future therapeutic interventions. Before we can think of such interventions, we need to first obtain a deeper understanding of the cause and effect relationship between JIA and the microbiome. In this review, we discuss the existing evidence for the involvement of the microbiome in JIA pathogenesis and explore the potential mechanisms through which the microbiome may influence the development of autoimmunity in general and JIA specifically.

  18. Lung microbiome dynamics in COPD exacerbations.

    Science.gov (United States)

    Wang, Zhang; Bafadhel, Mona; Haldar, Koirobi; Spivak, Aaron; Mayhew, David; Miller, Bruce E; Tal-Singer, Ruth; Johnston, Sebastian L; Ramsheh, Mohammadali Yavari; Barer, Michael R; Brightling, Christopher E; Brown, James R

    2016-04-01

    Increasing evidence suggests that the lung microbiome plays an important role in chronic obstructive pulmonary disease (COPD) severity. However, the dynamics of the lung microbiome during COPD exacerbations and its potential role in disease aetiology remain poorly understood.We completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on 476 sputum samples collected from 87 subjects with COPD at four visits defined as stable state, exacerbation, 2 weeks post-therapy and 6 weeks recovery.Our analysis revealed a dynamic lung microbiota where changes appeared to be associated with exacerbation events and indicative of specific exacerbation phenotypes. Antibiotic and steroid treatments appear to have differential effects on the lung microbiome. We depict a microbial interaction network for the lung microbiome and suggest that perturbation of a few bacterial operational taxonomic units, in particular Haemophilus spp., could greatly impact the overall microbial community structure. Furthermore, several serum and sputum biomarkers, in particular sputum interleukin-8, appear to be highly correlated with the structure and diversity of the microbiome.Our study furthers the understanding of lung microbiome dynamics in COPD patients and highlights its potential as a biomarker, and possibly a target, for future respiratory therapeutics.

  19. The Intestinal Microbiome in Spondyloarthritis

    Science.gov (United States)

    Gill, Tejpal; Asquith, Mark; Rosenbaum, James T.; Colbert, Robert A.

    2015-01-01

    Purpose of the review Microbial dysbiosis in the gut is emerging as a common component in various inflammatory disorders including spondyloarthritis (SpA). The depth of this influence has begun to be realized with next generation sequencing of the gut microbiome providing unbiased assessment of previously uncharted bacterial populations. Recent findings Decreased numbers of Firmicutes, a major phyla of gut commensals, especially the species Faecalibacterium prausnitzii and Clostridium leptum have been found in various inflammatory disorders including SpA and IBD, and could be an important link between SpA and gut inflammation. Multiple studies in ankylosing spondylitis, psoriatic arthritis, juvenile SpA and animals models of SpA are revealing common bacterial associations among these diseases as well as IBD. Summary We are beginning to appreciate the complex relationship between the gut microbiome and host immune regulation and dysregulation in health and disease. Potentially important differences have been revealed in SpA, but cause and effect relationships remain far from established. Many critical questions remain to be answered before we can apply new knowledge to improve therapeutics in SpA. PMID:26002022

  20. The gut microbiome modulates colon tumorigenesis.

    Science.gov (United States)

    Zackular, Joseph P; Baxter, Nielson T; Iverson, Kathryn D; Sadler, William D; Petrosino, Joseph F; Chen, Grace Y; Schloss, Patrick D

    2013-11-05

    Recent studies have shown that individuals with colorectal cancer have an altered gut microbiome compared to healthy controls. It remains unclear whether these differences are a response to tumorigenesis or actively drive tumorigenesis. To determine the role of the gut microbiome in the development of colorectal cancer, we characterized the gut microbiome in a murine model of inflammation-associated colorectal cancer that mirrors what is seen in humans. We followed the development of an abnormal microbial community structure associated with inflammation and tumorigenesis in the colon. Tumor-bearing mice showed enrichment in operational taxonomic units (OTUs) affiliated with members of the Bacteroides, Odoribacter, and Akkermansia genera and decreases in OTUs affiliated with members of the Prevotellaceae and Porphyromonadaceae families. Conventionalization of germfree mice with microbiota from tumor-bearing mice significantly increased tumorigenesis in the colon compared to that for animals colonized with a healthy gut microbiome from untreated mice. Furthermore, at the end of the model, germfree mice colonized with microbiota from tumor-bearing mice harbored a higher relative abundance of populations associated with tumor formation in conventional animals. Manipulation of the gut microbiome with antibiotics resulted in a dramatic decrease in both the number and size of tumors. Our results demonstrate that changes in the gut microbiome associated with inflammation and tumorigenesis directly contribute to tumorigenesis and suggest that interventions affecting the composition of the microbiome may be a strategy to prevent the development of colon cancer. The trillions of bacteria that live in the gut, known collectively as the gut microbiome, are important for normal functioning of the intestine. There is now growing evidence that disruptive changes in the gut microbiome are strongly associated with the development colorectal cancer. However, how the gut microbiome

  1. Activity of potent and selective host defense peptide mimetics in mouse models of oral candidiasis.

    Science.gov (United States)

    Ryan, Lisa K; Freeman, Katie B; Masso-Silva, Jorge A; Falkovsky, Klaudia; Aloyouny, Ashwag; Markowitz, Kenneth; Hise, Amy G; Fatahzadeh, Mahnaz; Scott, Richard W; Diamond, Gill

    2014-07-01

    There is a strong need for new broadly active antifungal agents for the treatment of oral candidiasis that not only are active against many species of Candida, including drug-resistant strains, but also evade microbial countermeasures which may lead to resistance. Host defense peptides (HDPs) can provide a foundation for the development of such agents. Toward this end, we have developed fully synthetic, small-molecule, nonpeptide mimetics of the HDPs that improve safety and other pharmaceutical properties. Here we describe the identification of several HDP mimetics that are broadly active against C. albicans and other species of Candida, rapidly fungicidal, and active against yeast and hyphal cultures and that exhibit low cytotoxicity for mammalian cells. Importantly, specificity for Candida over commensal bacteria was also evident, thereby minimizing potential damage to the endogenous microbiome which otherwise could favor fungal overgrowth. Three compounds were tested as topical agents in two different mouse models of oral candidiasis and were found to be highly active. Following single-dose administrations, total Candida burdens in tongues of infected animals were reduced up to three logs. These studies highlight the potential of HDP mimetics as a new tool in the antifungal arsenal for the treatment of oral candidiasis.

  2. Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients

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    Dang Angeline T

    2012-07-01

    Full Text Available Abstract Background Opportunistic oral infections can be found in over 80% of HIV + patients, often causing debilitating lesions that also contribute to deterioration in nutritional health. Although appreciation for the role that the microbiota is likely to play in the initiation and/or enhancement of oral infections has grown considerably in recent years, little is known about the impact of HIV infection on host-microbe interactions within the oral cavity. In the current study, we characterize modulations in the bacterial composition of the lingual microbiome in patients with treated and untreated HIV infection. Bacterial species profiles were elucidated by microarray assay and compared between untreated HIV infected patients, HIV infected patients receiving antiretroviral therapy, and healthy HIV negative controls. The relationship between clinical parameters (viral burden and CD4+ T cell depletion and the loss or gain of bacterial species was evaluated in each HIV patient group. Results In untreated HIV infection, elevated viremia was associated with significantly higher proportions of potentially pathogenic Veillonella, Prevotella, Megasphaera, and Campylobacter species in the lingual microbiome than observed in healthy controls. The upsurge in the prevalence of potential pathogens was juxtaposed by diminished representation of commensal Streptococcus and Veillonella species. Colonization of Neisseria flavescens was lower in the lingual microbiome of HIV infected patients receiving antiretroviral therapy than in uninfected controls. Conclusions Our findings provide novel insights into the potential impact of HIV infection and antiretroviral therapy on the community structure of the oral microbiome, and implicate potential mechanisms that may increase the capacity of non-commensal species to gain a stronger foothold.

  3. Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment

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    Christine V Avena

    2016-11-01

    Full Text Available Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States (n=45 and Colorado (n=119, as well as environmental samples (n=38 from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria. A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host

  4. Uncovering unseen fungal diversity from plant DNA banks

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    Erin M. Datlof

    2017-08-01

    Full Text Available Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms’ associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae. Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.

  5. Towards understanding oral health.

    Science.gov (United States)

    Zaura, Egija; ten Cate, Jacob M

    2015-01-01

    During the last century, dental research has focused on unraveling the mechanisms behind various oral pathologies, while oral health was typically described as the mere absence of oral diseases. The term 'oral microbial homeostasis' is used to describe the capacity of the oral ecosystem to maintain microbial community stability in health. However, the oral ecosystem itself is not stable: throughout life an individual undergoes multiple physiological changes while progressing through infancy, childhood, adolescence, adulthood and old age. Recent discussions on the definition of general health have led to the proposal that health is the ability of the individual to adapt to physiological changes, a condition known as allostasis. In this paper the allostasis principle is applied to the oral ecosystem. The multidimensionality of the host factors contributing to allostasis in the oral cavity is illustrated with an example on changes occurring in puberty. The complex phenomenon of oral health and the processes that prevent the ecosystem from collapsing during allostatic changes in the entire body are far from being understood. As yet individual components (e.g. hard tissues, microbiome, saliva, host response) have been investigated, while only by consolidating these and assessing their multidimensional interactions should we be able to obtain a comprehensive understanding of the ecosystem, which in turn could serve to develop rational schemes to maintain health. Adapting such a 'system approach' comes with major practical challenges for the entire research field and will require vast resources and large-scale multidisciplinary collaborations.

  6. Reproductive tract microbiome in assisted reproductive technologies.

    Science.gov (United States)

    Franasiak, Jason M; Scott, Richard T

    2015-12-01

    The human microbiome has gained much attention recently for its role in health and disease. This interest has come as we have begun to scratch the surface of the complexity of what has been deemed to be our "second genome" through initiatives such as the Human Microbiome Project. Microbes have been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction since before the first success in IVF. Although the data supporting or refuting this hypothesis remain somewhat sparse, thanks to sequencing data from the 16S rRNA subunit, we have begun to characterize the microbiome in the male and female reproductive tracts and understand how this may play a role in reproductive competence. In this review, we discuss what is known about the microbiome of the reproductive tract as it pertains to assisted reproductive technologies.

  7. Bioinformatics Approaches for Human Gut Microbiome Research

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    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  8. Microbiome Changes during Tuberculosis and Antituberculous Therapy.

    Science.gov (United States)

    Hong, Bo-Young; Maulén, Nancy Paula; Adami, Alexander J; Granados, Hector; Balcells, María Elvira; Cervantes, Jorge

    2016-10-01

    The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with Mycobacterium tuberculosis infection and TB therapy are presented and discussed.

  9. Novel Aggregation Properties of Candida albicans Secreted Aspartyl Proteinase Sap6 Mediate Virulence in Oral Candidiasis.

    Science.gov (United States)

    Kumar, Rohitashw; Saraswat, Darpan; Tati, Swetha; Edgerton, Mira

    2015-07-01

    Candida albicans, a commensal fungus of the oral microbiome, causes oral candidiasis in humans with localized or systemic immune deficiencies. Secreted aspartic proteinases (Saps) are a family of 10 related proteases and are virulence factors due to their proteolytic activity, as well as their roles in adherence and colonization of host tissues. We found that mice infected sublingually with C. albicans cells overexpressing Sap6 (SAP6 OE and a Δsap8 strain) had thicker fungal plaques and more severe oral infection, while infection with the Δsap6 strain was attenuated. These hypervirulent strains had highly aggregative colony structure in vitro and higher secreted proteinase activity; however, the levels of proteinase activity of C. albicans Saps did not uniformly match their abilities to damage cultured oral epithelial cells (SCC-15 cells). Hyphal induction in cells overexpressing Sap6 (SAP6 OE and Δsap8 cells) resulted in formation of large cell-cell aggregates. These aggregates could be produced in germinated wild-type cells by addition of native or heat-inactivated Sap6. Sap6 bound only to germinated cells and increased C. albicans adhesion to oral epithelial cells. The adhesion properties of Sap6 were lost upon deletion of its integrin-binding motif (RGD) and could be inhibited by addition of RGD peptide or anti-integrin antibodies. Thus, Sap6 (but not Sap5) has an alternative novel function in cell-cell aggregation, independent of its proteinase activity, to promote infection and virulence in oral candidiasis.

  10. Freshwater Fungal Infections

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    Dennis J. Baumgardner

    2017-01-01

    Full Text Available Fungal infections as a result of freshwater exposure or trauma are fortunately rare. Etiologic agents are varied, but commonly include filamentous fungi and Candida. This narrative review describes various sources of potential freshwater fungal exposure and the diseases that may result, including fungal keratitis, acute otitis externa and tinea pedis, as well as rare deep soft tissue or bone infections and pulmonary or central nervous system infections following traumatic freshwater exposure during natural disasters or near-drowning episodes. Fungal etiology should be suspected in appropriate scenarios when bacterial cultures or molecular tests are normal or when the infection worsens or fails to resolve with appropriate antibacterial therapy.

  11. Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity.

    Science.gov (United States)

    Brusca, Samuel B; Abramson, Steven B; Scher, Jose U

    2014-01-01

    Despite the progress toward understanding the molecular pathogenesis of rheumatoid arthritis (RA), its cause remains elusive. Genes are important but rather insufficient to explain the majority of RA cases. This review describes the novel data supporting the microbiome and its interactions with the human host as potential en('in')vironmental factors in RA pathogenesis. Animal models of inflammatory arthritis have shown that the presence of bacteria in mucosal surfaces is sufficient to alter local and systemic host immune responses and elicit joint inflammation. Human RA studies have focused on three mucosal sites: the gut, the gingiva, and the respiratory tree. The oral microbiome, and specifically Porphyromonas gingivalis, has long been implicated. Novel sequencing technologies have allowed investigations into the role of the gut microbiome in the development of autoimmune arthritis. Most recently, the pulmonary parenchyma has also been described as yet another possible mucosal site of initiation of autoimmunity in RA. Emerging data implicate the microbiome in RA pathogenesis. Mucosal sites exposed to a high load of bacterial antigens--such as the periodontium, lung, and gut--may represent the initial site of autoimmune generation. If validated, these findings could lead to the discovery of potential biomarkers and therapeutic approaches in the preclinical and clinical phases of RA.

  12. The establishment of the infant intestinal microbiome is not affected by rotavirus vaccination.

    Science.gov (United States)

    Ang, Li; Arboleya, Silvia; Lihua, Guo; Chuihui, Yuan; Nan, Qin; Suarez, Marta; Solís, Gonzalo; de los Reyes-Gavilán, Clara G; Gueimonde, Miguel

    2014-12-10

    The microbial colonization of the intestine during the first months of life constitutes the most important process for the microbiota-induced host-homeostasis. Alterations in this process may entail a high-risk for disease in later life. However, the potential factors affecting this process in the infant are not well known. Moreover, the potential impact of orally administered vaccines upon the establishing microbiome remains unknown. Here we assessed the intestinal microbiome establishment process and evaluated the impact of rotavirus vaccination upon this process. Metagenomic, PCR-DGGE and faecal short chain fatty acids analyses were performed on faecal samples obtained from three infants before and after the administration of each dose of vaccine. We found a high inter-individual variability in the early life gut microbiota at microbial composition level, but a large similarity between the infants' microbiomes at functional level. Rotavirus vaccination did not show any major effects upon the infant gut microbiota. Thus, the individual microbiome establishment and development process seems to occur in a defined manner during the first stages of life and rotavirus vaccination appears to be inconsequential for this process.

  13. Identifying personal microbiomes using metagenomic codes.

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    Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis

    2015-06-02

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.

  14. A parts list for fungal cellulosomes revealed by comparative genomics

    Energy Technology Data Exchange (ETDEWEB)

    Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K.; Solomon, Kevin V.; de Groot, Randall; Kuo, Alan; Mondo, Stephen J.; Salamov, Asaf A.; LaButti, Kurt; Zhao, Zhiying; Chiniquy, Jennifer; Barry, Kerrie; Brewer, Heather M.; Purvine, Samuel O.; Wright, Aaron T.; Hainaut, Matthieu; Boxma, Brigitte; van Alen, Theo; Hackstein, Johannes H. P.; Henrissat, Bernard; Baker, Scott E.; Grigoriev, Igor V.; O' Malley, Michelle A.

    2017-05-26

    chimeric structure – an independently evolved fungal complex that co-opted useful activities from bacterial neighbors within the gut microbiome.

  15. The alligator gut microbiome and implications for archosaur symbioses

    Science.gov (United States)

    Keenan, Sarah W.; Engel, Annette Summers; Elsey, Ruth M.

    2013-01-01

    Among vertebrate gastrointestinal microbiome studies, complete representation of taxa is limited, particularly among reptiles. Here, we provide evidence for previously unrecognized host-microbiome associations along the gastrointestinal tract from the American alligator, a crown archosaur with shared ancestry to extinct taxa, including dinosaurs. Microbiome compositional variations reveal that the digestive system consists of multiple, longitudinally heterogeneous microbiomes that strongly correlate to specific gastrointestinal tract organs, regardless of rearing histories or feeding status. A core alligator gut microbiome comprised of Fusobacteria, but depleted in Bacteroidetes and Proteobacteria common to mammalians, is compositionally unique from other vertebrate gut microbiomes, including other reptiles, fish, and herbivorous and carnivorous mammals. As such, modern alligator gut microbiomes advance our understanding of archosaur gut microbiome evolution, particularly if conserved host ecology has retained archosaur-specific symbioses over geologic time. PMID:24096888

  16. Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad

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    Vidya eDe Gannes

    2015-09-01

    Full Text Available Understanding how community structure of Bacteria, Archaea and Fungi varies as a function of edaphic characteristics is key to elucidating associations between soil ecosystem function and the microbiome that sustains it. In this study, non-managed tropical soils were examined that represented a range of edaphic characteristics, and a comprehensive soil microbiome analysis was done by Illumina sequencing of amplicon libraries that targeted Bacteria (universal prokaryotic 16S rRNA gene primers, Archaea (primers selective for archaeal 16S rRNA genes or Fungi (internal transcribed spacer region. Microbiome diversity decreased in the order: Bacteria > Archaea > Fungi. Bacterial community composition had a strong relationship to edaphic factors while that of Archaea and Fungi was comparatively weak. All communities were significantly more similar within soils, than they were between soils (ANOSIM p < 0.001; bacterial communities were 70-80% alike, while communities of Fungi and Archaea had 40-50% similarity. Communities differed in species turnover patterns, such that two soils with relatively similar bacterial communities could not be predicted to be similar in composition of Archaea or Fungi. Bacterial and archaeal diversity had significant (negative correlations to pH, whereas fungal diversity was not correlated to pH. Edaphic characteristics that best explained variation between soils in bacterial community structure were: total carbon, sodium, magnesium and zinc. For fungi, the best variables were: sodium, magnesium, phosphorus, boron and C/N. Archaeal communities had two sets of edaphic factors of equal strength, one contained sulphur, sodium, and ammonium-N and the other was composed of clay, potassium, ammonium-N, and nitrate-N. Collectively, the data indicate that Bacteria, Archaea and Fungi did not closely parallel one another in community structure development, and thus microbiomes in each soil acquired unique identities. This divergence

  17. Spatial Distribution of Fungal Communities in an Arable Soil

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    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment. PMID:26840453

  18. Spatial Distribution of Fungal Communities in an Arable Soil.

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    Julia Moll

    Full Text Available Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a ploughed soil in 0-10 cm, b rooted soil in 40-50 cm, c root-free soil in 60-70 cm soil depth and d maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit, occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment.

  19. Gut Microbiome of the Canadian Arctic Inuit

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    Tromas, Nicolas; Amyot, Marc

    2017-01-01

    ABSTRACT Diet is a major determinant of community composition in the human gut microbiome, and “traditional” diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome. We used deep sequencing of the 16S rRNA gene to compare the gut microbiomes of Montrealers with a Western diet to those of the Inuit consuming a range of traditional and Western diets. At the overall microbial community level, the gut microbiomes of Montrealers and Inuit were indistinguishable and contained similar levels of microbial diversity. However, we observed significant differences in the relative abundances of certain microbial taxa down to the subgenus level using oligotyping. For example, Prevotella spp., which have been previously associated with high-fiber diets, were enriched in Montrealers and among the Inuit consuming a Western diet. The gut microbiomes of Inuit consuming a traditional diet also had significantly less genetic diversity within the Prevotella genus, suggesting that a low-fiber diet might not only select against Prevotella but also reduce its diversity. Other microbes, such as Akkermansia, were associated with geography as well as diet, suggesting limited dispersal to the Arctic. Our report provides a snapshot of the Inuit microbiome as Western-like in overall community structure but distinct in the relative abundances and diversity of certain genera and strains. IMPORTANCE Non-Western populations have been shown to have distinct gut microbial communities shaped by traditional diets. The hitherto-uncharacterized microbiome of the Inuit may help us to

  20. Evaluation of the microbiome in children's appendicitis.

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    Salö, Martin; Marungruang, Nittaya; Roth, Bodil; Sundberg, Tiia; Stenström, Pernilla; Arnbjörnsson, Einar; Fåk, Frida; Ohlsson, Bodil

    2017-01-01

    The role of the microbiome has been widely discussed in the etiology of appendicitis. The primary aim was to evaluate the microbiome in the normal appendix and in appendicitis specifically divided into the three clinically and histopathologically defined grades of inflammation. Secondary aims were to examine whether there were any microbiome differences between proximal and distal appendices, and relate the microbiome with histopathological findings. A prospective pilot study was conducted of children undergoing appendectomy for appendicitis. The diagnosis was based on histopathological analysis. Children with incidental appendectomy were used as controls. The proximal and distal mucosa from the appendices were analyzed with 16S rRNA gene sequencing. A total of 22 children, 3 controls and 19 appendicitis patients; 11 phlegmonous, 4 gangrenous, and 4 perforated appendices, were prospectively included. The amount of Fusobacterium increased and Bacteroides decreased in phlegmonous and perforated appendicitis compared to controls, but statistical significance was not reached, and this pattern was not seen in gangrenous appendicitis. No relation could be seen between different bacteria and the grade of inflammation, and there was a wide variation of abundances at phylum, genus, and species level within every specific group of patients. Further, no significant differences could be detected when comparing the microbiome in proximal and distal mucosa, which may be because the study was underpowered. A trend with more abundance of Fusobacteria in the distal mucosa was seen in appendicitis patients with obstruction (25 and 13 %, respectively, p = 0.06). The pattern of microbiome differed not only between groups, but also within groups. However, no statistically significant differences could be found in the microbiome between groups or clinical conditions. No correlation between a specific bacteria and grade of inflammation was found. In the vast majority of cases of

  1. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  2. Fungal infections of the orbit

    Directory of Open Access Journals (Sweden)

    Bipasha Mukherjee

    2016-01-01

    Full Text Available Fungal infections of the orbit can lead to grave complications. Although the primary site of inoculation of the infective organism is frequently the sinuses, the patients can initially present to the ophthalmologist with ocular signs and symptoms. Due to its varied and nonspecific clinical features, especially in the early stages, patients are frequently misdiagnosed and even treated with steroids which worsen the situation leading to dire consequences. Ophthalmologists should be familiar with the clinical spectrum of disease and the variable presentation of this infection, as early diagnosis and rapid institution of appropriate therapy are crucial elements in the management of this invasive sino-orbital infection. In this review, relevant clinical, microbiological, and imaging findings are discussed along with the current consensus on local and systemic management. We review the recent literature and provide a comprehensive analysis. In the immunocompromised, as well as in healthy patients, a high index of suspicion must be maintained as delay in diagnosis of fungal pathology may lead to disfiguring morbidity or even mortality. Obtaining adequate diagnostic material for pathological and microbiological examination is critical. Newer methods of therapy, particularly oral voriconazole and topical amphotericin B, may be beneficial in selected patients.

  3. Gut inflammation and microbiome in spondyloarthritis.

    Science.gov (United States)

    Kabeerdoss, Jayakanthan; Sandhya, Pulukool; Danda, Debashish

    2016-04-01

    Spondyloarthritis (SpA) is chronic inflammatory disease involving joints and the spine. Bowel inflammation is common in SpA, which may be classified as acute or chronic. Chronic gut inflammation is most common in SpA patients with axial involvement as compared to those presenting with peripheral involvement alone. The pathogenesis of gut inflammation in SpA could be explained by two factors-over-activation of immunological cells and altered gut microbiome. This is exemplified by SpA animal models, namely HLA-B27-expressing transgenic animals and SKG mice models. Immunological mechanisms include homing of activated T cells from gut into synovium, excess pro-inflammatory cytokines secretion by immune cells such as IL-23 and genetic variations in immunological genes. The evidence for role of gut microbiome in SpA is gradually emerging. Recently, metagenomic study of gut microbiome by sequencing of microbial nucleic acids has enabled identification of new microbial taxa and their functions in gut of patients with SpA. In SpA, the gut microbiome could emerge as diagnostic and prognostic marker of disease. Modulation of gut microbiome is slated to have therapeutic potential as well.

  4. Scabies, lice, and fungal infections.

    Science.gov (United States)

    Taplin, D; Meinking, T L

    1989-09-01

    Scabies and pediculosis capitis are frequent and often unrecognized causes of multiple streptococcal and staphylococcal pyodermas. Permethrin 1 per cent creme rinse (NIX) for head lice, and permethrin 5 per cent topical cream for scabies are new, highly effective, safe, and cosmetically elegant treatments which have shown superiority over older remedies. In populations in which pediculosis and scabies have resisted traditional lindane therapy, patients promptly responded to these permethrin products. Scabies in nursing homes is a persistent and expanding problem which demands a high level of diagnostic suspicion and an integrated approach to management. For fungal infections, several new broad-spectrum oral and topical agents have been introduced. Their successful use is enhanced by appropriate diagnostic tests which can be performed in the office setting. Recommendations and references are given to assist the physician in diagnosis and choice of therapy.

  5. Fungal DNA barcoding.

    Science.gov (United States)

    Xu, Jianping

    2016-11-01

    Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

  6. Fungal arthritis and osteomyelitis.

    Science.gov (United States)

    Kohli, Rakhi; Hadley, Susan

    2005-12-01

    Fungal arthritis and osteomyelitis are uncommon diseases and generally present in an indolent fashion. The incidence of fungal bone and joint dis-ease is increasing with an increase in the prevalence of factors predisposing to invasive fungal disease, such as the use of central venous catheters, broad spectrum antibiotics, immunosuppression, and abdominal surgery. Definitive diagnosis relies on bone or synovial culture or biopsy. Successful management has traditionally consisted of amphotericin B in combination with surgical debridement. Given the rarity of this disease, treatment is not well defined, but reports of success with the use of azole antifungal agents, including itraconazole, fluconazole, voriconazole, and posaconazole, are promising.

  7. 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.

  8. Gut microbiome in Down syndrome.

    Directory of Open Access Journals (Sweden)

    Elena Biagi

    Full Text Available Premature aging seriously compromises the health status of Down Syndrome (DS persons. Since human aging has been associated with a deterioration of the gut microbiota (GM-host mutualism, here we investigated the composition of GM in DS.The observational study presented involved 17 adult DS persons. We characterized the GM structure by 454 pyrosequencing of the V4 region of the 16S rRNA gene. DS microbiome was compared with that of age-matched healthy non-trisomic adults enrolled in the same geographic area.The dominant GM fraction of DS persons showed an overall mutualistic immune-modulatory layout, comparable to that of healthy controls. This makes GM a possible factor counteracting the genetic determined acceleration of immune senescence in DS persons. However, we also found detectable signatures specific for DS among subdominant GM components, such as the increase of Parasporobacterium and Sutterella. In particular, the abundance of this last microorganism significantly correlated with the Aberrant Behavior Checklist (ABC total score, allowing us to hypothesize a possible role for this microbial genus in behavioral features in DS.

  9. Gut Microbiome in Down Syndrome

    Science.gov (United States)

    Biagi, Elena; Candela, Marco; Centanni, Manuela; Consolandi, Clarissa; Rampelli, Simone; Turroni, Silvia; Severgnini, Marco; Peano, Clelia; Ghezzo, Alessandro; Scurti, Maria; Salvioli, Stefano; Franceschi, Claudio; Brigidi, Patrizia

    2014-01-01

    Background Premature aging seriously compromises the health status of Down Syndrome (DS) persons. Since human aging has been associated with a deterioration of the gut microbiota (GM)-host mutualism, here we investigated the composition of GM in DS. Methods The observational study presented involved 17 adult DS persons. We characterized the GM structure by 454 pyrosequencing of the V4 region of the 16S rRNA gene. DS microbiome was compared with that of age-matched healthy non-trisomic adults enrolled in the same geographic area. Results and Conclusions The dominant GM fraction of DS persons showed an overall mutualistic immune-modulatory layout, comparable to that of healthy controls. This makes GM a possible factor counteracting the genetic determined acceleration of immune senescence in DS persons. However, we also found detectable signatures specific for DS among subdominant GM components, such as the increase of Parasporobacterium and Sutterella. In particular, the abundance of this last microorganism significantly correlated with the Aberrant Behavior Checklist (ABC) total score, allowing us to hypothesize a possible role for this microbial genus in behavioral features in DS. PMID:25386941

  10. Chronic granulomatous invasive fungal sinusitis: an evolving approach to management.

    Science.gov (United States)

    Halderman, Ashleigh; Shrestha, Rabin; Sindwani, Raj

    2014-04-01

    Chronic granulomatous invasive fungal sinusitis (CGIFS) is rare and a consensus on ideal management is lacking. We present an extensive case managed successfully with a conservative approach. Case report and literature review. The patient presented with unilateral proptosis, papilledema, and headache. Imaging revealed an infiltrative process with extensive intracranial and intraorbital involvement. Biopsy showed fungal elements and granulomatous reaction consistent with CGIFS. The patient was managed with conservative surgery and long-term oral voriconazole. This case supports a conservative surgical approach in some patients with extensive CGIFS. Oral voriconazole is effective and has significant advantages over more toxic agents administered intravenously. © 2014 ARS-AAOA, LLC.

  11. Insect pathology and fungal entomopathogens

    Science.gov (United States)

    Fungi that occur inside asymptomatic plant tissues are known as fungal endophytes. Different genera of fungal entomopathogens have been reported as naturally occurring fungal endophytes, and it has been shown that it is possible to inoculate plants with fungal entomopathogens, making them endophytic...

  12. Human genetic variation and the gut microbiome in disease.

    Science.gov (United States)

    Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J

    2017-08-21

    Taxonomic and functional changes to the composition of the gut microbiome have been implicated in multiple human diseases. Recent microbiome genome-wide association studies reveal that variants in many human genes involved in immunity and gut architecture are associated with an altered composition of the gut microbiome. Although many factors can affect the microbial organisms residing in the gut, a number of recent findings support the hypothesis that certain host genetic variants predispose an individual towards microbiome dysbiosis. This condition, in which the normal microbiome population structure is disturbed, is a key feature in disorders of metabolism and immunity.

  13. The microbiome of the chicken gastrointestinal tract.

    Science.gov (United States)

    Yeoman, Carl J; Chia, Nicholas; Jeraldo, Patricio; Sipos, Maksim; Goldenfeld, Nigel D; White, Bryan A

    2012-06-01

    The modern molecular biology movement was developed in the 1960s with the conglomeration of biology, chemistry, and physics. Today, molecular biology is an integral part of studies aimed at understanding the evolution and ecology of gastrointestinal microbial communities. Molecular techniques have led to significant gains in our understanding of the chicken gastrointestinal microbiome. New advances, primarily in DNA sequencing technologies, have equipped researchers with the ability to explore these communities at an unprecedented level. A reinvigorated movement in systems biology offers a renewed promise in obtaining a more complete understanding of chicken gastrointestinal microbiome dynamics and their contributions to increasing productivity, food value, security, and safety as well as reducing the public health impact of raising production animals. Here, we contextualize the contributions molecular biology has already made to our understanding of the chicken gastrointestinal microbiome and propose targeted research directions that could further exploit molecular technologies to improve the economy of the poultry industry.

  14. Metatranscriptomics of the human gut microbiome

    DEFF Research Database (Denmark)

    Sicheritz-Pontén, Thomas

    2011-01-01

    Our ‘other’ genome is the collective genetic information in all of the microorganisms that are living on and within us. Collectively known as the microbiome, these microbial cells outnumber human cells in the body by more than 10 to 1, and the genes carried by these organisms outnumber the genes...... in the human genome by more than 100 to 1. How these organisms contribute to and affect human health is poorly understood, but the emerging field of metagenomics promises a more comprehensive and complete understanding of the human microbiome. In the European-funded Metagenomics of the Human Intestinal Tract...... that there is a division of labor between the bacterial species in the human gut microbiome....

  15. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  16. Soil Influences Colonization of Root-Associated Fungal Endophyte Communities of Maize, Wheat, and Their Progenitors

    Directory of Open Access Journals (Sweden)

    Deepak Bokati

    2016-01-01

    Full Text Available Root-associated fungal endophytes are vital component of root microbiome as some mitigate their host’s abiotic and biotic stress. We characterized root-associated fungal endophytes in cereal grains and their progenitors grown on two different soil-types. We aimed at determining how clay and desert soil affects the colonization of root fungal community. Both culture-dependent and culture-independent methods were employed to identify endophytes that successfully colonized greenhouse-grown host plants. The Internal Transcriber Spacer region of fungal ribosomal DNA was utilized for identification purposes. This study revealed soil as a prominent factor influencing the composition of microfungal communities inhabiting the roots of maize (Zea mays subsp. mays and its conspecific progenitor, teosinte (Zea mays subsp. parviglumis. Similar results were found in wheat (Triticum aestivum subsp. aestivum and its progenitor (Triticum monococcum subsp. monococcum. The multidimensional comparisons of Morisita-Horn similarity values of fungal colonists of various host plant taxa indicated that soil plays a primary role in shaping the root fungal community; a secondary effect was plant host identity, even when the plant host is a conspecific. Future studies focused on characterizing root endophytes in other cereal grains, and studying the effect of edaphic factors on fungal colonization, can ultimately contribute to crop productivity.

  17. FungiQuant: A broad-coverage fungal quantitative real-time PCR assay

    Directory of Open Access Journals (Sweden)

    Liu Cindy M

    2012-11-01

    Full Text Available Abstract Background Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. Methods We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE guidelines. Results We designed FungiQuant, a TaqMan® qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant’s is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r2-values of >0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from Conclusions FungiQuant has comprehensive coverage against diverse fungi and is a robust quantification and detection tool for delineating between true fungal detection and non-target human DNA.

  18. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, M.; Raes, J.; Pelletier, E.

    2011-01-01

    Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previou......Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries...

  19. The Microbiome, Systemic Immune Function, and Allotransplantation.

    Science.gov (United States)

    Nellore, Anoma; Fishman, Jay A

    2016-01-01

    Diverse effects of the microbiome on solid organ transplantation are beginning to be recognized. In allograft recipients, microbial networks are disrupted by immunosuppression, nosocomial and community-based infectious exposures, antimicrobial therapies, surgery, and immune processes. Shifting microbial patterns, including acute infectious exposures, have dynamic and reciprocal interactions with local and systemic immune systems. Both individual microbial species and microbial networks have central roles in the induction and control of innate and adaptive immune responses, in graft rejection, and in ischemia-reperfusion injury. Understanding the diverse interactions between the microbiome and the immune system of allograft recipients may facilitate clinical management in the future.

  20. Respiratory Microbiome of New-born Infants

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    David John Gallacher

    2016-02-01

    Full Text Available The respiratory tract, once believed to be sterile, harbours diverse bacterial communities. The role of microorganisms within health and disease is slowly being unravelled. Evidence points to the neonatal period as a critical time for establishing stable bacterial communities and influencing immune responses important for long term respiratory health. This review summarises the evidence of early airway and lung bacterial colonisation and the role the microbiome has on respiratory health in the short and long term. The challenges of neonatal respiratory microbiome studies and future research directions are also discussed.

  1. The Lung Microbiome and Airway Disease.

    Science.gov (United States)

    Lynch, Susan V

    2016-12-01

    A growing body of literature has demonstrated relationships between the composition of the airway microbiota (mixed-species communities of microbes that exist in the respiratory tract) and critical features of immune response and pulmonary function. These studies provide evidence that airway inflammatory status and capacity for repair are coassociated with specific taxonomic features of the airway microbiome. Although directionality has yet to be established, the fact that microbes are known drivers of inflammation and tissue damage suggests that in the context of chronic inflammatory airway disease, the composition and, more importantly, the function, of the pulmonary microbiome represent critical factors in defining airway disease outcomes.

  2. Induced Systemic Resistance and the Rhizosphere Microbiome

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    Peter A.H.M. Bakker

    2013-06-01

    Full Text Available Microbial communities that are associated with plant roots are highly diverse and harbor tens of thousands of species. This so-called microbiome controls plant health through several mechanisms including the suppression of infectious diseases, which is especially prominent in disease suppressive soils. The mechanisms implicated in disease suppression include competition for nutrients, antibiosis, and induced systemic resistance (ISR. For many biological control agents ISR has been recognized as the mechanism that at least partly explains disease suppression. Implications of ISR on recruitment and functioning of the rhizosphere microbiome are discussed.

  3. [Pathogenesis of invasive fungal infections].

    Science.gov (United States)

    Garcia-Vidal, Carolina; Carratalà, Jordi

    2012-03-01

    Invasive fungal infections remain a life-threatening disease. The development of invasive fungal disease is dependent on multiple factors, such us colonization and efficient host immune response. We aimed to review the pathogenesis of invasive fungal infections, in particular, those caused by Candida and Aspergillus. For this we propose, to describe the fungal characteristics, to detail the host defence mechanisms against fungus and to analyse the host risk factors for invasive fungal infection.

  4. Fungal endocarditis: current challenges.

    Science.gov (United States)

    Tattevin, Pierre; Revest, Matthieu; Lefort, Agnès; Michelet, Christian; Lortholary, Olivier

    2014-10-01

    Whilst it used to affect mostly intravenous drug users and patients who underwent valvular surgery with suboptimal infection control procedures, fungal endocarditis is now mostly observed in patients with severe immunodeficiency (onco-haematology), in association with chronic central venous access and broad-spectrum antibiotic use. The incidence of fungal endocarditis has probably decreased in most developed countries with access to harm-reduction policies (i.e. needle exchange programmes) and with improved infection control procedures during cardiac surgery. Use of specific blood culture bottles for diagnosis of fungal endocarditis has decreased due to optimisation of media and automated culture systems. Meanwhile, the advent of rapid techniques, including fungal antigen detection (galactomannan, mannan/anti-mannan antibodies and β-1,3-d-glucans) and PCR (e.g. universal fungal PCR targeting 18S rRNA genes), shall improve sensitivity and reduce diagnostics delays, although limited data are available on their use for the diagnosis of fungal endocarditis. New antifungal agents available since the early 2000s may represent dramatic improvement for fungal endocarditis: (i) a new class, the echinocandins, has the potential to improve the management of Candida endocarditis owing to its fungicidal effect on yeasts as well as tolerability of increased dosages; and (ii) improved survival in patients with invasive aspergillosis with voriconazole compared with amphotericin B, and this may apply to Aspergillus sp. endocarditis as well, although its prognosis remains dismal. These achievements may allow selected patients to be cured with prolonged medical treatment alone when surgery is considered too risky.

  5. Sinonasal microbiome sampling: a comparison of techniques.

    Science.gov (United States)

    Bassiouni, Ahmed; Cleland, Edward John; Psaltis, Alkis James; Vreugde, Sarah; Wormald, Peter-John

    2015-01-01

    The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample. Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package. At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05). We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.

  6. The microbiome of New World vultures

    DEFF Research Database (Denmark)

    Roggenbuck, Michael; Schnell, Ida Baerholm; Blom, Nikolaj

    2014-01-01

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we...

  7. UNRAVELING THE FUNCTIONS OF THE MACROALGAL MICROBIOME

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    Ravindra Pal Singh

    2016-01-01

    Full Text Available Macroalgae are a diverse group of photosynthetic eukaryotic lower organisms and offer indispensable ecosystem services towards sustainable productivity of rocky coastal areas. The earlier studies have mainly focused on elucidation of the roles of the epiphytic bacterial communities in the ecophysiology of the host macroalga. However, mutualistic interactions have become topic of current interest. It is evident from recent studies that a fraction of epiphytic bacterial communities can be categorized as core microbial species, suggesting an obligate association. Epiphytic bacterial communities have also been reported to protect macroalgal surfaces from biofouling microorganisms through production of biologically active metabolites. Because of their intrinsic roles in the host life cycle, the host in turn may provide necessary organic nutrients in order to woo pelagic microbial communities to settle on the host surfaces. However, the precise composition of microbiomes and their functional partnership with hosts are hardly understood. In contrast, the microbial studies associated with human skin and gut and plants have significantly advanced our knowledge on microbiome and their functional interactions with the host. This has led to manipulation of the microbial flora of the human gut and of agricultural plants for improving health and performance. Therefore, it is highly imperative to investigate the functional microbiome that is closely involved in the life cycles of the host macroalgae using high-throughput techniques (metagenomics and metatranscriptomics. The findings from such investigations would help in promoting health and productivity in macroalgal species through regulation of functionally active microbiome.

  8. Metagenomic Systems Biology of the Human Microbiome

    DEFF Research Database (Denmark)

    Bonde, Ida

    The human microbiome is an integrated part of the human body, outnumbering the human cells by approximately a factor 10. These microorganisms are very important for human health, hence knowledge about this, ”our other genome”, has been growing rapidly in recent years. This is manly due to the adv......The human microbiome is an integrated part of the human body, outnumbering the human cells by approximately a factor 10. These microorganisms are very important for human health, hence knowledge about this, ”our other genome”, has been growing rapidly in recent years. This is manly due...... in the system. Applying the CAG clustering method to data from the human gut microbiome, we identified dependency-associations between plasmids, phages and clone-specific gene sets to their bacterial host. Connections between CRISPR-elements and phages were also observed. Additionally, the persistence of some...... bacterial species in the human gut could be predicted based on absence or presence of specific genetic modules. Based on the same CAG clustering of the human gut microbiome data, the link between bile acid degradation of bacteria in the gut and obesity was investigated. There seemed to be a slight...

  9. Proton pump inhibitors affect the gut microbiome

    NARCIS (Netherlands)

    Imhann, Floris; Bonder, Marc Jan; Vich Vila, Arnau; Fu, Jingyuan; Mujagic, Zlatan; Vork, Lisa; Tigchelaar, Ettje F; Jankipersadsing, Soesma A; Cenit, Maria Carmen; Harmsen, Hermie J M; Dijkstra, Gerard; Franke, Lude; Xavier, Ramnik J; Jonkers, Daisy; Wijmenga, Cisca; Weersma, Rinse K; Zhernakova, Alexandra

    2015-01-01

    BACKGROUND AND AIMS: Proton pump inhibitors (PPIs) are among the top 10 most widely used drugs in the world. PPI use has been associated with an increased risk of enteric infections, most notably Clostridium difficile. The gut microbiome plays an important role in enteric infections, by resisting or

  10. Childhood malnutrition and the intestinal microbiome.

    Science.gov (United States)

    Kane, Anne V; Dinh, Duy M; Ward, Honorine D

    2015-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 y, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections, and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it toward an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota, and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition.

  11. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, M.; Raes, J.; Pelletier, E.

    2011-01-01

    Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries...

  12. Social attraction mediated by fruit flies' microbiome.

    Science.gov (United States)

    Venu, Isvarya; Durisko, Zachary; Xu, Jianping; Dukas, Reuven

    2014-04-15

    Larval and adult fruit flies are attracted to volatiles emanating from food substrates that have been occupied by larvae. We tested whether such volatiles are emitted by the larval gut bacteria by conducting tests under bacteria-free (axenic) conditions. We also tested attraction to two bacteria species, Lactobacillus brevis, which we cultured from larvae in our lab, and L. plantarum, a common constituent of fruit flies' microbiome in other laboratory populations and in wild fruit flies. Neither larvae nor adults showed attraction to axenic food that had been occupied by axenic larvae, but both showed the previously reported attraction to standard food that had been occupied by larvae with an intact microbiome. Larvae also showed significant attraction to volatiles from axenic food and larvae to which we added only either L. brevis or L. plantarum, and volatiles from L. brevis reared on its optimal growth medium. Controlled learning experiments indicated that larvae experienced with both standard and axenic used food do not perceive either as superior, while focal larvae experienced with simulated used food, which contains burrows, perceive it as superior to unused food. Our results suggest that flies rely on microbiome-derived volatiles for long-distance attraction to suitable food patches. Under natural settings, fruits often contain harmful fungi and bacteria, and both L. brevis and L. plantarum produce compounds that suppress the growth of some antagonistic fungi and bacteria. The larval microbiome volatiles may therefore lead prospective fruit flies towards substrates with a hospitable microbial environment.

  13. Phenylketonuria: central nervous system and microbiome interaction

    Directory of Open Access Journals (Sweden)

    Demian Arturo Herrera Morban

    2017-06-01

    Full Text Available Phenylketonuria (PKU is an autosomal recessive inborn error of metabolism characterized by increased phenylalanine (Phe levels causing an inadequate neurodevelopment; the treatment of PKU is a Phe-restricting diet, and as such it can modulate the intestinal microbiome of the individual, generating central nervous system secondary disturbances that, added to the baseline disturbance, can influence the outcome of the disease.

  14. The role of microbiome in central nervous system disorders.

    Science.gov (United States)

    Wang, Yan; Kasper, Lloyd H

    2014-05-01

    Mammals live in a co-evolutionary association with the plethora of microorganisms that reside at a variety of tissue microenvironments. The microbiome represents the collective genomes of these co-existing microorganisms, which is shaped by host factors such as genetics and nutrients but in turn is able to influence host biology in health and disease. Niche-specific microbiome, prominently the gut microbiome, has the capacity to effect both local and distal sites within the host. The gut microbiome has played a crucial role in the bidirectional gut-brain axis that integrates the gut and central nervous system (CNS) activities, and thus the concept of microbiome-gut-brain axis is emerging. Studies are revealing how diverse forms of neuro-immune and neuro-psychiatric disorders are correlated with or modulated by variations of microbiome, microbiota-derived products and exogenous antibiotics and probiotics. The microbiome poises the peripheral immune homeostasis and predisposes host susceptibility to CNS autoimmune diseases such as multiple sclerosis. Neural, endocrine and metabolic mechanisms are also critical mediators of the microbiome-CNS signaling, which are more involved in neuro-psychiatric disorders such as autism, depression, anxiety, stress. Research on the role of microbiome in CNS disorders deepens our academic knowledge about host-microbiome commensalism in central regulation and in practicality, holds conceivable promise for developing novel prognostic and therapeutic avenues for CNS disorders. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. The microbiome and regulation of mucosal immunity.

    Science.gov (United States)

    McDermott, Andrew J; Huffnagle, Gary B

    2014-05-01

    The gastrointestinal tract is a mucosal surface constantly exposed to foreign antigens and microbes, and is protected by a vast array of immunologically active structures and cells. Epithelial cells directly participate in immunological surveillance and direction of host responses in the gut and can express numerous pattern recognition receptors, including Toll-like receptor 5 (TLR5), TLR1, TLR2, TLR3, TLR9, and nucleotide oligomerization domain 2, as well as produce chemotactic factors for both myeloid and lymphoid cells following inflammatory stimulation. Within the epithelium and in the underlying lamina propria resides a population of innate lymphoid cells that, following stimulation, can become activated and produce effector cytokines and exert both protective and pathogenic roles during inflammation. Lamina propria dendritic cells play a large role in determining whether the response to a particular antigen will be inflammatory or anti-inflammatory. It is becoming clear that the composition and metabolic activity of the intestinal microbiome, as a whole community, exerts a profound influence on mucosal immune regulation. The microbiome produces short-chain fatty acids, polysaccharide A, α-galactosylceramide and tryptophan metabolites, which can induce interleukin-22, Reg3γ, IgA and interleukin-17 responses. However, much of what is known about microbiome-host immune interactions has come from the study of single bacterial members of the gastrointestinal microbiome and their impact on intestinal mucosal immunity. Additionally, evidence continues to accumulate that alterations of the intestinal microbiome can impact not only gastrointestinal immunity but also immune regulation at distal mucosal sites.

  16. Pregnancy's stronghold on the vaginal microbiome.

    Directory of Open Access Journals (Sweden)

    Marina R S Walther-António

    Full Text Available OBJECTIVE: To assess the vaginal microbiome throughout full-term uncomplicated pregnancy. METHODS: Vaginal swabs were obtained from twelve pregnant women at 8-week intervals throughout their uncomplicated pregnancies. Patients with symptoms of vaginal infection or with recent antibiotic use were excluded. Swabs were obtained from the posterior fornix and cervix at 8-12, 17-21, 27-31, and 36-38 weeks of gestation. The microbial community was profiled using hypervariable tag sequencing of the V3-V5 region of the 16S rRNA gene, producing approximately 8 million reads on the Illumina MiSeq. RESULTS: Samples were dominated by a single genus, Lactobacillus, and exhibited low species diversity. For a majority of the patients (n = 8, the vaginal microbiome was dominated by Lactobacillus crispatus throughout pregnancy. Two patients showed Lactobacillus iners dominance during the course of pregnancy, and two showed a shift between the first and second trimester from L. crispatus to L. iners dominance. In all of the samples only these two species were identified, and were found at an abundance of higher than 1% in this study. Comparative analyses also showed that the vaginal microbiome during pregnancy is characterized by a marked dominance of Lactobacillus species in both Caucasian and African-American subjects. In addition, our Caucasian subject population clustered by trimester and progressed towards a common attractor while African-American women clustered by subject instead and did not progress towards a common attractor. CONCLUSION: Our analyses indicate normal pregnancy is characterized by a microbiome that has low diversity and high stability. While Lactobacillus species strongly dominate the vaginal environment during pregnancy across the two studied ethnicities, observed differences between the longitudinal dynamics of the analyzed populations may contribute to divergent risk for pregnancy complications. This helps establish a baseline for

  17. Sinonasal Fungal Infections and Complications: A Pictorial Review

    Directory of Open Access Journals (Sweden)

    Jose Gavito-Higuera

    2016-01-01

    Full Text Available Fungal infections of the nose and paranasal sinuses can be categorized into invasive and non-invasive forms. The clinical presentation and course of the disease is primarily determined by the immune status of the host and can range from harmless or subtle presentations to life threatening complications. Invasive fungal infections are categorized into acute, chronic or chronic granulomatous entities. Immunocompromised patients with poorly controlled diabetes mellitus, HIV and patients receiving chemotherapy or chronic oral corticosteroids are mostly affected. Mycetoma and Allergic Fungal Rhinosinusitis are considered non-invasive forms. Computer tomography is the gold-standard in sinonasal imaging and is complimented by Magnetic resonance imaging (MRI as it is superior in the evaluation of intraorbital and intracranial extensions. The knowledge and identification of the characteristic imaging patterns in invasive - and non- invasive fungal rhinosinusitis is crucial and the radiologist plays an important role in refining the diagnosis to prevent a possible fatal outcome.

  18. Allergic Fungal Rhinosinusitis.

    Science.gov (United States)

    Hoyt, Alice E W; Borish, Larry; Gurrola, José; Payne, Spencer

    2016-01-01

    This article reviews the history of allergic fungal rhinosinusitis and the clinical, pathologic, and radiographic criteria necessary to establish its diagnosis and differentiate this disease from other types of chronic rhinosinusitis. Allergic fungal rhinosinusitis is a noninvasive fungal form of sinus inflammation characterized by an often times unilateral, expansile process in which the typical allergic "peanut-butter-like" mucin contributes to the formation of nasal polyps, hyposmia/anosmia, and structural changes of the face. IgE sensitization to fungi is a necessary, but not sufficient, pathophysiologic component of the disease process that is also defined by microscopic visualization of mucin-containing fungus and characteristic radiological imaging. This article expounds on these details and others including the key clinical and scientific distinctions of this diagnosis, the pathophysiologic mechanisms beyond IgE-mediated hypersensitivity that must be at play, and areas of current and future research.

  19. Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs.

    Science.gov (United States)

    Segal, Leopoldo N; Rom, William N; Weiden, Michael D

    2014-01-01

    Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNA-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus-infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets.

  20. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  1. Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Crump, Alex R. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Resch, Charles T. [Geochemistry Department, Pacific Northwest National Laboratory, Richland WA USA; Fansler, Sarah [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Arntzen, Evan [Environmental Compliance and Emergency Preparation, Pacific Northwest National Laboratory, Richland WA USA; Kennedy, David W. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Fredrickson, Jim K. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Stegen, James C. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA

    2017-03-28

    Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets. The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.

  2. Estimated burden of fungal infections in Kenya.

    Science.gov (United States)

    Guto, John Abuga; Bii, Christine C; Denning, David W

    2016-08-31

    Kenya is a developing country with a high rate of tuberculosis (TB) and a moderate HIV infection burden. No estimate of the burden of fungal diseases in Kenya is published. We used specific populations at risk and fungal infection frequencies from the literature to estimate national incidence or prevalence of serious fungal infections. Used sources were: 2010 WHO TB statistics, Kenya Acquired Immunodeficiency Syndrome (AIDS) Epidemic Update 2012, Kenya Facts and figures 2012, Kenya Demographic and Health Survey 2008-2009. Of Kenya's population of ~40 million, 43% are under 15 years old and approximately 594,660 Kenyan women get >4 episodes Candida vulvovaginitis annually (2,988/100,000). The HIV/AIDS population at risk of opportunistic infections (OI) is 480,000 and the OI estimates include 306,000 patients with oral thrush (768/100,000), 114,000 with oesophageal candidiasis (286/100,000), 11,900 with cryptococcal meningitis (29/100,000) and 17,000 patients with Pneumocystis pneumonia (42/100,000). Chronic pulmonary aspergillosis following TB has a prevalence of 10,848 cases (32/100,000). The adult asthma prevalence is 3.1% and assuming 2.5% have allergic bronchopulmonary aspergillosis then 17,696 (44/100,000) are affected.  Invasive aspergillosis, candidaemia and Candida peritonitis are probably uncommon. Tinea capitis infects 9.6% of children in Kenya, while fungal keratitis and otomycoses are difficult to estimate. At any one time, about 7% of the Kenyan population suffers from a significant fungal infection, with recurrent vaginitis and tinea capitis accounting for 82% of the infections. These estimates require further epidemiological studies for validation.

  3. The evidence for microbiome manipulation in inflammatory arthritis.

    Science.gov (United States)

    Jethwa, Hannah; Abraham, Sonya

    2017-09-01

    The human body consists of millions of commensal bacteria (the microbiome), with the intestinal tract being the most prevalent site of colonization. This colonization process begins at birth, and despite numerous factors such as ageing, diet and drug use affecting the microbiome make-up, by adulthood the composition of the gut bacteria is relatively consistent across local populations. The recent advent of new scientific techniques has enabled us to explore how the microbiome affects health and, in particular, has shed light on the involvement of the microbiome in the pathogenesis of inflammatory disease. In this review we highlight the current evidence for microbiome manipulation in inflammatory arthritis in animal and human models and discuss potential therapeutics targeting the microbiome as treatment for these diseases. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. The human microbiome in rheumatic autoimmune diseases: A comprehensive review.

    Science.gov (United States)

    Coit, Patrick; Sawalha, Amr H

    2016-09-01

    The human microbiome consists of the total diversity of microbiota and their genes. High-throughput sequencing has allowed for inexpensive and rapid evaluation of taxonomic representation and functional capability of the microbiomes of human body sites. Autoimmune and inflammatory rheumatic diseases are characterized by dysbiosis of the microbiome. Microbiome dysbiosis can be influenced by host genetics and environmental factors. Dysbiosis is also associated with shifts in certain functional pathways. The goal of this article is to provide a current and comprehensive review of the unique characteristics of the microbiome of patients with autoimmune and inflammatory rheumatic diseases, measured using high-throughput sequencing. We also highlight the need for broader studies utilizing a longitudinal approach to better understand how the human microbiome contributes to disease susceptibility, and to characterize the role of the interaction between host genetics and microbial diversity in the pathogenesis of autoimmune diseases, disease manifestations, and progression.

  5. FISH 'N' Chips : a single cell genomic analyzer for the human microbiome.

    Energy Technology Data Exchange (ETDEWEB)

    Light, Yooli Kim; Perroud, Thomas D.; Hugenholtz, Philip (Joint Genome Institute, Walnut Creek, CA); Meagher, Robert J.; Singh, Anup K.; Malamud, Daniel (New York University, New York, NY); Saxena, Deepak (New York University, New York, NY); Liu, Peng

    2010-09-01

    Uncultivable microorganisms likely play significant roles in the ecology within the human body, with subtle but important implications for human health. Focusing on the oral microbiome, we are developing a processor for targeted isolation of individual microbial cells, facilitating whole-genome analysis without the need for isolation of pure cultures. The processor consists of three microfluidic modules: identification based on 16S rRNA fluorescence in situ hybridization (FISH), fluorescence-based sorting, and encapsulation of individual selected cells into small droplets for whole genome amplification. We present here a technique for performing microscale FISH and flow cytometry, as a prelude to single cell sorting.

  6. The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis.

    Science.gov (United States)

    Prince, Amanda L; Ma, Jun; Kannan, Paranthaman S; Alvarez, Manuel; Gisslen, Tate; Harris, R Alan; Sweeney, Emma L; Knox, Christine L; Lambers, Donna S; Jobe, Alan H; Chougnet, Claire A; Kallapur, Suhas G; Aagaard, Kjersti M

    2016-05-01

    Preterm birth (PTB) is a leading cause of neonatal morbidity and mortality and is not uncommonly associated with chorioamnionitis. We recently have demonstrated that the placenta harbors a unique microbiome with similar flora to the oral community. We also have shown an association of these placental microbiota with PTB, history of antenatal infection, and excess maternal weight gain. On the basis of these previous observations, we hypothesized that the placental membranes would retain a microbiome community that would vary in association with preterm birth and chorioamnionitis. In the current study, we aimed to examine the differences in the placental membrane microbiome in association with PTB in both the presence and absence of chorioamnionitis and/or funisitis using state-of-the-science whole-genome shotgun metagenomics. This was a cross-sectional analysis with 6 nested spontaneous birth cohorts (n = 9-15 subjects/cohort): Term gestations without chorioamnionitis, term with chorioamnionitis, preterm without chorioamnionitis, preterm with mild chorioamnionitis, preterm with severe chorioamnionitis, and preterm with chorioamnionitis and funisitis. Histologic analysis was performed with Redline's criteria, and inflammatory cytokines were analyzed in the cord blood. DNA from placental membranes was extracted from sterile swabs collected at delivery, and whole-genome shotgun sequencing was performed on the Illumina HiSeq platform. Filtered microbial DNA sequences were annotated and analyzed with MG-RAST (ie, Metagenomic Rapid Annotations using Subsystems Technology) and R. Subjects were assigned to cohorts on the basis of gestational age at delivery and independent scoring of histologic chorioamnionitis. We found that preterm subjects with severe chorioamnionitis and funisitis had increases in cord blood inflammatory cytokines. Of interest, although the placental membrane microbiome was altered in association with severity of histologic chorioamnionitis

  7. Frequent Replenishment Sustains the Beneficial Microbiome of Drosophila melanogaster

    OpenAIRE

    2013-01-01

    ABSTRACT We report that establishment and maintenance of the Drosophila melanogaster microbiome depend on ingestion of bacteria. Frequent transfer of flies to sterile food prevented establishment of the microbiome in newly emerged flies and reduced the predominant members, Acetobacter and Lactobacillus spp., by 10- to 1,000-fold in older flies. Flies with a normal microbiome were less susceptible than germfree flies to infection by Serratia marcescens and Pseudomonas aeruginosa. Augmentation ...

  8. Gut microbiome-host interactions in health and disease

    OpenAIRE

    Kinross, James M.; Darzi, Ara W; Nicholson, Jeremy K.

    2011-01-01

    The gut microbiome is the term given to describe the vast collection of symbiotic microorganisms in the human gastrointestinal system and their collective interacting genomes. Recent studies have suggested that the gut microbiome performs numerous important biochemical functions for the host, and disorders of the microbiome are associated with many and diverse human disease processes. Systems biology approaches based on next generation 'omics' technologies are now able to describe the gut mic...

  9. Molecular characterization of Candida in the oral cavity and factors involved in biofilm formation and virulence

    NARCIS (Netherlands)

    Kraneveld, E.A.

    2014-01-01

    The research described in this thesis addresses current issues related to oral Candida infections. Interactions of Candida with the oral microbiome were characterized and factors involved in biofilm formation and virulence were studied. All in all, the work described in this thesis contributes

  10. Fungal Wound Infection

    Centers for Disease Control (CDC) Podcasts

    2016-01-28

    Dr. David Tribble, acting director of the infectious disease clinical research program at Uniformed Services University of the Health Sciences, discusses fungal wound infections after combat trauma.  Created: 1/28/2016 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 1/28/2016.

  11. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2011-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  12. Fungal pathogens of Proteaceae

    NARCIS (Netherlands)

    Crous, P.W.; Summerell, B.A.; Swart, L.; Denman, S.; Taylor, J.E.; Bezuidenhout, C.M.; Palm, M.E.; Marincowitz, S.; Groenewald, J.Z.

    2012-01-01

    Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study

  13. The mPEG-PCL Copolymer for Selective Fermentation of Staphylococcus lugdunensis Against Candida parapsilosis in the Human Microbiome

    Science.gov (United States)

    Kao, Ming-Shan; Wang, Yanhan; Marito, Shinta; Huang, Stephen; Lin, Wan-Zhen; Gangoiti, Jon A; Barshop, Bruce A; Hyun, Choi; Lee, Woan-Ruah; Sanford, James A; Gallo, Richard L; Ran, Yuping; Chen, Wan-Tzu; Huang, Chun-Jen; Hsieh, Ming-Fa; Huang, Chun-Ming

    2017-01-01

    Many human skin diseases, such as seborrheic dermatitis, potentially occur due to the over-growth of fungi. It remains a challenge to develop fungicides with a lower risk of generating resistant fungi and non-specifically killing commensal microbes. Our probiotic approaches using a selective fermentation initiator of skin commensal bacteria, fermentation metabolites or their derivatives provide novel therapeutics to rein in the over-growth of fungi. Staphylococcus lugdunensis (S. lugdunensis) bacteria and Candida parapsilosis (C. parapsilosis) fungi coexist in the scalp microbiome. S. lugdunensis interfered with the growth of C. parapsilosis via fermentation. A methoxy poly(ethylene glycol)-b-poly(ε-caprolactone) (mPEG-PCL) copolymer functioned as a selective fermentation initiator of S. lugdunensis, selectively triggering the S. lugdunensis fermentation to produce acetic and isovaleric acids. The acetic acid and its pro-drug diethyleneglycol diacetate (Ac-DEG-Ac) effectively suppressed the growth of C. parapsilosis in vitro and impeded the fungal expansion in the human dandruff. We demonstrate for the first time that S. lugdunensis is a skin probiotic bacterium that can exploit mPEG-PCL to yield fungicidal short-chain fatty acids (SCFAs). The concept of bacterial fermentation as a part of skin immunity to re-balance the dysbiotic microbiome warrants a novel avenue for studying the probiotic function of the skin microbiome in promoting health.

  14. Advancing gut microbiome research using cultivation

    DEFF Research Database (Denmark)

    Sommer, Morten OA

    2015-01-01

    Culture-independent approaches have driven the field of microbiome research and illuminated intricate relationships between the gut microbiota and human health. However, definitively associating phenotypes to specific strains or elucidating physiological interactions is challenging for metagenomic...... approaches. Recently a number of new approaches to gut microbiota cultivation have emerged through the integration of high-throughput phylogenetic mapping and new simplified cultivation methods. These methodologies are described along with their potential use within microbiome research. Deployment of novel...... cultivation approaches should enable improved studies of xenobiotic tolerance and modification phenotypes and allow a drastic expansion of the gut microbiota reference genome catalogues. Furthermore, the new cultivation methods should facilitate systematic studies of the causal relationship between...

  15. Deciphering conjugative plasmid permissiveness in wastewater microbiomes

    DEFF Research Database (Denmark)

    Jacquiod, Samuel Jehan Auguste; Brejnrod, Asker Daniel; Milani, Stefan Morberg

    2017-01-01

    Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer between bacteria via...... still remains largely uncharted. Furthermore, current in vitro methods used to assess conjugation in complex microbiomes do not include in situ behaviours of recipient cells, resulting in partial understanding of transfers. We investigated the in vitro conjugation capacities of WWTP microbiomes from...... diversity of recipient bacterial phyla for the plasmid was observed, especially in WWTP outlets. We also identified permissive bacteria potentially able to cross WWTPs and engage in conjugation before and after water treatment. Bacterial activity and lifestyle seem to influence conjugation extent...

  16. Microbiome, Metabolome and Inflammatory Bowel Disease

    Science.gov (United States)

    Ahmed, Ishfaq; Roy, Badal C.; Khan, Salman A.; Septer, Seth; Umar, Shahid

    2016-01-01

    Inflammatory Bowel Disease (IBD) is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD) or Ulcerative Colitis (UC), two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome) and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis. PMID:27681914

  17. Microbiome, Metabolome and Inflammatory Bowel Disease

    Directory of Open Access Journals (Sweden)

    Ishfaq Ahmed

    2016-06-01

    Full Text Available Inflammatory Bowel Disease (IBD is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD or Ulcerative Colitis (UC, two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis.

  18. PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa.

    Science.gov (United States)

    Lebeis, Sarah L; Paredes, Sur Herrera; Lundberg, Derek S; Breakfield, Natalie; Gehring, Jase; McDonald, Meredith; Malfatti, Stephanie; Glavina del Rio, Tijana; Jones, Corbin D; Tringe, Susannah G; Dangl, Jeffery L

    2015-08-21

    Immune systems distinguish "self" from "nonself" to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

  19. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

    Directory of Open Access Journals (Sweden)

    Christian Hoffmann

    Full Text Available Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

  20. Host Genotype and Harvest Practices Shape the Leaf and Root Microbiomes of the Biofuel Crop Switchgrass

    Science.gov (United States)

    Singer, E.; Gonzalez, J.; Juenger, T. E.; Woyke, T.

    2016-12-01

    Growing energy demands and concerns for climate change have urgently pushed forward the timeline for the implementation of biofuel energies. Switchgrass (Panicum virgatum) is a leading biofuel crop in the United States. Bacteria living on and inside leaves and roots affect plant health, hence a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. We present a large-scale field experiment to untangle the effects of genotype, environment, soil horizon and harvest treatment practices on prokaryotic and fungal communities associated with leaves and roots of switchgrass. Using V4 16S rRNA and ITS gene as well as metagenome sequencing, we show that host genotype is significant in both, leaves and roots, and varies among sites. Microbiome composition along the rhizosphere also shifts with soil depth. Furthermore, plant harvest significantly changes both, leaf surface and rhizosphere communities, which can be seen a year after the harvest event. Gene function analysis shows that rhizosphere communities are enriched in genes encoding nitrate reduction, carbohydrate transport and metabolism, motility, and sensory and signal transduction proteins relative to leaf surface communities. Our results demonstrate how genotype-environment interactions contribute to the complexity of microbiome assembly in natural environments.

  1. The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux—A Prospective Longitudinal Interventional Study

    Directory of Open Access Journals (Sweden)

    Christoph Castellani

    2017-10-01

    Full Text Available Proton pump inhibitors (PPIs are the standard therapy for gastroesophageal reflux disease. In adults, PPI treatment is associated with Clostridium difficile infections (CDI. In contrast to adults the microbiome of infants develops from sterility at birth toward an adult-like profile in the first years of life. The effect of PPIs on this developing microbiome has never been studied. The aim of the present study was to determine the effect of oral PPIs on the fecal microbiome in infants with gastroesophageal reflux disease (GERD. In this prospective longitudinal study 12 infants with proven GERD received oral PPIs for a mean period of 18 weeks (range 8–44. Stool samples were collected before (“before PPI” and 4 weeks after initiation of PPI therapy (“on PPI”. A third sample was obtained 4 weeks after PPI discontinuation (“after PPI”. The fecal microbiome was determined by NGS based 16S rDNA sequencing. This trial was registered with clinicaltrials.gov (NCT02359604. In a comparison of “before PPI” and “on PPI” neither α- nor β-diversity changed significantly. On the genus level, however, the relative abundances showed a decrease of Lactobacillus and Stenotrophomonas and an increase of Haemophilus. After PPI therapy there was a significant increase of α- and β-diversity. Additionally, the relative abundances of the phyla Firmicutes, Bacteroidetes, and Proteobacteria were significantly changed and correlated to patients' age and the introduction of solid foods. PPI treatment has only minor effects on the fecal microbiome. After discontinuation of PPI treatment the fecal microbiome correlated to patients' age and nutrition.

  2. Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems.

    Science.gov (United States)

    Bourne, David G; Morrow, Kathleen M; Webster, Nicole S

    2016-09-01

    Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.

  3. Induced Systemic Resistance and the Rhizosphere Microbiome

    OpenAIRE

    Bakker, Peter A. H. M.; Doornbos, Rogier F.; Christos Zamioudis; Berendsen, Roeland L; Pieterse, Corné M. J.

    2013-01-01

    Microbial communities that are associated with plant roots are highly diverse and harbor tens of thousands of species. This so-called microbiome controls plant health through several mechanisms including the suppression of infectious diseases, which is especially prominent in disease suppressive soils. The mechanisms implicated in disease suppression include competition for nutrients, antibiosis, and induced systemic resistance (ISR). For many biological control agents ISR has been recognized...

  4. The fecal microbiome in cats with diarrhea.

    Directory of Open Access Journals (Sweden)

    Jan S Suchodolski

    Full Text Available Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21 and cats with acute (n = 19 or chronic diarrhea (n = 29 and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA effect size (LEfSe revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration, while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001 altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or

  5. Perna canaliculus and the Intestinal Microbiome

    Directory of Open Access Journals (Sweden)

    Emma Tali Saltzman

    2017-06-01

    Full Text Available Natural medicines are often an attractive option for patients diagnosed with chronic conditions. Three main classes of bioactives that have been reported from marine mussel extracts include proteins, lipids and carbohydrates. Commercially, the most relevant species of marine mollusks belong to two genera, Perna and Mytilus. Specifically, the Perna canaliculus species has been repeatedly demonstrated to harbor anti-inflammatory compounds such as omega-3 polyunsaturated fatty acids (ω-3 PUFAs that can ameliorate pro-inflammatory conditions, or proteins that can promote thrombin inhibitory activity. Recent clinical studies have posited that extracts from green-lipped mussels may lead to prebiotic activity in the intestinal microbiome that in turn has been reported to improve symptoms of osteoarthritis of the knee. Prebiotics have been reported to favorably interact with the intestinal microbiome through the proliferation of beneficial bacteria in the gut, suppressing exogenous and endogenous intestinal infections and promoting homeostasis by balancing local pro- and anti-inflammatory actions. Bioactive compounds from Perna canaliculus are functional foods and, in this regard, may positively interact with the intestinal microbiome and provide novel therapeutic solutions for intra-intestinal and extra-intestinal inflammatory conditions.

  6. Towards the human colorectal cancer microbiome.

    Directory of Open Access Journals (Sweden)

    Julian R Marchesi

    Full Text Available Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC. To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

  7. [Clinically documented fungal infections].

    Science.gov (United States)

    Kakeya, Hiroshi; Kohno, Shigeru

    2008-12-01

    Proven fungal infections are diagnosed by histological/microbiological evidence of fungi at the site of infection and positive blood culture (fungemia). However, invasive diagnosing examinations are not always applied for all of immunocompromised patients. Clinically documented invasive fungal infections are diagnosed by typical radiological findings such as halo sign on chest CT plus positive serological/molecular evidence of fungi. Serological tests of Aspergillus galactomannan antigen and beta-glucan for aspergillosis and cryptococcal glucuronoxylomannan antigen for cryptococcosis are useful. Hence, none of reliable serological tests for zygomycosis are available so far. In this article, risk factors, sign and symptoms, and diagnostic methods for clinically documented cases of invasive aspergillosis, pulmonary cryptococcosis, and zygomycosis with diabates, are reviewed.

  8. Can Your Microbiome Tell You What to Eat?

    Science.gov (United States)

    Vanamala, Jairam K P; Knight, Rob; Spector, Timothy D

    2015-12-01

    Prospects for using the gut microbiome for personalized medicine are substantial since the gut microbiome is known to modulate metabolism and varies substantially among individuals. Zeevi et al. (2015) demonstrate that the gut microbiota can be used to predict individualized blood glucose responses to particular foods, which differ between individuals.

  9. Gut microbiome and lipid metabolism : from associations to mechanisms

    NARCIS (Netherlands)

    Wang, Zheng; Koonen, Debby; Hofker, Marten; Fu, Jingyuan

    Purpose of review The gut microbiome has now been convincingly linked to human metabolic health but the underlying causality and mechanisms remain poorly understood. This review focuses on the recent progress in establishing the associations between gut microbiome species and lipid metabolism in

  10. The importance of the microbiome of the plant holobiont

    National Research Council Canada - National Science Library

    Vandenkoornhuyse, Philippe; Quaiser, Achim; Duhamel, Marie; Le Van, Amandine; Dufresne, Alexis

    2015-01-01

    ... colonizing roots. Over the last few years, research into plant microbiota (i.e. the diversity of plant‐associated microorganisms within the so‐called plant microbiome) has progressed significantly. Analysis of the plant microbiome involves linking microbial ecology and the plant host's biology and functioning, and viewing microorganisms as a reser...

  11. Emerging perspectives on the natural microbiome of fresh produce vegetables

    Science.gov (United States)

    Plants harbor a diverse microbiome existing as bacterial populations on the leaf surface (the phyllosphere) and within plant tissues (endophytes). The composition of this microbiome has been largely unexplored in fresh produce vegetables, where studies have tended to focus on pathogen detection and...

  12. Research priorities for harnessing plant microbiomes in sustainable agriculture.

    Science.gov (United States)

    Busby, Posy E; Soman, Chinmay; Wagner, Maggie R; Friesen, Maren L; Kremer, James; Bennett, Alison; Morsy, Mustafa; Eisen, Jonathan A; Leach, Jan E; Dangl, Jeffery L

    2017-03-01

    Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.

  13. Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children

    Directory of Open Access Journals (Sweden)

    Shan Jiang

    2016-11-01

    Full Text Available Dental caries (tooth decay is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3–4 years old with caries (n = 20 and without caries (n = 20 were recruited. Unstimulated saliva (2 mL was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children (p > 0.05. The relative abundance of several species (Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae, and Streptococcus mutans was higher in the caries-affected group than in the caries-free group (p < 0.05. Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children (p < 0.05. The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children’s risk of developing caries.

  14. Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children.

    Science.gov (United States)

    Jiang, Shan; Gao, Xiaoli; Jin, Lijian; Lo, Edward C M

    2016-11-25

    Dental caries (tooth decay) is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3-4 years old) with caries (n = 20) and without caries (n = 20) were recruited. Unstimulated saliva (2 mL) was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children (p > 0.05). The relative abundance of several species (Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae, and Streptococcus mutans) was higher in the caries-affected group than in the caries-free group (p < 0.05). Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children (p < 0.05). The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children's risk of developing caries.

  15. Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children

    Science.gov (United States)

    Jiang, Shan; Gao, Xiaoli; Jin, Lijian; Lo, Edward C. M.

    2016-01-01

    Dental caries (tooth decay) is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3–4 years old) with caries (n = 20) and without caries (n = 20) were recruited. Unstimulated saliva (2 mL) was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children (p > 0.05). The relative abundance of several species (Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae, and Streptococcus mutans) was higher in the caries-affected group than in the caries-free group (p < 0.05). Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children (p < 0.05). The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children’s risk of developing caries. PMID:27898021

  16. [Prevention of fungal infections in hospitalized patients].

    Science.gov (United States)

    Seeliger, H P; Schröter, G

    1984-06-01

    Hospital acquired infections due to fungi are primarily caused by yeast species of the genus Candida and mould species of the genus Aspergillus. Underlying disease with severely impaired defence mechanisms as well as certain forms of immunosuppressive and aggressive chemotherapy are the most important prerequisites for such secondary fungal infections. Aspergillus spec. usually infect man via exogenous routes, whereas Candida spec. mostly originate from the patient's own microbial flora. Under certain circumstances invasion of tissues follows (endomycosis). Exogenous Candida infections may likewise occur through contaminated hands of personnel and medical devices. The density of yeast cell distribution in hospital wards decreases with the distance from the primary source: the Candida infected human patient. Preventive measures protecting the patient at risk include: Permanent surveillance by routine cultural and serological examinations for the detection of an early infection of the skin, mouth, oesophagus, urinary tract, vagina and the bowel. Monitoring of patients is essential for early detection of dissemination and contributes to the control of fungal decontamination measures. Selective local decontamination is effected by the use of nonabsorbable compounds such as nystatin and amphotericin B in the gastrointestinal tract, and in oral and genital mucous membranes. Oral administration of ketoconazole has also been recommended. For the disinfection of skin appropriate chemicals are available. In the control of the environment of the endangered patient special attention must be paid to meticulous management of catheters. These measures are to be supported by careful disinfection policy concerning the hands of personnel and medical equipment.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses

    Science.gov (United States)

    Doroud, Ladan; Firl, Alana J.; Hird, Sarah M.; Eisen, Jonathan A.

    2017-01-01

    ABSTRACT Waterfowl, especially ducks and geese, are primary reservoirs for influenza A viruses (IAVs) that evolve and emerge as important pathogens in domestic animals and humans. In contrast to humans, where IAVs infect the respiratory tract and cause significant morbidity and mortality, IAVs infect the gastrointestinal tract of waterfowl and cause little or no pathology and are spread by fecal-oral transmission. For this reason, we examined whether IAV infection is associated with differences in the cloacal microbiome of mallards (Anas platyrhyncos), an important host of IAVs in North America and Eurasia. We characterized bacterial community composition by sequencing the V4 region of 16S rRNA genes. IAV-positive mallards had lower species diversity, richness, and evenness than IAV-negative mallards. Operational taxonomic unit (OTU) cooccurrence patterns were also distinct depending on infection status. Network analysis showed that IAV-positive mallards had fewer significant cooccurring OTUs and exhibited fewer coassociation patterns among those OTUs than IAV-negative mallards. These results suggest that healthy mallards have a more robust and complex cloacal microbiome. By combining analytical approaches, we identified 41 bacterial OTUs, primarily representatives of Streptococcus spp., Veillonella dispar, and Rothia mucilaginosa, contributing to the observed differences. This study found that IAV-infected wild mallards exhibited strong differences in microbiome composition relative to noninfected mallards and identified a concise set of putative biomarker OTUs. Using Random Forest, a supervised machine learning method, we verified that these 41 bacterial OTUs are highly predictive of infection status. IMPORTANCE Seasonal influenza causes 3 to 5 million severe illnesses and 250,000 to 500,000 human deaths each year. While pandemic influenza viruses emerge only periodically, they can be devastating—for example, the 1918 H1N1 pandemic virus killed more than 20

  18. Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas.

    Science.gov (United States)

    Luan, Chunguang; Xie, Lingling; Yang, Xi; Miao, Huifang; Lv, Na; Zhang, Ruifen; Xiao, Xue; Hu, Yongfei; Liu, Yulan; Wu, Na; Zhu, Yuanmin; Zhu, Baoli

    2015-01-23

    The fungal microbiota is an important component of the human gut microbiome and may be linked to gastrointestinal disease. In this study, the fungal microbiota of biopsy samples from adenomas and adjacent tissues was characterized by deep sequencing. Ascomycota, Glomeromycota and Basidiomycota were identified as the dominant phyla in both adenomas and adjacent tissues from all subjects. Among the 60 genera identified, the opportunist pathogens Phoma and Candida represented an average of 45% of the fungal microbiota. When analyzed at the operational taxonomic unit (OTU) level, however, a decreased diversity in adenomas was observed, and three OTUs differed significantly from the adjacent tissues. Principal Component Analysis (PCA) revealed that the core OTUs formed separate clusters for advanced and non-advanced adenomas for which the abundance of four OTUs differed significantly. Moreover, the size of adenomas and the disease stage were closely related to changes in the fungal microbiota in subjects with adenomas. This study characterized the fungal microbiota profile of subjects with adenomas and identified potential diagnostic biomarkers closely related to different stages of adenomas.

  19. The gut microbiome: a clinically significant player in transplantation?

    Science.gov (United States)

    Vindigni, Stephen M; Surawicz, Christina M

    2015-01-01

    The intestinal microbiome is critical to digestion, metabolism and protection from pathogenic organisms. Dysbiosis, or alteration of this microbiome, can result in Clostridium difficile infection and may play a role in other conditions. Patients undergoing solid organ transplantation (e.g., kidney, lung, liver, small bowel) and hematopoietic stem cell transplantation have a shift in the gut microbiome with a decrease in predominant organisms, a loss of bacterial diversity and emergence of a new dominant population. This translates into increased morbidity and mortality with risk of infection and rejection. We discuss the changes seen in the microbiome and its possible consequences. It may be important to develop strategies to restore the normal microbiome in such patients.

  20. What Makes Oral Candidiasis Recurrent Infection? A Clinical View

    Directory of Open Access Journals (Sweden)

    Azmi M. G. Darwazeh

    2014-01-01

    Full Text Available Clinical oral Candida infection (candidiasis is one of the common oral mucosal infections, and its management is usually frustrating due to either treatment failure or recurrence. Historically, oral candidiasis has been branded as disease of diseased. The unsuccessful management of oral candidiasis can due to either incorrect diagnosis, failure to identify (or correct the underlying predisposing factor(s, or inaccurate prescription of antifungal agents. Failure to properly treat oral candidiasis will lead to persistence of the fungal cell in the oral cavity and hence recurrence of infection. The oral health care provider should be aware of these fall pits in order to successfully manage oral candidiasis.

  1. Eosinophils, probiotics, and the microbiome.

    Science.gov (United States)

    Rosenberg, Helene F; Masterson, Joanne C; Furuta, Glenn T

    2016-11-01

    There is currently substantial interest in the therapeutic properties of probiotic microorganisms as recent research suggests that oral administration of specific bacterial strains may reduce inflammation and alter the nature of endogenous microflora in the gastrointestinal tract. Eosinophils are multifunctional tissue leukocytes, prominent among the resident cells of the gastrointestinal mucosa that promote local immunity. Recent studies with genetically altered mice indicate that eosinophils not only participate in maintaining gut homeostasis, but that the absence of eosinophils may have significant impact on the nature of the endogenous gut microflora and responses to gut pathogens, notably Clostridium difficile Furthermore, in human subjects, there is an intriguing relationship between eosinophils, allergic inflammation, and the nature of the lung microflora, notably a distinct association between eosinophil infiltration and detection of bacteria of the phylum Actinobacteria. Among topics for future research, it will be important to determine whether homeostatic mechanisms involve direct interactions between eosinophils and bacteria or whether they involve primarily eosinophil-mediated responses to cytokine signaling in the local microenvironment. Likewise, although is it clear that eosinophils can and do interact with bacteria in vivo, their ability to discern between pathogenic and probiotic species in various settings remains to be explored.

  2. What every dentist needs to know about the human microbiome and probiotics.

    Science.gov (United States)

    Klish, Andrew J; Porter, Judith A; Bashirelahi, Nasir

    2014-01-01

    Bacterial cells in the human body outnumber human cells by a ratio of 10:1. Apart from their well-known pathogenic potential, bacteria are proving to be integral to the overall health of the body. Residential microbes have critical roles in diverse processes, such as nutrient harvesting, internal environment regulation, immune system development, neurological modulation, and drug metabolism, as well as providing protection against pathogens. There is a growing body of research on the microbiome and probiotic therapies to restore or augment these functions throughout the body. In particular, increasing numbers of bacterial species and bacterial interactions have been discovered in the oral cavity, and probiotic interventions for common dental problems such as caries, periodontal diseases, and oral malodor are being developed and reviewed.

  3. As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases

    Directory of Open Access Journals (Sweden)

    José F. Siqueira

    2013-05-01

    Full Text Available It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease.

  4. Fungal osteomyelitis and septic arthritis.

    Science.gov (United States)

    Bariteau, Jason T; Waryasz, Gregory R; McDonnell, Matthew; Fischer, Staci A; Hayda, Roman A; Born, Christopher T

    2014-06-01

    Management of fungal osteomyelitis and fungal septic arthritis is challenging, especially in the setting of immunodeficiency and conditions that require immunosuppression. Because fungal osteomyelitis and fungal septic arthritis are rare conditions, study of their pathophysiology and treatment has been limited. In the literature, evidence-based treatment is lacking and, historically, outcomes have been poor. The most common offending organisms are Candida and Aspergillus, which are widely distributed in humans and soil. However, some fungal pathogens, such as Histoplasma, Blastomyces, Coccidioides, Cryptococcus, and Sporothrix, have more focal areas of endemicity. Fungal bone and joint infections result from direct inoculation, contiguous infection spread, or hematogenous seeding of organisms. These infections may be difficult to diagnose and eradicate, especially in the setting of total joint arthroplasty. Although there is no clear consensus on treatment, guidelines are available for management of many of these pathogens.

  5. Analyses of the stability and core taxonomic memberships of the human microbiome.

    Science.gov (United States)

    Li, Kelvin; Bihan, Monika; Methé, Barbara A

    2013-01-01

    Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.

  6. [Oral microbiota: a promising predictor of human oral and systemic diseases].

    Science.gov (United States)

    Xin, Xu; Junzhi, He; Xuedong, Zhou

    2015-12-01

    A human oral microbiota is the ecological community of commensal, symbiotic, and pathogenic microorganisms found in human oral cavity. Oral microbiota exists mostly in the form of a biofilm and maintains a dynamic ecological equilibrium with the host body. However, the disturbance of this ecological balance inevitably causes oral infectious diseases, such as dental caries, apical periodontitis, periodontal diseases, pericoronitis, and craniofacial bone osteomyelitis. Oral microbiota is also correlated with many systemic diseases, including cancer, diabetes mellitus, rheumatoid arthritis, cardiovascular diseases, and preterm birth. Hence, oral microbiota has been considered as a potential biomarker of human diseases. The "Human Microbiome Project" and other metagenomic projects worldwide have advanced our knowledge of the human oral microbiota. The integration of these metadata has been the frontier of oral microbiology to improve clinical translation. By reviewing recent progress on studies involving oral microbiota-related oral and systemic diseases, we aimed to propose the essential role of oral microbiota in the prediction of the onset, progression, and prognosis of oral and systemic diseases. An oral microbiota-based prediction model helps develop a new paradigm of personalized medicine and benefits the human health in the post-metagenomics era.

  7. The fungal microbiota of de-novo paediatric inflammatory bowel disease.

    Science.gov (United States)

    Mukhopadhya, I; Hansen, R; Meharg, C; Thomson, J M; Russell, R K; Berry, S H; El-Omar, E M; Hold, G L

    2015-04-01

    Inflammatory bowel disease (IBD) is characterised by an inappropriate chronic immune response against resident gut microbes. This may be on account of distinct changes in the gut microbiota termed as dysbiosis. The role of fungi in this altered luminal environment has been scarcely reported. We studied the fungal microbiome in de-novo paediatric IBD patients utilising next generation sequencing and compared with adult disease and normal controls. We report a distinct difference in fungal species with Ascomycota predominating in control subjects compared to Basidiomycota dominance in children with IBD, which could be as a result of altered tolerance in these patients. Copyright © 2015 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  8. Pathogens and host immunity in the ancient human oral cavity.

    Science.gov (United States)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank; Cappellini, Enrico

    2014-04-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.

  9. Pathogens and host immunity in the ancient human oral cavity

    DEFF Research Database (Denmark)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak

    2014-01-01

    cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction......Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral...... of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental...

  10. The human microbiome and probiotics: implications for pediatrics.

    Science.gov (United States)

    Versalovic, James

    2013-01-01

    Steady advances in our knowledge of the composition and function of the human microbiome at multiple body sites including the gut, skin and airways will likely contribute to our understanding of mechanisms of probiotic action by beneficial microbes. Microbe:microbe and microbe:human interactions are important considerations as we select probiotics for pediatric patients in the future. Although our knowledge about the composition of the microbiome is progressing rapidly, many gaps exist about the functional capacity and metabolic machinery of the human microbiome. Based on a limited amount of data, probiotics appear capable of altering the composition and function of the microbiome. Probiotics may be part of dietary strategies that combine ways to enhance microbiome function with nutrients that may be converted to active compounds promoting human health. Probiotics have yielded beneficial effects in numerous studies in the context of different diseases in pediatric gastroenterology. These disease states include necrotizing enterocolitis, antibiotic-associated diarrhea and colitis, acute gastroenteritis and irritable bowel syndrome. In the skin and airways, it is unclear if probiotics can affect the function of the microbiome to reduce the impact of diseases such as asthma and atopic dermatitis. An enhanced understanding of the effects of probiotics on the microbiome should facilitate selection of optimal probiotic strains for specific diseases in the future.

  11. Human Microbiome: When a Friend Becomes an Enemy.

    Science.gov (United States)

    Muszer, Magdalena; Noszczyńska, Magdalena; Kasperkiewicz, Katarzyna; Skurnik, Mikael

    2015-08-01

    The microorganisms that inhabit humans are very diverse on different body sites and tracts. Each specific niche contains a unique composition of the microorganisms that are important for a balanced human physiology. Microbial cells outnumber human cells by tenfold and they function as an invisible organ that is called the microbiome. Excessive use of antibiotics and unhealthy diets pose a serious danger to the composition of the microbiome. An imbalance in the microbial community may cause pathological conditions of the digestive system such as obesity, cancer and inflammatory bowel disease; of the skin such as atopic dermatitis, psoriasis and acne and of the cardiovascular system such as atherosclerosis. An unbalanced microbiome has also been associated with neurodevelopmental disorders such as autism and multiple sclerosis. While the microbiome has a strong impact on the development of the host immune system, it is suspected that it can also be the cause of certain autoimmune diseases, including diabetes or rheumatoid arthritis. Despite the enormous progress in the field, the interactions between the human body and its microbiome still remain largely unknown. A better characterization of the interactions may allow for a deeper understanding of human disease states and help to elucidate a possible association between the composition of the microbiome and certain pathologies. This review focuses on general findings that are related to the area and provides no detailed information about the case of study. The aim is to give some initial insight on the studies of the microbiome and its connection with human health.

  12. Application of metagenomics in the human gut microbiome.

    Science.gov (United States)

    Wang, Wei-Lin; Xu, Shao-Yan; Ren, Zhi-Gang; Tao, Liang; Jiang, Jian-Wen; Zheng, Shu-Sen

    2015-01-21

    There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

  13. Dynamics of the human gut microbiome in inflammatory bowel disease

    Energy Technology Data Exchange (ETDEWEB)

    Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina; Vázquez-Baeza, Yoshiki; Walters, William A.; Bramer, Lisa M.; D' Amato, Mauro; Bonfiglio, Ferdinando; McDonald, Daniel; Gonzalez, Antonio; McClure, Erin E.; Dunklebarger, Mitchell F.; Knight, Rob; Jansson, Janet K.

    2017-02-13

    Inflammatory bowel disease (IBD) is characterized by flares of inflammation with periodic need for increased medication and sometimes even surgery. IBD etiology is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD diseases, including ulcerative colitis (UC), colonic Crohn’s Disease (CCD), and ileal CD (ICD). Although IBD is dynamic, microbiome studies have primarily focused on single timepoints or few individuals. Here we dissect the long-term dynamic behavior of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than healthy individuals, based on deviation from a newly-defined healthy plane (HP). ICD subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results help guide therapies that will re-direct the gut microbiome towards a healthy state and maintain remission in IBD.

  14. Research priorities for harnessing plant microbiomes in sustainable agriculture

    Science.gov (United States)

    Soman, Chinmay; Wagner, Maggie R.; Friesen, Maren L.; Kremer, James; Bennett, Alison; Morsy, Mustafa; Eisen, Jonathan A.; Leach, Jan E.; Dangl, Jeffery L.

    2017-01-01

    Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes—i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance—into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host–microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply. PMID:28350798

  15. Fungal biodiversity to biotechnology.

    Science.gov (United States)

    Chambergo, Felipe S; Valencia, Estela Y

    2016-03-01

    Fungal habitats include soil, water, and extreme environments. With around 100,000 fungus species already described, it is estimated that 5.1 million fungus species exist on our planet, making fungi one of the largest and most diverse kingdoms of eukaryotes. Fungi show remarkable metabolic features due to a sophisticated genomic network and are important for the production of biotechnological compounds that greatly impact our society in many ways. In this review, we present the current state of knowledge on fungal biodiversity, with special emphasis on filamentous fungi and the most recent discoveries in the field of identification and production of biotechnological compounds. More than 250 fungus species have been studied to produce these biotechnological compounds. This review focuses on three of the branches generally accepted in biotechnological applications, which have been identified by a color code: red, green, and white for pharmaceutical, agricultural, and industrial biotechnology, respectively. We also discuss future prospects for the use of filamentous fungi in biotechnology application.

  16. Biomarkers for the 21st century: listening to the microbiome.

    Science.gov (United States)

    Dietert, Rodney Reynolds; Silbergeld, Ellen Kovner

    2015-04-01

    The field of environmental research has benefited greatly from the concept of biomarkers, which originally expanded our thinking by opening the "black box" between environmental exposures and manifestations of disease and dysfunction in exposed populations, as laid out in a highly influential article published in 1987 by an expert committee convened by the National Research Council. Advances in biomedical research now challenge us to revise this concept to include the microbiome as a critical stage in the progression from exposure to outcome. Incorporating the microbiome into the basic 1987 model can spur new advances and understanding in environmental health. The human microbiome as a whole comprises the majority of cells and genes of the super-organism (host and microbiome). Site-specific microbiomes are the first to encounter xenobiotics, prior to absorption across gut, skin, or respiratory system. A growing literature indicates that these microbial communities may participate in biotransformation and thus constitute a compartment to add to the original biomarker schematic. In addition, these microbiomes interact with the "niche" in which they are located and thus transduce responses to and from the host organism. Incorporating the microbiome into the environmental health paradigm will enlarge our concepts of susceptibility as well as the interactions between xenobiotics and other factors that influence the status and function of these barrier systems. This article reviews the complexities of host:microbiome responses to xenobiotics in terms of redefining toxicokinetics and susceptibility. Our challenge is to consider these multiple interactions between and within the microbiome, the immune system, and other systems of the host in terms of exposure to exogenous agents, including environmental toxicants.

  17. 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

  18. Unravelling the diversity of grapevine microbiome.

    Science.gov (United States)

    Pinto, Cátia; Pinho, Diogo; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C

    2014-01-01

    Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

  19. Unravelling the diversity of grapevine microbiome.

    Directory of Open Access Journals (Sweden)

    Cátia Pinto

    Full Text Available Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

  20. Performing Skin Microbiome Research: A Method to the Madness.

    Science.gov (United States)

    Kong, Heidi H; Andersson, Björn; Clavel, Thomas; Common, John E; Jackson, Scott A; Olson, Nathan D; Segre, Julia A; Traidl-Hoffmann, Claudia

    2017-03-01

    Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  1. The core gut microbiome, energy balance and obesity.

    Science.gov (United States)

    Turnbaugh, Peter J; Gordon, Jeffrey I

    2009-09-01

    Metagenomics is an emerging field focused on characterizing the structures, functions and dynamic operations of microbial communities sampled in their native habitats without the need for culture. Here, we present findings from a 16S rRNA gene sequence- and whole community DNA shotgun sequencing-based analysis of the adult human gut microbiomes of lean and obese mono- and dizygotic twins. Our findings indicate that a core microbiome can be found at the gene level, despite large variation in community membership, and that variations from the core are associated with obesity. These findings have implications for ongoing Human Microbiome Project(s), and highlight important challenges to the field of metagenomics.

  2. Managing acute invasive fungal sinusitis.

    Science.gov (United States)

    Dwyhalo, Kristina M; Donald, Carrlene; Mendez, Anthony; Hoxworth, Joseph

    2016-01-01

    Acute invasive fungal sinusitis is the most aggressive form of fungal sinusitis and can be fatal, especially in patients who are immunosuppressed. Early diagnosis and intervention are crucial and potentially lifesaving, so primary care providers must maintain a high index of suspicion for this disease. Patients may need to be admitted to the hospital for IV antifungal therapy and surgical debridement.

  3. Current management of fungal infections.

    NARCIS (Netherlands)

    Meis, J.F.G.M.; Verweij, P.E.

    2001-01-01

    The management of superficial fungal infections differs significantly from the management of systemic fungal infections. Most superficial infections are treated with topical antifungal agents, the choice of agent being determined by the site and extent of the infection and by the causative organism,

  4. The evolution of fungal epiphytes

    NARCIS (Netherlands)

    Hongsanan, S.; Sánchez-Ramírez, S.; Crous, P.W.; Ariyawansa, H.A.; Zhao, R.L.; Hyde, K.D.

    2016-01-01

    Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors o

  5. Melatonin and oral cavity.

    Science.gov (United States)

    Cengiz, Murat İnanç; Cengiz, Seda; Wang, Hom-Lay

    2012-01-01

    While initially the oral cavity was considered to be mainly a source of various bacteria, their toxins and antigens, recent studies showed that it may also be a location of oxidative stress and periodontal inflammation. Accordingly, this paper focuses on the involvement of melatonin in oxidative stress diseases of oral cavity as well as on potential therapeutic implications of melatonin in dental disorders. Melatonin has immunomodulatory and antioxidant activities, stimulates the proliferation of collagen and osseous tissue, and acts as a protector against cellular degeneration associated with aging and toxin exposure. Arising out of its antioxidant actions, melatonin protects against inflammatory processes and cellular damage caused by the toxic derivates of oxygen. As a result of these actions, melatonin may be useful as a coadjuvant in the treatment of certain conditions of the oral cavity. However, the most important effect of melatonin seems to result from its potent antioxidant, immunomodulatory, protective, and anticancer properties. Thus, melatonin could be used therapeutically for instance, locally, in the oral cavity damage of mechanical, bacterial, fungal, or viral origin, in postsurgical wounds caused by tooth extractions and other oral surgeries. Additionally, it can help bone formation in various autoimmunological disorders such as Sjorgen syndrome, in periodontal diseases, in toxic effects of dental materials, in dental implants, and in oral cancers.

  6. Melatonin and Oral Cavity

    Directory of Open Access Journals (Sweden)

    Murat İnanç Cengiz

    2012-01-01

    Full Text Available While initially the oral cavity was considered to be mainly a source of various bacteria, their toxins and antigens, recent studies showed that it may also be a location of oxidative stress and periodontal inflammation. Accordingly, this paper focuses on the involvement of melatonin in oxidative stress diseases of oral cavity as well as on potential therapeutic implications of melatonin in dental disorders. Melatonin has immunomodulatory and antioxidant activities, stimulates the proliferation of collagen and osseous tissue, and acts as a protector against cellular degeneration associated with aging and toxin exposure. Arising out of its antioxidant actions, melatonin protects against inflammatory processes and cellular damage caused by the toxic derivates of oxygen. As a result of these actions, melatonin may be useful as a coadjuvant in the treatment of certain conditions of the oral cavity. However, the most important effect of melatonin seems to result from its potent antioxidant, immunomodulatory, protective, and anticancer properties. Thus, melatonin could be used therapeutically for instance, locally, in the oral cavity damage of mechanical, bacterial, fungal, or viral origin, in postsurgical wounds caused by tooth extractions and other oral surgeries. Additionally, it can help bone formation in various autoimmunological disorders such as Sjorgen syndrome, in periodontal diseases, in toxic effects of dental materials, in dental implants, and in oral cancers.

  7. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.

    Science.gov (United States)

    2014-09-10

    Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Treatment of lingual traumatic ulcer accompanied with fungal infections

    Directory of Open Access Journals (Sweden)

    Sella Sella

    2011-09-01

    Full Text Available Background: Traumatic ulcer is a common form of ulceration occured in oral cavity caused by mechanical trauma, either acute or chronic, resulting in loss of the entire epithelium. Traumatic ulcer often occurs in children that are usually found on buccal mucosa, labial mucosa of upper and lower lip, lateral tongue, and a variety of areas that may be bitten. To properly diagnose the ulcer, dentists should evaluate the history and clinical description in detail. If the lesion is allegedly accompanied by other infections, such as fungal, bacterial or viral infections, microbiological or serological tests will be required. One of the initial therapy given for fungal infection is nystatin which aimed to support the recovery and repair processes of epithelial tissue in traumatic ulcer case. Purpose: This case report is aimed to emphasize the importance of microbiological examination in suspected cases of ulcer accompanied with traumatic fungal infection. Case: A 12-year-old girl came to the clinic of Pediatric Dentistry, Faculty of Dentistry, University of Indonesia on June 9, 2011 accompanied with her mother. The patient who had a history of geographic tongue came with complaints of injury found in the middle of the tongue. The main diagnosis was ulcer accompanied with traumatic fungal infection based on the results of swab examination. Case management: This traumatic ulcer case was treated with Dental Health Education, oral prophylaxis, as well as prescribing and usage instructions of nystatin. The recovery and repair processes of mucosal epithelium of the tongue then occured after the use of nystatin. Conclusion: It can be concluded that microbiological examination is important to diagnose suspected cases of ulcer accompanied with traumatic fungal infection. The appropriate treatment such as nystatin can be given for traumatic fungal infection.Latar belakang: Ulkus traumatic merupakan bentuk umum dari ulserasi rongga mulut yang terjadi akibat trauma

  9. Salivary inflammatory markers and microbiome in normoglycemic lean and obese children compared to obese children with type 2 diabetes

    Science.gov (United States)

    Sabharwal, Amarpeet; Tsompana, Maria; Berman, Harvey A.; Haase, Elaine M.; Miecznikowski, Jeffrey C.

    2017-01-01

    Background There is emerging evidence linking diabetes with periodontal disease. Diabetes is a well-recognized risk factor for periodontal disease. Conversely, pro-inflammatory molecules released by periodontally-diseased tissues may enter the circulation to induce insulin resistance. While this association has been demonstrated in adults, there is little information regarding periodontal status in obese children with and without type 2 diabetes (T2D). We hypothesized that children with T2D have higher rates of gingivitis, elevated salivary inflammatory markers, and an altered salivary microbiome compared to children without T2D. Methods Three pediatric cohorts ages 10–19 years were studied: lean (normal weight—C), obese (Ob), and obese with T2D (T2D). Each subject completed an oral health survey, received a clinical oral examination, and provided unstimulated saliva for measurement of inflammatory markers and microbiome analysis. Results The diabetes group was less likely to have had a dental visit within the last six months. Body mass index (BMI) Z-scores and waist circumference/height ratios were similar between Ob and T2D cohorts. The number of carious lesions and fillings were similar for all three groups. The gingival index was greater in the T2D group compared to the Ob and C groups. Although salivary microbial diversity was minimal between groups, a few differences in bacterial genus composition were noted. Conclusions Obese children with T2D show a trend toward poorer oral health compared to normal weight and obese children without T2D. This study characterizes the salivary microbiome of children with and without obesity and T2D. This study supports a modest link between T2D and periodontal inflammation in the pediatric population. PMID:28253297

  10. Alterations of the human gut microbiome in multiple sclerosis

    Science.gov (United States)

    Jangi, Sushrut; Gandhi, Roopali; Cox, Laura M.; Li, Ning; von Glehn, Felipe; Yan, Raymond; Patel, Bonny; Mazzola, Maria Antonietta; Liu, Shirong; Glanz, Bonnie L.; Cook, Sandra; Tankou, Stephanie; Stuart, Fiona; Melo, Kirsy; Nejad, Parham; Smith, Kathleen; Topçuolu, Begüm D.; Holden, James; Kivisäkk, Pia; Chitnis, Tanuja; De Jager, Philip L.; Quintana, Francisco J.; Gerber, Georg K.; Bry, Lynn; Weiner, Howard L.

    2016-01-01

    The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis. PMID:27352007

  11. Novel microbiome-based therapeutics for chronic rhinosinusitis.

    Science.gov (United States)

    Cope, E K; Lynch, S V

    2015-03-01

    The human microbiome, i.e. the collection of microbes that live on, in and interact with the human body, is extraordinarily diverse; microbiota have been detected in every tissue of the human body interrogated to date. Resident microbiota interact extensively with immune cells and epithelia at mucosal surfaces including the airways, and chronic inflammatory and allergic respiratory disorders are associated with dysbiosis of the airway microbiome. Chronic rhinosinusitis (CRS) is a heterogeneous disease with a large socioeconomic impact, and recent studies have shown that sinus inflammation is associated with decreased sinus bacterial diversity and the concomitant enrichment of specific sinus pathogens. Here, we discuss the potential role for probiotic supplementation for CRS in light of this increasing understanding of the airway microbiome and microbial interactions with the host. We focus on the ecological significance of microbiome-based probiotic supplementation and potential interactions with the gastrointestinal tract and consider microbial administration methods for treatment of CRS.

  12. The Hoops, Hopes, and Hypes of Human Microbiome Research

    Science.gov (United States)

    Bik, Elisabeth M.

    2016-01-01

    Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research. PMID:27698620

  13. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

    NARCIS (Netherlands)

    Cremers, Amelieke Jh; Zomer, Aldert L; Gritzfeld, Jenna F; Ferwerda, Gerben; van Hijum, Sacha Aft; Ferreira, Daniela M; Shak, Joshua R; Klugman, Keith P; Boekhorst, Jos|info:eu-repo/dai/nl/302571523; Timmerman, Harro M; de Jonge, Marien I; Gordon, Stephen B; Hermans, Peter Wm

    2014-01-01

    BACKGROUND: Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volu

  14. Metagenomics of prebiotic and probiotic supplemented broilers gastrointestinal tract microbiome

    Science.gov (United States)

    Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) is a recently developed computational approach for prediction of functional composition of a microbiome comparing marker gene data with a reference genome database. The procedure established significant link ...

  15. Changes of Cattle Fecal Microbiome Under Field Conditions

    Science.gov (United States)

    Next generation sequencing (NGS) has been applied to study the microbiome in wastewater, sewage sludge, and feces. Previous microbial survival studies have shown different fecal-associated microbes have different decay rates and regrowth behaviors.

  16. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

    NARCIS (Netherlands)

    Cremers, Amelieke Jh; Zomer, Aldert L; Gritzfeld, Jenna F; Ferwerda, Gerben; van Hijum, Sacha Aft; Ferreira, Daniela M; Shak, Joshua R; Klugman, Keith P; Boekhorst, Jos; Timmerman, Harro M; de Jonge, Marien I; Gordon, Stephen B; Hermans, Peter Wm

    2014-01-01

    BACKGROUND: Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volu

  17. The core gut microbiome, energy balance and obesity

    National Research Council Canada - National Science Library

    Peter J. Turnbaugh; Jeffrey I. Gordon

    2009-01-01

    .... Here, we present findings from a 16S rRNA gene sequence- and whole community DNA shotgun sequencing-based analysis of the adult human gut microbiomes of lean and obese mono- and dizygotic twins...

  18. Epidemiologic studies of the human microbiome and cancer

    National Research Council Canada - National Science Library

    Vogtmann, Emily; Goedert, James J

    2016-01-01

    .... Previously detected associations of individual bacteria (e.g., Helicobacter pylori), periodontal disease, and inflammation with specific cancers have motivated studies considering the association between the human microbiome and cancer risk...

  19. The human salivary microbiome exhibits temporal stability in bacterial diversity.

    Science.gov (United States)

    Cameron, Simon J S; Huws, Sharon A; Hegarty, Matthew J; Smith, Daniel P M; Mur, Luis A J

    2015-09-01

    The temporal variability of the human microbiome may be an important factor in determining its relationship with health and disease. In this study, the saliva of 40 participants was collected every 2 months over a one-year period to determine the temporal variability of the human salivary microbiome. Salivary pH and 16S rRNA gene copy number were measured for all participants, with the microbiome of 10 participants assessed through 16S rRNA amplicon sequencing. In February 2013, 16S rRNA gene copy number was significantly (P Salivary pH levels were significantly (P salivary pH (R(2) = 7.8%; P = 0.019). At the phylum level, significant differences were evident between participants in the Actinobacteria (P salivary microbiome, suggesting that bacterial diversity is stable, but that 16S rRNA gene copy number may be subject to seasonal flux.

  20. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities

    Science.gov (United States)

    Nawaz, Ali; Purahong, Witoon; Lehmann, Robert; Herrmann, Martina; Küsel, Kirsten; Totsche, Kai U.; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis. PMID:27242696

  1. Functional soil microbiome: belowground solutions to an aboveground problem.

    Science.gov (United States)

    Lakshmanan, Venkatachalam; Selvaraj, Gopinath; Bais, Harsh P

    2014-10-01

    There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.

  2. Structure and function of the human skin microbiome

    OpenAIRE

    Schommer, Nina N.; Gallo, Richard L.

    2013-01-01

    An abundant and diverse collection of bacteria, fungi and viruses inhabit the human skin. These microorganisms have been reported to vary between individuals and between different sites on the skin. The factors responsible for the unique variability of the skin microbiome are only partially understood, but results suggest host genetic and environmental influences play a major role. Today, the steady accumulation of data describing the skin microbiome, combined with experiments designed to tes...

  3. Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

    Science.gov (United States)

    Moeller, Andrew H.; Goodman, Andrew L.; Ochman, Howard

    2017-01-01

    ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis

  4. Diversity of the Human Skin Microbiome Early in Life

    OpenAIRE

    Capone, Kimberly A; Scot E Dowd; Georgios N. Stamatas; Nikolovski, Janeta

    2011-01-01

    Within days after birth, rapid surface colonization of infant skin coincides with significant functional changes. Gradual maturation of skin function, structure, and composition continues throughout the first years of life. Recent reports have revealed topographical and temporal variations in the adult skin microbiome. Here we address the question of how the human skin microbiome develops early in life. We show that the composition of cutaneous microbial communities evolves over the first yea...

  5. Oral and nasal microbiota in Parkinson's disease.

    Science.gov (United States)

    Pereira, Pedro A B; Aho, Velma T E; Paulin, Lars; Pekkonen, Eero; Auvinen, Petri; Scheperjans, Filip

    2017-05-01

    Parkinson's disease (PD) is associated with neuropathological changes in olfactory and gastrointestinal tissues, and PD patients frequently suffer from hyposmia, hyposalivation, and dysphagia. Since hyposmia and gastrointestinal dysfunction are frequently premotor symptoms, it has been speculated that an external, for example microbial, agent could trigger the pathologic process in the corresponding organs, subsequently spreading to the central nervous system. We recently showed evidence for compositional differences between the fecal microbiota of PD patients and control subjects. In this study, our objective was to explore a possible connection between nasal and oral microbiota and PD. We compared the oral and nasal bacterial communities of PD patients (oral: n = 72, nasal: n = 69) and control subjects (oral: n = 76, nasal: n = 67) using a 16S rRNA gene amplicon sequencing approach. Oral and nasal microbiota differed markedly from each other, with no notable similarity within subjects. Oral microbiota of PD patients and control subjects had differences in beta diversity and abundances of individual bacterial taxa. An increase in the abundance of opportunistic oral pathogens was detected in males, both with and without PD. Our data did not reveal convincing differences between the nasal microbiota of control subjects and PD patients. The oral microbiome deserves additional research regarding its connection to PD and its biomarker potential. The higher abundance of oral pathogens in men underlines the importance of monitoring and promoting male dental health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. The plant microbiome explored: implications for experimental botany

    Energy Technology Data Exchange (ETDEWEB)

    Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

    2015-11-07

    The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are coevolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.

  7. Stability of the gorilla microbiome despite simian immunodeficiency virus infection.

    Science.gov (United States)

    Moeller, Andrew H; Peeters, Martine; Ayouba, Ahidjo; Ngole, Eitel Mpoudi; Esteban, Amadine; Hahn, Beatrice H; Ochman, Howard

    2015-02-01

    Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees, SIVgor-infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf-based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla-specific enterotype was enabled by lowered immune system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV-1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority.

  8. The plant microbiome explored: implications for experimental botany.

    Science.gov (United States)

    Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

    2016-02-01

    The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.

  9. Integrating the microbiome as a resource in the forensics toolkit.

    Science.gov (United States)

    Clarke, Thomas H; Gomez, Andres; Singh, Harinder; Nelson, Karen E; Brinkac, Lauren M

    2017-09-01

    The introduction of DNA fingerprinting to forensic science rapidly expanded the available evidence that could be garnered from a crime scene and used in court cases. Next generation sequencing technologies increased available genetic data that could be used as evidence by orders of magnitude, and as such, significant additional genetic information is now available for use in forensic science. This includes DNA from the bacteria that live in and on humans, known as the human microbiome. Next generation sequencing of the human microbiome demonstrates that its bacterial DNA can be used to uniquely identify an individual, provide information about their life and behavioral patterns, determine the body site where a sample came from, and estimate postmortem intervals. Bacterial samples from the environment and objects can also be leveraged to address similar questions about the individual(s) who interacted with them. However, the applications of this new field in forensic sciences raises concerns on current methods used in sample processing, including sample collection, storage, and the statistical power of published studies. These areas of human microbiome research need to be fully addressed before microbiome data can become a regularly incorporated evidence type and routine procedure of the forensic toolkit. Here, we summarize information on the current status of microbiome research as applies to the forensic field, the mathematical models used to make predictions, and the possible legal and practical difficulties that can limit the application of microbiomes in forensic science. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways.

    Energy Technology Data Exchange (ETDEWEB)

    Denner, Darcy R.; Sangwan, Naseer; Becker, Julia B.; Hogarth, D. Kyle; Oldham, Justin; Castillo, Jamee; Sperling, Anne I.; Solway, Julian; Naureckas, Edward T.; Gilbert, Jack A.; White, Steven R.

    2016-05-01

    Abstract BACKGROUND: The lung has a diverse microbiome that is modest in biomass. This microbiome differs in asthmatic patients compared with control subjects, but the effects of clinical characteristics on the microbial community composition and structure are not clear. OBJECTIVES: We examined whether the composition and structure of the lower airway microbiome correlated with clinical characteristics of chronic persistent asthma, including airflow obstruction, use of corticosteroid medications, and presence of airway eosinophilia. METHODS: DNA was extracted from endobronchial brushings and bronchoalveolar lavage fluid collected from 39 asthmatic patients and 19 control subjects, along with negative control samples. 16S rRNA V4 amplicon sequencing was used to compare the relative abundance of bacterial genera with clinical characteristics. RESULTS: Differential feature selection analysis revealed significant differences in microbial diversity between brush and lavage samples from asthmatic patients and control subjects. Lactobacillus, Pseudomonas, and Rickettsia species were significantly enriched in samples from asthmatic patients, whereas Prevotella, Streptococcus, and Veillonella species were enriched in brush samples from control subjects. Generalized linear models on brush samples demonstrated oral corticosteroid use as an important factor affecting the relative abundance of the taxa that were significantly enriched in asthmatic patients. In addition, bacterial α-diversity in brush samples from asthmatic patients was correlated with FEV1 and the proportion of lavage eosinophils. CONCLUSION: The diversity and composition of the bronchial airway microbiome of asthmatic patients is distinct from that of nonasthmatic control subjects and influenced by worsening airflow obstruction and corticosteroid use. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  11. Diet effects in gut microbiome and obesity.

    Science.gov (United States)

    Chen, Jia; He, Xianzhi; Huang, Jinhai

    2014-04-01

    The 100 trillion microbes in human gut coevolve with the host and exert significant influences on human health. The gut microbial composition presents dynamic changes correlated with various factors including host genotypes, age, and external environment. Effective manipulation of the gut microbiota through diets (both long-term and short-term diet patterns), probiotics and/or prebiotics, and antibiotics has been proved being potential to prevent from metabolic disorders such as obesity in many studies. The dietary regulation exerts influences on microbial metabolism and host immune functions through several pathways, of which may include selectively bacterial fermentation of nutrients, lower intestinal barrier function, overexpression of genes associated with disorders, and disruptions to both innate and adaptive immunity. Discoveries in the interrelationship between diet, intestinal microbiome, and body immune system provide us novel perceptions to the specific action mechanisms and will promote the development of therapeutic approaches for obesity. © 2014 Institute of Food Technologists®

  12. 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.

  13. The rhizosphere microbiome and plant health.

    Science.gov (United States)

    Berendsen, Roeland L; Pieterse, Corné M J; Bakker, Peter A H M

    2012-08-01

    The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications.

    Science.gov (United States)

    DeLeon-Rodriguez, Natasha; Lathem, Terry L; Rodriguez-R, Luis M; Barazesh, James M; Anderson, Bruce E; Beyersdorf, Andreas J; Ziemba, Luke D; Bergin, Michael; Nenes, Athanasios; Konstantinidis, Konstantinos T

    2013-02-12

    The composition and prevalence of microorganisms in the middle-to-upper troposphere (8-15 km altitude) and their role in aerosol-cloud-precipitation interactions represent important, unresolved questions for biological and atmospheric science. In particular, airborne microorganisms above the oceans remain essentially uncharacterized, as most work to date is restricted to samples taken near the Earth's surface. Here we report on the microbiome of low- and high-altitude air masses sampled onboard the National Aeronautics and Space Administration DC-8 platform during the 2010 Genesis and Rapid Intensification Processes campaign in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses before, during, and after two major tropical hurricanes, Earl and Karl. Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range and were at least an order of magnitude more abundant than fungal cells, suggesting that bacteria represent an important and underestimated fraction of micrometer-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Nonetheless, 17 bacterial taxa, including taxa that are known to use C1-C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms possess traits that allow survival in the troposphere. The findings presented here suggest that the microbiome is a dynamic and underappreciated aspect of the upper troposphere with potentially important impacts on the hydrological cycle, clouds, and climate.

  15. Power law analysis of the human microbiome.

    Science.gov (United States)

    Ma, Zhanshan Sam

    2015-11-01

    Taylor's (1961, Nature, 189:732) power law, a power function (V = am(b) ) describing the scaling relationship between the mean and variance of population abundances of organisms, has been found to govern the population abundance distributions of single species in both space and time in macroecology. It is regarded as one of few generalities in ecology, and its parameter b has been widely applied to characterize spatial aggregation (i.e. heterogeneity) and temporal stability of single-species populations. Here, we test its applicability to bacterial populations in the human microbiome using extensive data sets generated by the US-NIH Human Microbiome Project (HMP). We further propose extending Taylor's power law from the population to the community level, and accordingly introduce four types of power-law extensions (PLEs): type I PLE for community spatial aggregation (heterogeneity), type II PLE for community temporal aggregation (stability), type III PLE for mixed-species population spatial aggregation (heterogeneity) and type IV PLE for mixed-species population temporal aggregation (stability). Our results show that fittings to the four PLEs with HMP data were statistically extremely significant and their parameters are ecologically sound, hence confirming the validity of the power law at both the population and community levels. These findings not only provide a powerful tool to characterize the aggregations of population and community in both time and space, offering important insights into community heterogeneity in space and/or stability in time, but also underscore the three general properties of power laws (scale invariance, no average and universality) and their specific manifestations in our four PLEs.

  16. Management of Patients with Oral Candidiasis

    DEFF Research Database (Denmark)

    Kragelund, Camilla; Reibel, Jesper; Pedersen, Anne Marie Lynge

    2016-01-01

    Oral candidal infections are medically treated with antifungal agents. In the fungal cell membrane, steroid ergosterol is the target of the antifungals on the market, but similarity with the human cell membrane may cause host toxicity and unintended reactions. Management of oral candidiasis depends...... in particular in patients with recurrent oral candidiasis. This risk can be reduced if different types of antifungal drugs are used over time or are combined. This chapter focuses on antifungal treatment of the medically compromised patient with oral candidiasis by highlighting the advantages and disadvantages...

  17. Hospitalized Patients and Fungal Infections

    Science.gov (United States)

    ... These types of infections are called healthcare-associated infections (HAIs). Hospital staff and healthcare providers do everything they can ... IV tube) can increase your risk for fungal infection. During your hospital stay you may need a central venous catheter, ...

  18. Fungal Entomopathogens in the Rhizosphere

    Science.gov (United States)

    Entomopathogenic fungi are found in a wide variety of fungal groups. The order Hypocreales contains the largest number of entomogenous fungi, including two of the most widely studied, Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Clavicipitaceae) and Metarhizium anisopliae (Metchnikoff) Sorok...

  19. Fungal genomics beyond Saccharomyces cerevisiae?

    DEFF Research Database (Denmark)

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens

    2003-01-01

    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious that the a......Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...... that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential....

  20. [Oral candidiasis: clinical features and control].

    Science.gov (United States)

    Yamamoto, Tetsuya

    2010-10-01

    Candidiasis is the most commonly encountered fungal infection, and oral candidiasis is often observed as a local opportunistic infection. Oral candidiasis is clinically divided into three types: acute forms, chronic forms, and Candida-associated lesions. Candida adhesion and multiplication are largely regulated by the local and systemic factors of the host. The local factors include impairment of the oral mucosal integrity, which is usually impaired by hyposalivation, anticancer drugs/radiation for head and neck cancers, denture wearing, a decrease in the oral bacterial population, and poor oral hygiene. Among Candida species, oral candidiasis is mostly caused by Candida albicans (C. albicans), C. glabrata, or C. tropicalis. Oral Candida induces a variety of symptoms, such as oral mucosal inflammation manifesting as an uncomfortable feeling, pain, erythema, erosion, taste abnormalities, and hyperplasia of the oral mucosa. Candida overgrowth in the oral cavity may disseminate to distant organs. Therefore, in order to avoid the sequelae of systemic candidiasis, oral candidiasis should be rapidly controlled. Oral candidiasis is usually treated by the local application of antifungal drugs. However, oral candidiasis occasionally escapes the control of such local treatment due to the development of multi-drug resistant Candida strains and species or due to the suppression of salivation or cellular immune activity. When drug-resistant strains are suspected as the pathogens and when the host is generally compromised, the oral administration of combinations of antifungal drugs, enhancement of cellular immune activity, and improvement of the nutritional condition are recommended.

  1. Fungal microbiota dysbiosis in IBD

    Science.gov (United States)

    Sokol, Harry; Leducq, Valentin; Aschard, Hugues; Pham, Hang-Phuong; Jegou, Sarah; Landman, Cecilia; Cohen, David; Liguori, Giuseppina; Bourrier, Anne; Nion-Larmurier, Isabelle; Cosnes, Jacques; Seksik, Philippe; Langella, Philippe; Skurnik, David; Richard, Mathias L; Beaugerie, Laurent

    2017-01-01

    Objective The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. Design Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. Results We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. Conclusions Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis. PMID:26843508

  2. Oral Medication

    Science.gov (United States)

    ... Size: A A A Listen En Español Oral Medication The first treatment for type 2 diabetes blood ... new — even over-the-counter items. Explore: Oral Medication How Much Do Oral Medications Cost? Save money ...

  3. The microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications

    Science.gov (United States)

    Nenes, A.; DeLeon-Rodriguez, N.; Lathem, T. L.; Rodriguez-Rojas, L. M.; Barazesh, J.; Anderson, B. E.; Beyersdorf, A.; Ziemba, L. D.; Bergin, M. H.; Konstantinidis, K.

    2012-12-01

    The composition and prevalence of microorganisms in the middle to upper troposphere (8-15 km altitude) and their role in aerosol-cloud-precipitation interactions represent important, unresolved questions for biological and atmospheric science. Here we report on the microbiome of low and high altitude air masses sampled onboard the NASA DC-8 platform during the 2010 Genesis and Rapid Intensification Processes (GRIP) campaign in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses, before, during, and after two major tropical hurricanes, Earl and Karl. Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25-1μm diameter range and were at least an order of magnitude more abundant compared to fungal cells, suggesting that bacteria represent an important and underestimated fraction of micron-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Nonetheless, 17 bacterial taxa, including taxa that are known to utilize C1-C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms have developed adaptations to survive in the troposphere. The findings presented here suggest that the microbiome is a dynamic and underappreciated aspect of the upper troposphere with potentially profound impacts on the water cycle, clouds, and climate.

  4. Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Kevin McKernan

    2016-05-01

    Full Text Available The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and even concentrated Cannabis products . As a result, third party microbial testing has become a regulatory requirement in the medical and recreational Cannabis markets, yet knowledge of the Cannabis microbiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary based Cannabis flowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenic Penicillium and Aspergillus species, including P. citrinum and P. paxilli, that were not detected by one or more culture-based methods currently in use for safety testing.

  5. Oral myiasis

    OpenAIRE

    Thalaimalai Saravanan; Mathan A Mohan; Meera Thinakaran; Saneem Ahammed

    2015-01-01

    Myiasis is a pathologic condition in humans occurring because of parasitic infestation. Parasites causing myiasis belong to the order Diptera. Oral myiasis is seen secondary to oral wounds, suppurative lesions, and extraction wounds, especially in individuals with neurological deficit. In such cases, neglected oral hygiene and halitosis attracts the flies to lay eggs in oral wounds resulting in oral myiasis. We present a case of oral myiasis in 40-year-old male patient with mental disability ...

  6. An integrated catalog of reference genes in the human gut microbiome

    DEFF Research Database (Denmark)

    Li, Junhua; Jia, Huijue; Cai, Xianghang

    2014-01-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly...... signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease....

  7. Progress in oral personalized medicine: contribution of ‘omics’

    Directory of Open Access Journals (Sweden)

    Ingrid Glurich

    2015-09-01

    Full Text Available Background: Precision medicine (PM, representing clinically applicable personalized medicine, proactively integrates and interprets multidimensional personal health data, including clinical, ‘omics’, and environmental profiles, into clinical practice. Realization of PM remains in progress. Objective: The focus of this review is to provide a descriptive narrative overview of: 1 the current status of oral personalized medicine; and 2 recent advances in genomics and related ‘omic’ and emerging research domains contributing to advancing oral-systemic PM, with special emphasis on current understanding of oral microbiomes. Design: A scan of peer-reviewed literature describing oral PM or ‘omic’-based research conducted on humans/data published in English within the last 5 years in journals indexed in the PubMed database was conducted using mesh search terms. An evidence-based approach was used to report on recent advances with potential to advance PM in the context of historical critical and systematic reviews to delineate current state-of-the-art technologies. Special focus was placed on oral microbiome research associated with health and disease states, emerging research domains, and technological advances, which are positioning realization of PM. Results: This review summarizes: 1 evolving conceptualization of personalized medicine; 2 emerging insight into roles of oral infectious and inflammatory processes as contributors to both oral and systemic diseases; 3 community shifts in microbiota that may contribute to disease; 4 evidence pointing to new uncharacterized potential oral pathogens; 5 advances in technological approaches to ‘omics’ research that will accelerate PM; 6 emerging research domains that expand insights into host–microbe interaction including inter-kingdom communication, systems and network analysis, and salivaomics; and 7 advances in informatics and big data analysis capabilities to facilitate interpretation of

  8. MetaCoMET: a web platform for discovery and visualization of the core microbiome

    Science.gov (United States)

    A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome. Results: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome an...

  9. An integrated catalog of reference genes in the human gut microbiome

    NARCIS (Netherlands)

    Li, J.; Jia, H.; Cai, X.; Zhong, H.; Feng, Q.; Sunagawa, S.; Arumugam, M.; Kultima, J.R.; Prifti, E.; Nielsen, T.; Juncker, A.S.; Manichanh, C.; Chen, B.; Zhang, W.; Levenez, F.; Xu, X.; Xiao, L.; Liang, S.; Zhang, D.; Zhang, Z.; Chen, W.; Zhao, H.; Al-Aama, J.Y.; Edris, S.; Yang, H.; Hansen, H.; Nielsen, H.B.; Brunak, S.; Kristiansen, K.; Guarner, F.; Pedersen, O.; Doré, J.; Ehrlich, S.D.; Bork, P.; Wang, J.; Vos, de W.M.; Tims, S.; Zoetendal, E.G.; Kleerebezem, M.

    2014-01-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly

  10. Fungal-Fungal Interactions in Leaf-Cutting Ant Agriculture

    Directory of Open Access Journals (Sweden)

    Sunshine A. Van Bael

    2011-01-01

    Full Text Available Many organisms participate in symbiotic relationships with other organisms, yet studies of symbioses typically have focused on the reciprocal costs and benefits within a particular host-symbiont pair. Recent studies indicate that many ecological interactions involve alliances of symbionts acting together as mutualistic consortia against other consortia. Such interacting consortia are likely to be widespread in nature, even if the interactions often occur in a cryptic fashion. Little theory and empirical data exist concerning how these complex interactions shape ecological outcomes in nature. Here, we review recent work on fungal-fungal interactions between two consortia: (i leaf-cutting ants and their symbiotic fungi (the latter grown as a food crop by the former and (ii tropical plants and their foliar endophytes (the cryptic symbiotic fungi within leaves of the former. Plant characteristics (e.g., secondary compounds or leaf physical properties of leaves are involved in leaf-cutting ant preferences, and a synthesis of published information suggests that these plant traits could be modified by fungal presence. We discuss potential mechanisms for how fungal-fungal interactions proceed in the leaf-cutting ant agriculture and suggest themes for future research.

  11. Photoletter to the editor: Disseminated histoplasmosis with initial oral manifestations

    OpenAIRE

    Sinha, Surabhi; Sardana, Kabir; Vijay K Garg

    2013-01-01

    Histoplasmosis is a systemic fungal disease that may present in a variety of clinical manifestations. Involvment of the oral mucosa is very rare and may occur as part of disseminated histoplasmosis or as isolated involvement. We present a patient with disseminated histoplasmosis, in whom oral lesions were the initial manifestation of the disease.

  12. Serious fungal infections in Ecuador.

    Science.gov (United States)

    Zurita, J; Denning, D W; Paz-Y-Miño, A; Solís, M B; Arias, L M

    2017-06-01

    There is a dearth of data from Ecuador on the burden of life-threatening fungal disease entities; therefore, we estimated the burden of serious fungal infections in Ecuador based on the populations at risk and available epidemiological databases and publications. A full literature search was done to identify all epidemiology papers reporting fungal infection rates. WHO, ONU-AIDS, Index Mundi, Global Asthma Report, Globocan, and national data [Instituto Nacional de Estadística y Censos (INEC), Ministerio de Salud Pública (MSP), Sociedad de Lucha Contra el Cáncer (SOLCA), Instituto Nacional de Donación y Trasplante de Órganos, Tejidos y Células (INDOT)] were reviewed. When no data existed, risk populations were used to estimate frequencies of fungal infections, using previously described methodology by LIFE. Ecuador has a variety of climates from the cold of the Andes through temperate to humid hot weather at the coast and in the Amazon basin. Ecuador has a population of 15,223,680 people and an average life expectancy of 76 years. The median estimate of the human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) population at risk for fungal disease (<200 CD4 cell counts) is ∼10,000, with a rate of 11.1% (1100) of histoplasma, 7% (700) of cryptococcal meningitis, and 11% (1070) of Pneumocystis pneumonia. The burden of candidemia is 1037. Recurrent Candida vaginitis (≥4 episodes per year) affects 307,593 women aged 15-50 years. Chronic pulmonary aspergillosis probably affects ∼476 patients following tuberculosis (TB). Invasive aspergillosis is estimated to affect 748 patients (∼5.5/100,000). In addition, allergic bronchopulmonary aspergillosis (ABPA) in asthma and severe asthma with fungal sensitization (SAFS) were estimated to affect 26,642 and 45,013 people, respectively. Our estimates indicate that 433,856 (3%) of the population in Ecuador is affected by serious fungal infection.

  13. Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test.

    Science.gov (United States)

    Zhao, Ni; Chen, Jun; Carroll, Ian M; Ringel-Kulka, Tamar; Epstein, Michael P; Zhou, Hua; Zhou, Jin J; Ringel, Yehuda; Li, Hongzhe; Wu, Michael C

    2015-05-01

    High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Distance-based analysis is a popular strategy for evaluating the overall association between microbiome diversity and outcome, wherein the phylogenetic distance between individuals' microbiome profiles is computed and tested for association via permutation. Despite their practical popularity, distance-based approaches suffer from important challenges, especially in selecting the best distance and extending the methods to alternative outcomes, such as survival outcomes. We propose the microbiome regression-based kernel association test (MiRKAT), which directly regresses the outcome on the microbiome profiles via the semi-parametric kernel machine regression framework. MiRKAT allows for easy covariate adjustment and extension to alternative outcomes while non-parametrically modeling the microbiome through a kernel that incorporates phylogenetic distance. It uses a variance-component score statistic to test for the association with analytical p value calculation. The model also allows simultaneous examination of multiple distances, alleviating the problem of choosing the best distance. Our simulations demonstrated that MiRKAT provides correctly controlled type I error and adequate power in detecting overall association. "Optimal" MiRKAT, which considers multiple candidate distances, is robust in that it suffers from little power loss in comparison to when the best distance is used and can achieve tremendous power gain in comparison to when a poor distance is chosen. Finally, we applied MiRKAT to real microbiome datasets to show that microbial communities are associated with smoking and with fecal protease levels after confounders are controlled for.

  14. Cultivable microbiome of fresh white button mushrooms.

    Science.gov (United States)

    Rossouw, W; Korsten, L

    2017-02-01

    Microbial dynamics on commercially grown white button mushrooms is of importance in terms of food safety assurance and quality control. The purpose of this study was to establish the microbial profile of fresh white button mushrooms. The total microbial load was determined through standard viable counts. Presence and isolation of Gram-negative bacteria including coagulase-positive Staphylococci were performed using a selective enrichment approach. Dominant and presumptive organisms were confirmed using molecular methods. Total mushroom microbial counts ranged from 5·2 to 12·4 log CFU per g, with the genus Pseudomonas being most frequently isolated (45·37% of all isolations). In total, 91 different microbial species were isolated and identified using Matrix-assisted laser desorption ionization-time of flight mass spectrophotometry, PCR and sequencing. Considering current food safety guidelines in South Africa for ready-to-eat fresh produce, coliform counts exceeded the guidance specifications for fresh fruit and vegetables. Based on our research and similar studies, it is proposed that specifications for microbial loads on fresh, healthy mushrooms reflect a more natural microbiome at the point-of-harvest and point-of-sale. Presence and persistence of micro-organisms within the microbiome of fresh produce is important when identifying a potential niche for foodborne pathogens. Most foodborne outbreaks can be attributed to microbial imbalances or lack of diversity within the associated host surface and residing microbial population. Agaricus bisporus samples analysed during this study showed a higher microbial load (5·2 up to 12·4 log CFU per g) compared to known values for other fresh produce. These mushrooms were considered to carry microbial loads representing a healthy and safe product, fit for consumption, despite showing a high indicator incidence. Although foodborne pathogens may be associated on occasion with fresh mushrooms, it remains a low

  15. Microbiome mediation of infections in the cancer setting.

    Science.gov (United States)

    Taur, Ying; Pamer, Eric G

    2016-04-18

    Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic barriers, and exposure to nosocomial (hospital-acquired) pathogens. Consequently, cancer-related infections are unique and epidemiologically distinct from those in other patient populations and may be particularly challenging for clinicians to treat. There is increasing evidence that the microbiome is a crucial factor in the cancer patient's risk for infectious complications. Frequently encountered pathogens with observed ties to the microbiome include vancomycin-resistant Enterococcus, Enterobacteriaceae, and Clostridium difficile; these organisms can exist in the human body without disease under normal circumstances, but all can arise as infections when the microbiome is disrupted. In the cancer patient, such disruptions may result from interventions such as chemotherapy, broad-spectrum antibiotics, or anatomic alteration through surgery. In this review, we discuss evidence of the significant role of the microbiome in cancer-related infections; how a better understanding of the role of the microbiome can facilitate our understanding of these complications; and how this knowledge might be exploited to improve outcomes in cancer patients and reduce risk of infection.

  16. Geochemical influences and mercury methylation of a dental wastewater microbiome.

    Science.gov (United States)

    Rani, Asha; Rockne, Karl J; Drummond, James; Al-Hinai, Muntasar; Ranjan, Ravi

    2015-08-14

    The microbiome of dental clinic wastewater and its impact on mercury methylation remains largely unknown. Waste generated during dental procedures enters the sewer system and contributes a significant fraction of the total mercury (tHg) and methyl mercury (MeHg) load to wastewater treatment facilities. Investigating the influence of geochemical factors and microbiome structure is a critical step linking the methylating microorganisms in dental wastewater (DWW) ecosystems. DWW samples from a dental clinic were collected over eight weeks and analyzed for geochemical parameters, tHg, MeHg and bacterio-toxic heavy metals. We employed bacterial fingerprinting and pyrosequencing for microbiome analysis. High concentrations of tHg, MeHg and heavy metals were detected in DWW. The microbiome was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and many unclassified bacteria. Significant correlations were found between the bacterial community, Hg levels and geochemical factors including pH and the predicted total amount (not fraction) of neutral Hg-sulfide species. The most prevalent known methylators included Desulfobulbus propionicus, Desulfovibrio desulfuricans, Desulfovibrio magneticus and Geobacter sulfurreducens. This study is the first to investigate the impact of high loads of Hg, MeHg and other heavy metals on the dental clinic wastewater microbiome, and illuminates the role of many known and unknown sulfate-reducing bacteria in Hg methylation.

  17. Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype.

    Science.gov (United States)

    Tyler, Andrea D; Kirsch, Richard; Milgrom, Raquel; Stempak, Joanne M; Kabakchiev, Boyko; Silverberg, Mark S

    2016-04-01

    Inflammatory bowel disease has been associated with differential abundance of numerous organisms when compared to healthy controls (HCs); however, few studies have investigated variability in the microbiome across intestinal locations and how this variability might be related to disease location and phenotype. In this study, we have analyzed the microbiome of a large cohort of individuals recruited at Mount Sinai Hospital in Toronto, Canada. Biopsies were taken from subjects with Crohn's disease, ulcerative colitis, and HC, and also individuals having undergone ileal pouch-anal anastomosis for treatment of ulcerative colitis or familial adenomatous polyposis. Microbial 16S rRNA was sequenced using the Illumina MiSeq platform. We observed a great deal of variability in the microbiome characterizing different sampling locations. Samples from pouch and afferent limb were comparable in microbial composition. When comparing sigmoid and terminal ileum samples, more differences were observed. The greatest number of differentially abundant microbes was observed when comparing either pouch or afferent limb samples to sigmoid or terminal ileum. Despite these differences, we were able to observe modest microbial variability between inflammatory bowel disease phenotypes and HCs, even when controlling for sampling location and additional experimental factors. Most detected associations were observed between HCs and Crohn's disease, with decreases in specific genera in the families Ruminococcaceae and Lachnospiraceae characterizing tissue samples from individuals with Crohn's disease. This study highlights important considerations when analyzing the composition of the microbiome and also provides useful insight into differences in the microbiome characterizing these seemingly related phenotypes.

  18. Impact of plant domestication on rhizosphere microbiome assembly and functions.

    Science.gov (United States)

    Pérez-Jaramillo, Juan E; Mendes, Rodrigo; Raaijmakers, Jos M

    2016-04-01

    The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.

  19. Microbiological diagnostics of fungal infections

    Directory of Open Access Journals (Sweden)

    Corrado Girmenia

    2013-07-01

    Full Text Available Laboratory tests for the detection of fungal infections are easy to perform. The main obstacle to a correct diagnosis is the correlation between the laboratory findings and the clinical diagnosis. Among pediatric patients, the most common fungal pathogen is Candida. The detection of fungal colonization may be performed through the use of chromogenic culture media, which allows also the identification of Candida subspecies, from which pathogenicity depends. In neonatology, thistest often drives the decision to begin a empiric therapy; in this regard, a close cooperation between microbiologists and clinicians is highly recommended. Blood culture, if positive, is a strong confirmation of fungal infection; however, its low sensitivity results in a high percentage of false negatives, thus decreasing its reliability. Molecular diagnostics is still under evaluation, whereas the detection of some fungal antigens, such as β-D-glucan, galactomannan, mannoprotein, and cryptococcal antigen in the serum is used for adults, but still under evaluations for pediatric patients.http://dx.doi.org/10.7175/rhc.v4i1S.862

  20. Fungal artificial chromosomes for mining of the fungal secondary metabolome

    OpenAIRE

    2015-01-01

    Background With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30–80 kb in size, breakthrough techniques are needed to characterize this SM wealth. Results Here we describe a novel system-level methodology for unbiased cloning of intact large SM clusters from a single fungal genome for one-step transformation and expression in a model host. All 56 intact SM clusters from Aspergillus terreus were individually captured in self-rep...

  1. Interactions between Host and Oral Commensal Microorganisms are Key Events in Health and Disease Status

    Directory of Open Access Journals (Sweden)

    Mahmoud Rouabhia

    2002-01-01

    Full Text Available The oral cavity has sometimes been described as a mirror that reflects a person's health. Systemic diseases such as diabetes or vitamin deficiency may be seen as alterations in the oral mucosa. A variety of external factors cause changes in the oral mucosa, thus altering mucosal structure and function, and promoting oral pathologies (most frequently bacterial, fungal and viral infections. Little is known, however, about immune surveillance mechanisms that involve the oral mucosa.

  2. The salivary microbiome is altered in the presence of a high salivary glucose concentration

    Science.gov (United States)

    Hartman, Mor-Li; Shi, Ping; Hasturk, Hatice; Yaskell, Tina; Vargas, Jorel; Song, Xiaoqing; Cugini, Maryann; Barake, Roula; Alsmadi, Osama; Al-Mutawa, Sabiha; Ariga, Jitendra; Soparkar, Pramod; Behbehani, Jawad; Behbehani, Kazem

    2017-01-01

    Background Type II diabetes (T2D) has been associated with changes in oral bacterial diversity and frequency. It is not known whether these changes are part of the etiology of T2D, or one of its effects. Methods We measured the glucose concentration, bacterial counts, and relative frequencies of 42 bacterial species in whole saliva samples from 8,173 Kuwaiti adolescents (mean age 10.00 ± 0.67 years) using DNA probe analysis. In addition, clinical data related to obesity, dental caries, and gingivitis were collected. Data were compared between adolescents with high salivary glucose (HSG; glucose concentration ≥ 1.0 mg/d, n = 175) and those with low salivary glucose (LSG, glucose concentration gingivitis in the study population. The overall salivary bacterial load in saliva decreased with increasing salivary glucose concentration. Under HSG conditions, the bacterial count for 35 (83%) of 42 species was significantly reduced, and relative bacterial frequencies in 27 species (64%) were altered, as compared with LSG conditions. These alterations were stronger predictors of high salivary glucose than measures of oral disease, obesity, sleep or fitness. Conclusions HSG was associated with a reduction in overall bacterial load and alterations to many relative bacterial frequencies in saliva when compared with LSG in samples from adolescents. We propose that hyperglycemia due to obesity and/or T2D results in HSG and subsequent acidification of the oral environment, leading to a generalized perturbation in the oral microbiome. This suggests a basis for the observation that hyperglycemia is associated with an increased risk of dental erosion, dental caries, and gingivitis. We conclude that HSG in adolescents may be predicted from salivary microbial diversity or frequency, and that the changes in the oral microbial composition seen in adolescents with developing metabolic disease may the consequence of hyperglycemia. PMID:28249034

  3. Defining the core Arabidopsis thaliana root microbiome

    Science.gov (United States)

    Gehring, Jase; Malfatti, Stephanie; Tremblay, Julien; Engelbrektson, Anna; Kunin, Victor; del Rio, Tijana Glavina; Edgar, Robert C.; Eickhorst, Thilo; Ley, Ruth E.; Hugenholtz, Philip; Tringe, Susannah Green; Dangl, Jeffery L.

    2014-01-01

    Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing therhizosphere(immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1-3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plantmicrobe interactions derived from complex soil communities. PMID:22859206

  4. Forest microbiome: diversity, complexity and dynamics.

    Science.gov (United States)

    Baldrian, Petr

    2016-11-16

    Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.

  5. The human gut microbiome, a taxonomic conundrum.

    Science.gov (United States)

    Sankar, Senthil Alias; Lagier, Jean-Christophe; Pontarotti, Pierre; Raoult, Didier; Fournier, Pierre-Edouard

    2015-06-01

    From culture to metagenomics, within only 130 years, our knowledge of the human microbiome has considerably improved. With >1000 microbial species identified to date, the gastro-intestinal microbiota is the most complex of human biotas. It is composed of a majority of Bacteroidetes and Firmicutes and, although exhibiting great inter-individual variations according to age, geographic origin, disease or antibiotic uptake, it is stable over time. Metagenomic studies have suggested associations between specific gut microbiota compositions and a variety of diseases, including irritable bowel syndrome, Crohn's disease, colon cancer, type 2 diabetes and obesity. However, these data remain method-dependent, as no consensus strategy has been defined to decipher the complexity of the gut microbiota. High-throughput culture-independent techniques have highlighted the limitations of culture by showing the importance of uncultured species, whereas modern culture methods have demonstrated that metagenomics underestimates the microbial diversity by ignoring minor populations. In this review, we highlight the progress and challenges that pave the way to a complete understanding of the human gastrointestinal microbiota and its influence on human health.

  6. The vent microbiome: patterns and drivers

    Science.gov (United States)

    Pachiadaki, M.

    2015-12-01

    Microbial processes within deep-sea hydrothermal vents affect the global biogeochemical cycles. Still, there are significant gaps in our understanding of the microbiology and the biogeochemistry of deep-sea hydrothermal systems. Vents differ in temperature, host rock composition and fluid chemistry; factors that are hypothesized to shape the distribution of the microbial communities, their metabolic capabilities and their activities. Using large-scale single cell genomics, we obtained insights into the genomic content of several linkages of a diffuse flow vent. The genomes show high metabolic versatility. Sulfur oxidation appears to be predominant but there is the potential of using a variety of e- donors and acceptors to obtain energy. To further assess the ecological importance of the vent auto- and heterotrophs, the global biogeography of the analyzed lineages will be investigated by fragment recruitment of metagenomes produced from the same site as well as other hydrothermal systems. Metatranscriptomic and metaproteomic data will be integrated to examine the expression of the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production. The comparative analysis of the key players and associated pathways among various vent sites that differ in physicochemical characteristics is anticipated to decipher the patterns and drivers of the global dispersion and the local diversification of the vent microbiome.

  7. The developing intestinal microbiome: probiotics and prebiotics.

    Science.gov (United States)

    Neu, Josef

    2014-01-01

    The microbes in the human intestinal tract interact with the host to form a 'superorganism'. The functional aspects of the host microbe interactions are being increasingly scrutinized and it is becoming evident that this interaction in early life is critical for development of the immune system and metabolic function and aberrations may result in life-long health consequences. Evidence is suggesting that such interactions occur even before birth, where the microbes may be either beneficial or harmful, and possibly even triggering preterm birth. Mode of delivery, use of antibiotics, and other perturbations may have life-long consequences in terms of health and disease. Manipulating the microbiota by use of pro- and prebiotics may offer a means for maintenance of 'healthy' host microbe interactions, but over-exuberance in their use also has the potential to cause harm. Considerable controversy exists concerning the routine use of probiotics in the prevention of necrotizing enterocolitis. This chapter will provide a brief overview of the developing intestinal microbiome and discuss the use of pro- and prebiotics in preterm infants.

  8. Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change.

    Science.gov (United States)

    Gehring, Catherine; Flores-Rentería, Dulce; Sthultz, Christopher M; Leonard, Tierra M; Flores-Rentería, Lluvia; Whipple, Amy V; Whitham, Thomas G

    2014-03-01

    Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary. © 2013 John Wiley & Sons Ltd.

  9. The genetic predisposition and the interplay of host genetics and gut microbiome in Crohn disease.

    Science.gov (United States)

    Jianzhong, Hu

    2014-12-01

    Extensive genetic studies have identified more than 140 loci predisposing to Crohn disease (CD). Several major CD susceptibility genes have been shown to impair biological function with regard to immune response to recognizing and clearance of bacterial infection. Recent human microbiome studies suggest that the gut microbiome composition is differentiated in carriers of many risk variants of major CD susceptibility genes. This interplay between host genetics and its associated gut microbiome may play an essential role in the pathogenesis of CD. The ongoing microbiome research is aimed to investigate the detailed host genetics-microbiome interacting mechanism. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Microbiome-wide association studies link dynamic microbial consortia to disease

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Jack A.; Quinn, Robert A.; Debelius, Justine; Xu, Zhenjiang Z.; Morton, James; Garg, Neha; Jansson, Janet K.; Dorrestein, Pieter C.; Knight, Rob

    2016-07-06

    Rapid advances in DNA sequencing, metabolomics, proteomics and computation dramatically increase accessibility of microbiome studies and identify links between the microbiome and disease. Microbial time-series and multiple molecular perspectives enable Microbiome-Wide Association Studies (MWAS), analogous to Genome-Wide Association Studies (GWAS). Rapid research advances point towards actionable results, although approved clinical tests based on MWAS are still in the future. Appreciating the complexity of interactions between diet, chemistry, health and the microbiome, and determining the frequency of observations needed to capture and integrate this dynamic interface, is paramount for addressing the need for personalized and precision microbiome-based diagnostics and therapies.

  11. Microbiome and Asthma: What Have Experimental Models Already Taught Us?

    Directory of Open Access Journals (Sweden)

    R. Bonamichi-Santos

    2015-01-01

    Full Text Available Asthma is a chronic inflammatory disease that imposes a substantial burden on patients, their families, and the community. Although many aspects of the pathogenesis of classical allergic asthma are well known by the scientific community, other points are not yet understood. Experimental asthma models, particularly murine models, have been used for over 100 years in order to better understand the immunopathology of asthma. It has been shown that human microbiome is an important component in the development of the immune system. Furthermore, the occurrence of many inflammatory diseases is influenced by the presence of microbes. Again, experimental models of asthma have helped researchers to understand the relationship between the microbiome and respiratory inflammation. In this review, we discuss the evolution of murine models of asthma and approach the major studies involving the microbiome and asthma.

  12. The past, present and future of microbiome analyses

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.; Baker, Erin S.; Jansson, Janet K.

    2016-09-29

    Microbes evolved on Earth approximately 3.5 billion years ago and eventually occupied every habitable environment in its biosphere. While microorganisms are responsible for key functions on Earth including carbon and nutrient cycling and determining the health and disease of its inhabitants (i.e. plants and animals), >99% of the estimated trillions of microbes have yet to be discovered.1 In addition, high microbial diversity has made it difficult to study specific functions carried out by complex microbial communities within "microbiomes", such as those inhabiting the soil and human gut.2,3 Fortunately, technological advances over the last few decades have greatly facilitated studies of complex microbiomes and their functions. Here we will specifically discuss advances related to nucleic acid sequencing and mass spectrometry analyses that have enabled exploration and understanding of complex microbiomes in a range of environments and our own bodies.4,5,6,7

  13. Structure and function of the human skin microbiome.

    Science.gov (United States)

    Schommer, Nina N; Gallo, Richard L

    2013-12-01

    An abundant and diverse collection of bacteria, fungi, and viruses inhabits the human skin. These microorganisms vary between individuals and between different sites on the skin. The factors responsible for the unique variability of the skin microbiome are only partly understood, but results suggest that host genetic and environmental influences play a major role. Today, the steady accumulation of data describing the skin microbiome, combined with experiments designed to test the biological functions of surface microbes, has provided new insights into links between human physiology and skin microbiota. This review describes some of the current information regarding the skin microbiome and its impact on human health. Specifically, we summarize the present understanding of the function of microbe-host interactions on the skin and highlight some unique features that distinguish skin commensal organisms from pathogenic microbes.

  14. Social networks predict gut microbiome composition in wild baboons.

    Science.gov (United States)

    Tung, Jenny; Barreiro, Luis B; Burns, Michael B; Grenier, Jean-Christophe; Lynch, Josh; Grieneisen, Laura E; Altmann, Jeanne; Alberts, Susan C; Blekhman, Ran; Archie, Elizabeth A

    2015-01-01

    Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments. They therefore strongly implicate direct physical contact among social partners in the transmission of gut microbial species. We identified 51 socially structured taxa, which were significantly enriched for anaerobic and non-spore-forming lifestyles. Our results argue that social interactions are an important determinant of gut microbiome composition in natural animal populations-a relationship with important ramifications for understanding how social relationships influence health, as well as the evolution of group living.

  15. Social behavior shapes the chimpanzee pan-microbiome.

    Science.gov (United States)

    Moeller, Andrew H; Foerster, Steffen; Wilson, Michael L; Pusey, Anne E; Hahn, Beatrice H; Ochman, Howard

    2016-01-01

    Animal sociality facilitates the transmission of pathogenic microorganisms among hosts, but the extent to which sociality enables animals' beneficial microbial associations is poorly understood. The question is critical because microbial communities, particularly those in the gut, are key regulators of host health. We show evidence that chimpanzee social interactions propagate microbial diversity in the gut microbiome both within and between host generations. Frequent social interaction promotes species richness within individual microbiomes as well as homogeneity among the gut community memberships of different chimpanzees. Sampling successive generations across multiple chimpanzee families suggests that infants inherited gut microorganisms primarily through social transmission. These results indicate that social behavior generates a pan-microbiome, preserving microbial diversity across evolutionary time scales and contributing to the evolution of host species-specific gut microbial communities.

  16. A hundred-year-old insight into the gut microbiome!

    Directory of Open Access Journals (Sweden)

    Aziz Ramy

    2009-12-01

    Full Text Available Abstract As the National Institutes of Health-funded Human Microbiome Project enters its second phase, and as a major part of this project focuses on the human gut microbiome and its effects on human health, it might help us to travel a century back in time and examine how microbiologists dealt with microbiome-related challenges similar to those of the 21st century using the tools of their time. An article by Arthur I. Kendall, published in The Journal of Biological Chemistry in November 1909 (Some observations on the study of the intestinal bacteria J Biol Chem 1909, 6:499-507, offers a visionary insight into many of today's hot research questions.

  17. Chronic obstructive pulmonary disease and infection. Disruption of the microbiome?

    Science.gov (United States)

    Sethi, Sanjay

    2014-01-01

    The dynamics of infection in chronic obstructive pulmonary disease (COPD) are complex, and microbiome technology has provided us with a new research tool for its better understanding. There is compartmentalization of the microbiota in the various parts of the lung. Studies of the lower airway lumen microbiota in COPD have yielded confusing results, and additional studies with scrupulous attention to prevent and account for upper airway contamination of bronchoalveolar lavage samples are required. Lung tissue microbiota has been examined in three studies, which also demonstrate varied results based on the site of sampling (bronchial mucosa, lung parenchyma), and this variation extends to sampling sites within a lobe of the lung. The Vicious Circle Hypothesis embodies how an altered lung microbiome could contribute to COPD progression. Relating microbiota composition to airway and systemic inflammation and clinical outcomes are important research questions. Although various obstacles need to be surmounted, ultimately lung microbiome studies will provide new insights into how infection contributes to COPD.

  18. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.

    Science.gov (United States)

    Huang, Yvonne J; Sethi, Sanjay; Murphy, Timothy; Nariya, Snehal; Boushey, Homer A; Lynch, Susan V

    2014-08-01

    Specific bacterial species are implicated in the pathogenesis of exacerbations of chronic obstructive pulmonary disease (COPD). However, recent studies of clinically stable COPD patients have demonstrated a greater diversity of airway microbiota, whose role in acute exacerbations is unclear. In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD. Microbiome composition and predicted functions were examined using 16S rRNA-based culture-independent profiling methods. Shifts in the abundance (≥ 2-fold, P microbiome could be useful indicators of exacerbation development or outcome.

  19. The skin microbiome: Associations between altered microbial communities and disease.

    Science.gov (United States)

    Weyrich, Laura S; Dixit, Shreya; Farrer, Andrew G; Cooper, Alan J; Cooper, Alan J

    2015-11-01

    A single square centimetre of the human skin can contain up to one billion microorganisms. These diverse communities of bacteria, fungi, mites and viruses can provide protection against disease, but can also exacerbate skin lesions, promote disease and delay wound healing. This review addresses the current knowledge surrounding the healthy skin microbiome and examines how different alterations to the skin microbial communities can contribute to disease. Current methodologies are considered, changes in microbial diversity and colonisation by specific microorganisms are discussed in the context of atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. The recent impact of modern Westernised lifestyles on the human skin microbiome is also examined, as well as the potential benefits and pitfalls of novel therapeutic strategies. Further analysis of the human skin microbiome, and its interactions with the host immune system and other commensal microorganisms, will undoubtedly elucidate molecular mechanisms for disease and reveal gateways for novel therapeutic treatment strategies.

  20. Metabolic modeling with Big Data and the gut microbiome.

    Science.gov (United States)

    Sung, Jaeyun; Hale, Vanessa; Merkel, Annette C; Kim, Pan-Jun; Chia, Nicholas

    2016-09-01

    The recent advances in high-throughput omics technologies have enabled researchers to explore the intricacies of the human microbiome. On the clinical front, the gut microbial community has been the focus of many biomarker-discovery studies. While the recent deluge of high-throughput data in microbiome research has been vastly informative and groundbreaking, we have yet to capture the full potential of omics-based approaches. Realizing the promise of multi-omics data will require integration of disparate omics data, as well as a biologically relevant, mechanistic framework - or metabolic model - on which to overlay these data. Also, a new paradigm for metabolic model evaluation is necessary. Herein, we outline the need for multi-omics data integration, as well as the accompanying challenges. Furthermore, we present a framework for characterizing the ecology of the gut microbiome based on metabolic network modeling.

  1. Fungal infection following renal transplantation.

    Science.gov (United States)

    Gallis, H A; Berman, R A; Cate, T R; Hamilton, J D; Gunnells, J C; Stickel, D L

    1975-09-01

    Twenty-seven deep fungal infections developed in 22 of 171 patients following renal transplantation. These infections included cryptococcosis (ten), nocardiosis (seven), candidiasis (four), aspergillosis (two), phycomycosis (two), chromomycosis (one), and subcutaneous infection with Phialophora gougeroti (one). Twelve infections occurred in living-related and ten in cadaveric recipients. Nineteen of the 22 patients were male. Infections occurred from 0 to 61 months after transplantation. Complicating non-fungal infections were present concomitantly in 15 patients. Thirteen patients died, eight probably as a result of fungal infection. Appropriate diagnostic procedures yielded a diagnosis in 20 of 27 infections, and therapy was begun in 18 patients. Serologic, culture, and biopsy procedures useful in making rapid diagnoses are advocated in the hope of increasing survival.

  2. The Fungal Defensin Family Enlarged

    Directory of Open Access Journals (Sweden)

    Jiajia Wu

    2014-08-01

    Full Text Available Fungi are an emerging source of peptide antibiotics. With the availability of a large number of model fungal genome sequences, we can expect that more and more fungal defensin-like peptides (fDLPs will be discovered by sequence similarity search. Here, we report a total of 69 new fDLPs encoded by 63 genes, in which a group of fDLPs derived from dermatophytes are defined as a new family (fDEF8 according to sequence and phylogenetic analyses. In the oleaginous fungus Mortierella alpine, fDLPs have undergone extensive gene expansion. Our work further enlarges the fungal defensin family and will help characterize new peptide antibiotics with therapeutic potential.

  3. Emerging fungal infections among children: A review on its clinical manifestations, diagnosis, and prevention.

    Science.gov (United States)

    Jain, Akansha; Jain, Shubham; Rawat, Swati

    2010-10-01

    The incidence of fungal infections is increasing at an alarming rate, presenting an enormous challenge to healthcare professionals. This increase is directly related to the growing population of immunocompromised individuals especially children resulting from changes in medical practice such as the use of intensive chemotherapy and immunosuppressive drugs. Although healthy children have strong natural immunity against fungal infections, then also fungal infection among children are increasing very fast. Virtually not all fungi are pathogenic and their infection is opportunistic. Fungi can occur in the form of yeast, mould, and dimorph. In children fungi can cause superficial infection, i.e., on skin, nails, and hair like oral thrush, candida diaper rash, tinea infections, etc., are various types of superficial fungal infections, subcutaneous fungal infection in tissues under the skin and lastly it causes systemic infection in deeper tissues. Most superficial and subcutaneous fungal infections are easily diagnosed and readily amenable to treatment. Opportunistic fungal infections are those that cause diseases exclusively in immunocompromised individuals, e.g., aspergillosis, zygomycosis, etc. Systemic infections can be life-threatening and are associated with high morbidity and mortality. Because diagnosis is difficult and the causative agent is often confirmed only at autopsy, the exact incidence of systemic infections is difficult to determine. The most frequently encountered pathogens are Candida albicans and Aspergillus spp. But other fungi such as non-albicans Candida spp. are increasingly important.

  4. Emerging fungal infections among children: A review on its clinical manifestations, diagnosis, and prevention

    Directory of Open Access Journals (Sweden)

    Akansha Jain

    2010-01-01

    Full Text Available The incidence of fungal infections is increasing at an alarming rate, presenting an enormous challenge to healthcare professionals. This increase is directly related to the growing population of immunocompromised individuals especially children resulting from changes in medical practice such as the use of intensive chemotherapy and immunosuppressive drugs. Although healthy children have strong natural immunity against fungal infections, then also fungal infection among children are increasing very fast. Virtually not all fungi are pathogenic and their infection is opportunistic. Fungi can occur in the form of yeast, mould, and dimorph. In children fungi can cause superficial infection, i.e., on skin, nails, and hair like oral thrush, candida diaper rash, tinea infections, etc., are various types of superficial fungal infections, subcutaneous fungal infection in tissues under the skin and lastly it causes systemic infection in deeper tissues. Most superficial and subcutaneous fungal infections are easily diagnosed and readily amenable to treatment. Opportunistic fungal infections are those that cause diseases exclusively in immunocompromised individuals, e.g., aspergillosis, zygomycosis, etc. Systemic infections can be life-threatening and are associated with high morbidity and mortality. Because diagnosis is difficult and the causative agent is often confirmed only at autopsy, the exact incidence of systemic infections is difficult to determine. The most frequently encountered pathogens are Candida albicans and Aspergillus spp. But other fungi such as non-albicans Candida spp. are increasingly important.

  5. Antifungal activity of some Tanzanian plants used traditionally for the treatment of fungal infections.

    NARCIS (Netherlands)

    Hamza, O.; Beukel, C. van den; Matee, M.I.N.; Moshi, M.J.; Mikx, F.H.M.; Selemani, H.O.; Mbwambo, Z.H.; Ven, A.J.A.M. van der; Verweij, P.E.

    2006-01-01

    Using the ethnobotanical approach, some Tanzanian plants reported to be used by traditional healers for the treatment of oral candidiasis and fungal infections of the skin were collected and screened for their antifungal activity against Candida albicans, Candida glabrata, Candida tropicalis, Candid

  6. Oral geotrichosis: report of 12 cases.

    Science.gov (United States)

    Bonifaz, Alexandro; Vázquez-González, Denisse; Macías, Berenice; Paredes-Farrera, Fernando; Hernández, Marco A; Araiza, Javier; Ponce, Rosa M

    2010-09-01

    Oral geotrichosis is an uncommon opportunistic infection caused by Geotrichum candidum, a habitual contaminant and component of the flora of various parts of the body. This communication reports both a 20-year retrospective study of clinically and mycologically proven cases of oral geotrichosis, and a prospective study of fungal oral flora in 200 individuals divided into two groups: normal individuals and individuals with associated conditions. Twelve patients with proven oral geotrichosis were included: 9 females and 3 males, with a mean age of 48.5 years; the associated conditions were diabetes mellitus (66.6%), leukemia, Hodgkin's lymphoma and HIV/AIDS infection. The oral geotrichoses showed three clinical varieties: pseudomembranous (75%), hyperplastic, and palatine ulcer. G. candidum was isolated in 11 cases and G. capitatum in one. Positive fungal cultures were obtained from the two groups, and 48% and 78% of cultures were positive, respectively, for Candida spp. In 2.8% and 6.33% of the cases, G. candidum was isolated, respectively, together with one strain of G. capitatum. Oral geotrichosis is an exceptional infection that clinically presents, and is treated, as oral candidiasis. G. candidum may be isolated from the oral flora of a small proportion of patients, either normal individuals or those with associated conditions.

  7. Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Kimberly D Cephas

    Full Text Available Bacterial contribution to oral disease has been studied in young children, but there is a lack of data addressing the developmental perspective in edentulous infants. Our primary objectives were to use pyrosequencing to phylogenetically characterize the salivary bacterial microbiome of edentulous infants and to make comparisons against their mothers. Saliva samples were collected from 5 edentulous infants (mean age = 4.6±1.2 mo old and their mothers or primary care givers (mean age = 30.8±9.5 y old. Salivary DNA was extracted, used to generate DNA amplicons of the V4-V6 hypervariable region of the bacterial 16S rDNA gene, and subjected to 454-pyrosequencing. On average, over 80,000 sequences per sample were generated. High bacterial diversity was noted in the saliva of adults [1012 operational taxonomical units (OTU at 3% divergence] and infants (578 OTU at 3% divergence. Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria were predominant bacterial phyla present in all samples. A total of 397 bacterial genera were present in our dataset. Of the 28 genera different (P<0.05 between infants and adults, 27 had a greater prevalence in adults. The exception was Streptococcus, which was the predominant genera in infant saliva (62.2% in infants vs. 20.4% in adults; P<0.05. Veillonella, Neisseria, Rothia, Haemophilus, Gemella, Granulicatella, Leptotrichia, and Fusobacterium were also predominant genera in infant samples, while Haemophilus, Neisseria, Veillonella, Fusobacterium, Oribacterium, Rothia, Treponema, and Actinomyces were predominant in adults. Our data demonstrate that although the adult saliva bacterial microbiome had a greater OTU count than infants, a rich bacterial community exists in the infant oral cavity prior to tooth eruption. Streptococcus, Veillonella, and Neisseria are the predominant bacterial genera present in infants. Further research is required to characterize the development of oral microbiota early in life

  8. The microbiome of the built environment and mental health.

    Science.gov (United States)

    Hoisington, Andrew J; Brenner, Lisa A; Kinney, Kerry A; Postolache, Teodor T; Lowry, Christopher A

    2015-12-17

    The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is little knowledge of the impacts of the MoBE on mental health. Depending on the specific microbial species involved, the transfer of microorganisms from the built environment to occupant's cutaneous or mucosal membranes has the potential to increase or disrupt immunoregulation and/or exaggerate or suppress inflammation. Preclinical evidence highlighting the influence of the microbiota on systemic inflammation supports the assertion that microorganisms, including those originating from the built environment, have the potential to either increase or decrease the risk of inflammation-induced psychiatric conditions and their symptom severity. With advanced understanding of both the ecology of the built environment, and its influence on the human microbiome, it may be possible to develop bioinformed strategies for management of the built environment to promote mental health. Here we present a brief summary of microbiome research in both areas and highlight two interdependencies including the following: (1) effects of the MoBE on the human microbiome and (2) potential opportunities for manipulation of the MoBE in order to improve mental health. In addition, we propose future research directions including strategies for assessment of changes in the microbiome of common areas of built environments shared by multiple human occupants, and associated cohort-level changes in the mental health of those who spend time in the buildings. Overall, our understanding of the fields of both the MoBE and influence of host-associated microorganisms on mental health are advancing at a rapid pace and, if linked, could offer considerable benefit to health and wellness.

  9. Current state of knowledge: the canine gastrointestinal microbiome.

    Science.gov (United States)

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

    2012-06-01

    Gastrointestinal (GI) microbes have important roles in the nutritional, immunological, and physiologic processes of the host. Traditional cultivation techniques have revealed bacterial density ranges from 10(4) to 10(5) colony forming units (CFU)/g in the stomach, from 10(5) to 10(7) CFU/g in the small intestine, and from 10(9) to 10(11) CFU/g in the colon of healthy dogs. As a small number of bacterial species can be grown and studied in culture, however, progress was limited until the recent emergence of DNA-based techniques. In recent years, DNA sequencing technology and bioinformatics have allowed for better phylogenetic and functional/metabolic characterization of the canine gut microbiome. Predominant phyla include Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. Studies using 16S ribosomal RNA (rRNA) gene pyrosequencing have demonstrated spatial differences along the GI tract and among microbes adhered to the GI mucosa compared to those in intestinal contents or feces. Similar to humans, GI microbiome dysbiosis is common in canine GI diseases such as chronic diarrhea and inflammatory bowel diseases. DNA-based assays have also identified key pathogens contributing to such conditions, including various Clostridium, Campylobacter, Salmonella, and Escherichia spp. Moreover, nutritionists have applied DNA-based techniques to study the effects of dietary interventions such as dietary fiber, prebiotics, and probiotics on the canine GI microbiome and associated health indices. Despite recent advances in the field, the canine GI microbiome is far from being fully characterized and a deeper characterization of the phylogenetic and functional/metabolic capacity of the GI microbiome in health and disease is needed. This paper provides an overview of recent studies performed to characterize the canine GI microbiome.

  10. The possible mechanisms of the human microbiome in allergic diseases.

    Science.gov (United States)

    Ipci, Kagan; Altıntoprak, Niyazi; Muluk, Nuray Bayar; Senturk, Mehmet; Cingi, Cemal

    2017-02-01

    In the present paper, we discuss the importance of the microbiome in allergic disease. In this review paper, the data from the Medline (PubMed) and search engine of Kirikkale University were systematically searched for all relevant articles in June 15th, 2015 for the past 30 years. The keywords of "microbiome", "dysbiosis", "allergy", "allergic rhinitis", "allergic disease", "mechanisms" and "treatment" were used alone or together. In this paper, microbiomes were presented in terms of "Definition", "Influence of \\the human microbiome on health", "The microbiome and allergic diseases", and "Modulation of the gut microbiota in terms of treatment and prevention". Microbiological dysbiosis is also reviewed. The microbiome is the genetic material of all microbes (bacteria, fungi, protozoa, and viruses) that live on or in the human body. Microbes outnumber human cells in a 10:1 ratio. Most microbes live in the gut, particularly the large intestine. Changes in the immune function of the respiratory tract are (at least in theory) linked to the immunomodulatory activity of the gut microbiota via the concept of a "common mucosal response". The gut microbiota shapes systemic immunity, thus affecting the lung mucosa. Alternatively, changes in the gut microbiota may reflect alterations in the oropharyngeal microbiota, which may in turn directly affect the lung microbiota and host immune responses via microaspiration. Dysbiosis is defined as qualitative and quantitative changes in the intestinal flora; and modern diet and lifestyle, antibiotics, psychological and physical stress result in alterations in bacterial metabolism, as well as the overgrowth of potentially pathogenic microorganisms. All immune system components are directly or indirectly regulated by the microbiota. The nature of microbial exposure early in life appears to be important for the development of robust immune regulation; disruption of either the microbiota or the host response can trigger chronic

  11. Clinical cases of parasitoses and fungal infections important from medical point of view

    Science.gov (United States)

    Błaszkowska, Joanna; Góralska, Katarzyna

    Most important infectious diseases which pose a risk to human health and life are associated with parasites transmitted by a variety of arthropod vectors, or from animal to man. Some of these (malaria, toxoplasmosis, leishmaniosis, dirofilariosis, alveococcosis, cystic echinococcosis) still represent a serious public health problem in many regions in the world. This review describes the epidemiological and clinical aspects of important parasitoses and fungal infections from a medical point of view. It should be emphasized that the development of invasive disease depends on both host (susceptibility/resistance) and parasite factors (pathogenicity/virulence); an immunocompromised state can favour opportunistic parasitic infections: toxoplasmosis, cryptosporidiosis, giardiosis, cyclosporidiosis, blastocystosis and strongyloidosis. This article highlights the role of free-living amoebae in the pathogenesis and transmission of human diseases, the high pathogenicity of Echinococcus multilocularis, and the growing importance of ticks as a reservoir and vector for numerous dangerous pathogens (e.g., Borrelia burgdorferi, Anaplasma phagocytophilum, Babesia microti). It also discusses the diagnostic problems of toxoplasmosis including cross-reactions in serological tests and reviews the search for new drugs and vaccines against toxoplasmosis. Attention is increasingly paid to the role played by the human microbiome in maintaining homeostasis and in the development of fungal infections. This review also presents the most common human superficial fungal infections and the role of Candida albicans infection in the pathogenesis of irritable bowel syndrome.

  12. Fungal infection risk groups among school children

    Directory of Open Access Journals (Sweden)

    Elżbieta Ejdas

    2014-08-01

    Full Text Available The aim of the study was to evaluate the relationship between ocurrence of fungi in children and living environment (city - countryside, sex, age, diet, undergone diseases therapy with antibiotics and exposure to hospital environment, and to indicate children potentially vulnerable to fungal infections. The material was consisted of swabs collected from the oral cavily, the throat and the nose of healthy children, aged 6-9 and 10-15, from both urban and rural environmens. Candida albicans, the basic aetiological factor in thc majority of mycoses recorded in humans, unquestionably prevailed in the group of the 13 speciec of yeast-like fungi and yeasts isolated. Records of C. glabrata and C. krusei increasing numbers of whose strains show resistance to basic antimycoties, as well as relatively frequent records of Trichosporon beigelii, Saccharomycopsis capsularis and Saccharomyces sp., fungi whose expansiveness and enzymatic activity have been growing, may be considered disconcerting. Vulnerability to fungal infection increases following anti-bacterial antibiotic therapy in the majority of subjects regardless season or age. This is particularly true primarily of the most stable ontocoenosis of the throat. Younger children, on the other hand, are the most vulnerable foUowing infection of the respiratory system. Fungi are likely to colonise the nose in this case. Children living in the countryside who had been ll immediately prior to the collection of the material constitute the highest risk group of the occurrence of fungi in any of the ontocoenoses studied. A greater number of positive inoculations were recorded in these children in comparison to the children from the city. It may be indicative of a more extensive spectrum of natural reservoirs of fungi and the vectors of their transmission in rural areas than those in the city, lower health hygiene and lower immunity or of a more common carriage of fungi among rural children.

  13. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

    Science.gov (United States)

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-07-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.

  14. Geriatric oral health and pneumonia risk.

    Science.gov (United States)

    Terpenning, Margaret

    2005-06-15

    The oral cavity is a complex microenvironment consisting of multiple bacterial and fungal species, their associated biofilms, and a cytokine milieu influenced by constant inflammatory stimulation. Multiple infectious consequences of poor oral health have been extensively described and primarily affect older adults. Probably the most common sequelae of poor oral health in aged persons is a risk of aspiration pneumonia. The risk of aspiration pneumonia is greatest when periodontal disease, dental caries, and poor oral hygiene are compounded by swallowing disease, feeding problems, and poor functional status. The effectiveness of oral hygiene interventions for preventing aspiration pneumonia and barriers to oral care of nursing home patients require additional study, but the current state of research in these areas is reviewed in this manuscript. The expense of aspiration pneumonia as a nursing home complication makes dental hygiene a potentially cost-saving intervention.

  15. Does the change on gastrointestinal tract microbiome affects host?

    Directory of Open Access Journals (Sweden)

    Elisa M. Beirão

    2014-12-01

    Full Text Available During the past decade, studies on the composition of human microbiota and its relation to the host became one of the most explored subjects of the medical literature. The development of high-throughput molecular technologies allowed a deeper characterization of human microbiota and a better understanding of its relationship with health and disease. Changes in human habits including wide use of antimicrobials can result in dysregulation of host–microbiome homeostasis, with multiple consequences. The purpose of this review is to highlight the most important evidence in the literature of host–microbiome interactions and illustrate how these intriguing relations may lead to new treatment and prevention strategies.

  16. Capturing One of the Human Gut Microbiome's Most Wanted

    DEFF Research Database (Denmark)

    Jeraldo, Patricio; Hernandez, Alvaro; Nielsen, Henrik Bjørn

    2016-01-01

    The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent...... allowed us to assemble "most wanted" genomes from metagenomic data collected from four stool samples. Using a combination of both de novo and guided assembly methods, we assembled and binned over 100 genomes from an initial data set of over 1,300 Gbp. One of these genome bins, which met HMP's criteria...

  17. The enteric microbiome in hepatobiliary health and disease.

    Science.gov (United States)

    Tabibian, James H; Varghese, Cyril; LaRusso, Nicholas F; O'Hara, Steven P

    2016-04-01

    Increasing evidence points to the contribution of the intestinal microbiome as a potentially key determinant in the initiation and/or progression of hepatobiliary disease. While current understanding of this dynamic is incomplete, exciting insights are continually being made and more are expected given the developments in molecular and high-throughput omics techniques. In this brief review, we provide a practical and updated synopsis of the interaction of the intestinal microbiome with the liver and its downstream impact on the initiation, progression and complications of hepatobiliary disease.

  18. Part 1: The Human Gut Microbiome in Health and Disease

    OpenAIRE

    Bull, Matthew J.; Plummer, Nigel T.

    2014-01-01

    The bacterial cells harbored within the human gastrointestinal tract (GIT) outnumber the host’s cells by a factor of 10 and the genes encoded by the bacteria resident within the GIT outnumber their host’s genes by more than 100 times. These human digestive-tract associated microbes are referred to as the gut microbiome. The human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physi...

  19. Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

    Directory of Open Access Journals (Sweden)

    Yang SONG,Chen ZHU,Waseem RAZA,Dongsheng WANG,Qiwei HUANG,Shiwei GUO,Ning LING,Qirong SHEN

    2016-09-01

    Full Text Available Grafting is commonly used to overcome soil-borne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper, significant negative correlations between the bacterial alpha diversity and both the disease incidence (r = -0.832, P = 0.005 and pathogen population (r = - 0.786, P = 0.012 were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure (beta diversity in the rhizosphere. Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

  20. Current treatment of oral candidiasis: a literature review

    OpenAIRE

    Garcia Cuesta, Carla; Sarrión Pérez, María Gracia; Bagán Sebastián, José Vicente

    2014-01-01

    Candidiasis or oral candidosis is one of the most common human opportunistic fungal infections of the oral cavity. This pathology has a wide variety of treatment which has been studied until these days. The present study offers a literature review on the treatment of oral candidiasis, with the purpose of establish which treatment is the most suitable in each case. Searching the 24 latest articles about treatment of candidiasis it concluded that the incidence depends on the type of the candidi...