WorldWideScience

Sample records for human fecal microbial

  1. Assessment and impact of microbial fecal pollution and human enteric pathogens in a coastal community.

    Science.gov (United States)

    Lipp, E K; Farrah, S A; Rose, J B

    2001-04-01

    The goals of this study were to assess watersheds impacted by high densities of OSDS (onsite sewage disposal systems) for evidence of fecal contamination and evaluate the occurrence of human pathogens in coastal waters off west Florida. Eleven stations (representing six watersheds) were intensively sampled for microbial indicators of fecal pollution (fecal coliform bacteria, enterococci, Clostridium perfringens and coliphage) and the human enteric pathogens, Cryptosporidium, Giardia, and enteroviruses during the summer rainy season (May-September 1996). Levels of all indicators ranged between 4000 CFU/100 ml. Cryptosporidium and Giardia were detected infrequently (6.8% and 2.3% of samples tested positive, respectively). Conversely, infectious enteroviruses were detected at low levels in 5 of the 6 watersheds sampled. Using cluster analysis, sites were grouped into two categories, high and low risks, based on combined levels of indicators. These results suggest that stations of highest pollution risk were located within areas of high OSDS densities. Furthermore, data indicate a subsurface transport of contaminated water to surface waters. The high prevalence of enteroviruses throughout the study area suggests a chronic pollution problem and potential risk to recreational swimmers in and around Sarasota Bay.

  2. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  3. PCR-DGGE-Based Study of Fecal Microbial Stability during the Long-Term Chitosan Supplementation of Humans

    Czech Academy of Sciences Publication Activity Database

    Mrázek, Jakub; Koppová, Ingrid; Kopečný, Jan; Šimůnek, Jiří; Fliegerová, Kateřina

    2010-01-01

    Roč. 55, č. 4 (2010), s. 352-358 ISSN 0015-5632 R&D Projects: GA ČR(CZ) GA525/08/0803 Institutional research plan: CEZ:AV0Z50450515 Keywords : Chitosan * Microbial stability * Microflora Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 0.977, year: 2010

  4. Dietary effects on human fecal microbiota

    OpenAIRE

    Simões, Catarina

    2013-01-01

    The establishment of microbial populations in the gastrointestinal (GI)-tract is a complex process, involving microbial and host interactions eventually resulting in a dense and stable population. Recently, the identification of microbial species from fecal samples has become more accurate with the use of 16S RNA gene-based methods. However, although these molecular-based detection methods have apparent benefits over culture-based techniques, they involve potential pitfalls that should be tak...

  5. Microbial quality of tilapia reared in fecal-contaminated ponds

    International Nuclear Information System (INIS)

    El-Shafai, S.A.; Gijzen, H.J.; Nasr, F.A.; El-Gohary, F.A.

    2004-01-01

    The microbial quality of tilapia reared in four fecal-contaminated fishponds was investigated. One of the fishponds (TDP) received treated sewage with an average fecal coliform count of 4x10 3 cfu/100 mL, and feed of fresh duckweed grown on treated sewage was used. The number of fecal coliform bacteria attached to duckweed biomass ranged between 4.1x10 2 and 1.6x10 4 cfu/g fresh weight. The second fishpond (TWP) received treated sewage, and the feed used was wheat bran. The third fishpond (FDP) received freshwater, and the feed used was the same duckweed. Pond 4 (SSP) received only settled sewage with an average fecal coliform count of 2.1x10 8 /100 mL. The average counts in the fishponds were 2.2x10 3 , 1.7x10 3 , 1.7x10 2 , and 9.4x10 3 cfu/100 mL in TDP, TWP, FDP, and SSP, respectively. FDP had a significantly (P gills>skin>liver. Poor water quality (ammonia and nitrite) in SSP resulted in statistically higher fecal coliform numbers in fish organs of about 1 log 10 than in treatments with good water quality. Pretreatment of sewage is therefore recommended

  6. Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study.

    Science.gov (United States)

    Flores, Roberto; Shi, Jianxin; Fuhrman, Barbara; Xu, Xia; Veenstra, Timothy D; Gail, Mitchell H; Gajer, Pawel; Ravel, Jacques; Goedert, James J

    2012-12-21

    High systemic estrogen levels contribute to breast cancer risk for postmenopausal women, whereas low levels contribute to osteoporosis risk. Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identify members and functions of the intestinal microbial community associated with estrogen levels via enterohepatic recirculation. Fifty-one epidemiologists at the National Institutes of Health, including 25 men, 7 postmenopausal women, and 19 premenopausal women, provided urine and aliquots of feces, using methods proven to yield accurate and reproducible results. Estradiol, estrone, 13 estrogen metabolites (EM), and their sum (total estrogens) were quantified in urine and feces by liquid chromatography/tandem mass spectrometry. In feces, β-glucuronidase and β-glucosidase activities were determined by realtime kinetics, and microbiome diversity and taxonomy were estimated by pyrosequencing 16S rRNA amplicons. Pearson correlations were computed for each loge estrogen level, loge enzymatic activity level, and microbiome alpha diversity estimate. For the 55 taxa with mean relative abundance of at least 0.1%, ordinal levels were created [zero, low (below median of detected sequences), high] and compared to loge estrogens, β-glucuronidase and β-glucosidase enzymatic activity levels by linear regression. Significance was based on two-sided tests with α=0.05. In men and postmenopausal women, levels of total urinary estrogens (as well as most individual EM) were very strongly and directly associated with all measures of fecal microbiome richness and alpha diversity (R≥0.50, P≤0.003). These non-ovarian systemic estrogens also were strongly and significantly associated with fecal Clostridia taxa, including non-Clostridiales and three genera in the Ruminococcaceae family (R=0.57-0.70, P=0.03-0.002). Estrone, but not other EM, in urine correlated significantly with functional activity of fecal β-glucuronidase (R=0.36, P=0

  7. Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders.

    Science.gov (United States)

    Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G; Hoyt, David W; Howsmon, Daniel P; Shaffer, Michael; Lozupone, Catherine A; Hahn, Juergen; Adams, James B; Krajmalnik-Brown, Rosa

    2018-02-01

    Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Using 1 H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. Despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further

  8. Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.; Hoyt, David W.; Howsmon, Daniel P.; Shaffer, Michael; Lozupone, Catherine A.; Hahn, Juergen; Adams, James B.; Krajmalnik-Brown, Rosa

    2018-02-01

    Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Using NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites- caprate, nicotinate, glutamine, thymine, and aspartate- may potentially function as a biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. Despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.

  9. Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

    Science.gov (United States)

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

  10. The Microbial Fecal Indicator Paradigm: Tools in the Toolbox Applications in Recreational Waters

    Science.gov (United States)

    Summary of ORD’s recent research to develop tools for assessing microbial water quality in recreational waters. Methods discussed include the development of health associations between microbial fecal indicators and the development of culture, and molecular methods for fec...

  11. Origin of fecal contamination in waters from contrasted areas: stanols as Microbial Source Tracking markers.

    Science.gov (United States)

    Derrien, M; Jardé, E; Gruau, G; Pourcher, A M; Gourmelon, M; Jadas-Hécart, A; Pierson Wickmann, A C

    2012-09-01

    Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5β-cholestan-3β-ol (coprostanol), 5β-cholestan-3α-ol (epicoprostanol), 24-methyl-5α-cholestan-3β-ol (campestanol), 24-ethyl-5α-cholestan-3β-ol (sitostanol), 24-ethyl-5β-cholestan-3β-ol (24-ethylcoprostanol) and 24-ethyl-5β-cholestan-3α-ol (24-ethylepicoprostanol)) was shown to be suitable for distinguishing between porcine and bovine feces. In this study, we tested if this PCA method, using the above six stanols, could be used as a tool in "Microbial Source Tracking (MST)" methods in water from areas of intensive agriculture where diffuse fecal contamination is often marked by the co-existence of human and animal sources. In particular, well-defined and stable clusters were found in PCA score plots clustering samples of "pure" human, bovine and porcine feces along with runoff and diluted waters in which the source of contamination is known. A good consistency was also observed between the source assignments made by the 6-stanol-based PCA method and the microbial markers for river waters contaminated by fecal matter of unknown origin. More generally, the tests conducted in this study argue for the addition of the PCA method based on six stanols in the MST toolbox to help identify fecal contamination sources. The data presented in this study show that this addition would improve the determination of fecal contamination sources when the contamination levels are low to moderate. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Microbial diversity in fecal samples depends on DNA extraction method

    DEFF Research Database (Denmark)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten

    2014-01-01

    was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France......BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study...... by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA...

  13. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.

    Science.gov (United States)

    Kerr, B J; Weber, T E; Ziemer, C J

    2015-05-01

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate digesta rate of passage and nutrient digestibility. Yet, the potential impact of indigestible markers on fecal microbial ecology and subsequent VFA generation is not known. Two experiments utilizing a total of 72 individually fed finishing pigs were conducted to describe the impact of dietary markers on fecal microbial ecology, fecal ammonia and VFA concentrations, nutrient digestibility, and pig performance. All pigs were fed a common diet with no marker or with 0.5% Cr2O3, Fe2O3, or TiO2. In Exp. 1, after 33 d of feeding, fresh fecal samples were collected for evaluation of microbial ecology, fecal ammonia and VFA concentrations, and nutrient digestibility, along with measures of animal performance. No differences were noted in total microbes or bacterial counts in pig feces obtained from pigs fed the different dietary markers while Archaea counts were decreased (P = 0.07) in feces obtained from pigs fed the diet containing Fe2O 3compared to pigs fed the control diet. Feeding Cr2O3, Fe2O3, or TiO2 increased fecal bacterial richness (P = 0.03, 0.01, and 0.10; respectively) when compared to pigs fed diets containing no marker, but no dietary marker effects were noted on fecal microbial evenness or the Shannon-Wiener index. Analysis of denaturing gradient gel electrophoresis gels did not reveal band pattern alterations due to inclusion of dietary markers in pig diets. There was no effect of dietary marker on fecal DM, ammonia, or VFA concentrations. Pigs fed diets containing Cr2O3 had greater Ca, Cu, Fe, and P (P ≤ 0.02), but lower Ti ( P= 0.08) digestibility compared to pigs fed the control diet. Pigs fed diets containing Fe2O3 had greater Ca (P = 0.08) but lower Ti (P = 0.01) digestibility compared to pigs fed the control diet. Pigs fed diets containing TiO2 had greater Fe and Zn (P ≤ 0.09), but lower Ti ( P= 0.01) digestibility compared to pigs fed the

  14. Trail Creek I: Assessing the Water Quality of Streams using Fecal Indicator Bacteria and Microbial Source Tracking

    Science.gov (United States)

    Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Kannan, A.

    2017-12-01

    Fecal coliforms are indicators for disease-causing pathogens. The United States Environmental Protection Agency (US. EPA) recommends the use of E. coli and Enterococci because they are highly correlated with pathogenic organisms in recreational waters. This standard method helps to determine the overall water quality and the potential health risks. Studies have shown that it is difficult to estimate the exact sources of fecal contamination because both human and certain animal species contain E. coli and Enterococci in their waste. Certain strains of E. coli and Enterococci are also able to survive outside of their hosts, which should not be the case for an appropriate fecal indicator. As a result, microbial source tracking (MST) studies use gene specific markers to identify the possible contributors to water pollution whether human or animal. Trail Creek is a second-order stream located in Athens-Clarke County, GA. The 33-km2 watershed is approximately 64% forests, 18% pastures and 16% residential communities. Trail Creek is on the TMDL list and an extended study on the relationships between the different factors causing elevated fecal bacteria is needed. Synoptic sampling events were conducted during baseflow conditions at six locations. Storm sampling events (> 8 mm) were captured using automated samplers at two locations. These samplers were equipped with pressure transducers which record stage at 30-minute intervals. The samples were analyzed for fecal coliform, E. Coli and Enterococci. Water quality parameters including temperature, specific conductance, dissolved oxygen, pH, and turbidity were also recorded. Relationships between the parameters and fecal indicator bacteria show inconsistent patterns and high variability. Using quantitative PCR and MST techniques, the human specific marker (HF183) and ruminant marker (Rum2Bac) were used to identify the fecal sources in both baseflow and storm samples. The presence and abundance of the different markers at

  15. Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

    Science.gov (United States)

    Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

    2016-01-01

    Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

  16. Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes.

    Science.gov (United States)

    Abeles, Shira R; Ly, Melissa; Santiago-Rodriguez, Tasha M; Pride, David T

    2015-01-01

    Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances.

  17. Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake.

    Science.gov (United States)

    Staley, Christopher; Reckhow, Kenneth H; Lukasik, Jerzy; Harwood, Valerie J

    2012-11-01

    We investigated the potential for a variety of environmental reservoirs to harbor or contribute fecal indicator bacteria (FIB), DNA markers of human fecal contamination, and human pathogens to a freshwater lake. We hypothesized that submerged aquatic vegetation (SAV), sediments, and stormwater act as reservoirs and/or provide inputs of FIB and human pathogens to this inland water. Analysis included microbial source tracking (MST) markers of sewage contamination (Enterococcus faecium esp gene, human-associated Bacteroides HF183, and human polyomaviruses), pathogens (Salmonella, Cryptosporidium, Giardia, and enteric viruses), and FIB (fecal coliforms, Escherichia coli, and enterococci). Bayesian analysis was used to assess relationships among microbial and physicochemical variables. FIB in the water were correlated with concentrations in SAV and sediment. Furthermore, the correlation of antecedent rainfall and major rain events with FIB concentrations and detection of human markers and pathogens points toward multiple reservoirs for microbial contaminants in this system. Although pathogens and human-source markers were detected in 55% and 21% of samples, respectively, markers rarely coincided with pathogen detection. Bayesian analysis revealed that low concentrations (<45 CFU × 100 ml(-1)) of fecal coliforms were associated with 93% probability that pathogens would not be detected; furthermore the Bayes net model showed associations between elevated temperature and rainfall with fecal coliform and enterococci concentrations, but not E. coli. These data indicate that many under-studied matrices (e.g. SAV, sediment, stormwater) are important reservoirs for FIB and potentially human pathogens and demonstrate the usefulness of Bayes net analysis for water quality assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Torrefaction Processing of Human Fecal Waste, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — New technology is needed to collect, stabilize, safen, recover useful materials, and store human fecal waste for long duration missions. The current SBIR Phase I...

  19. Quantitative CrAssphage PCR Assays for Human Fecal ...

    Science.gov (United States)

    Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal indicator bacteria are used; however, they cannot distinguish human fecal waste from pollution from other animals. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based upon initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against a large animal fecal reference library and were highly abundant in raw sewage and sewage impacted water samples. In addition, CPQ_056 and CPQ_064 assay performance was compared to HF183/BacR287 and HumM2 methods in paired experiments. Findings confirm viral crAssphage qPCR assays perform at a similar level to well established bacterial human-associated fecal source identification technologies. These new viral based assays could become important water quality management and research tools. To inform the public.

  20. Decay of Fecal Indicator Bacteria and Microbial Source Tracking Markers in Cattle Feces

    Science.gov (United States)

    The survival of fecal indicator bacteria (FIB) and microbial source tracking (MST) markers in water microcosms and manure amended soils has been well documented; however, little is known about the survival of MST markers in bovine feces deposited on pastures. We conducted a study...

  1. Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement

    Science.gov (United States)

    Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal indicator bacteria are used; however, they cannot distinguish human fecal waste from pollution from other animals. Recently, a novel bacteriophage, cr...

  2. Human fecal source identification with real-time quantitative PCR

    Science.gov (United States)

    Waterborne diseases represent a significant public health risk worldwide, and can originate from contact with water contaminated with human fecal material. We describe a real-time quantitative PCR (qPCR) method that targets a Bacteroides dori human-associated genetic marker for...

  3. Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor▿†

    Science.gov (United States)

    Newton, Ryan J.; VandeWalle, Jessica L.; Borchardt, Mark A.; Gorelick, Marc H.; McLellan, Sandra L.

    2011-01-01

    The complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within the Lachnospiraceae family, which was closely related to the genus Blautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for human Bacteroidales (based on the HF183 genetic marker), total Bacteroidales spp., and enterococci and the conventional Escherichia coli and enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and human Bacteroidales increased specificity to

  4. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

    Directory of Open Access Journals (Sweden)

    Jitendra Kumar

    2016-12-01

    Full Text Available Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23 kb metagenomic DNA (260/280 ratio >1.8 with a good yield (55.8 ± 3.8 ng/mg of feces. We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes = 227.9:1 in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

  5. A human fecal contamination index for ranking impaired ...

    Science.gov (United States)

    Human fecal pollution of surface water remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for recreational water quality risk management. The transition from a research subject to a management tool requires the integration of standardized water sampling, laboratory, and data analysis procedures. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and Bayesian data algorithm to establish a human fecal contamination index that can be used to rank impaired recreational water sites polluted with human waste. Stability and bias of index predictions were investigated under various parameters including siteswith different pollution levels, sampling period time range (1-15 weeks), and number of qPCR replicates per sample (2-14 replicates). Sensitivity analyses were conducted with simulated data sets (100 iterations) seeded with HF183/BacR287 qPCR laboratory measurements from water samples collected from three Southern California sites (588 qPCR measurements). Findings suggest that site ranking is feasible and that all parameters tested influence stability and bias in human fecal contamination indexscoring. Trends identified by sensitivity analyses will provide managers with the information needed to design and conduct field studies to rank impaired recreational water sites based

  6. Fecal specimens preparation methods for PCR diagnosis of human taeniosis

    Directory of Open Access Journals (Sweden)

    Nunes Cáris Maroni

    2006-01-01

    Full Text Available Sample preparation and DNA extraction protocols for DNA amplification by PCR, which can be applied in human fecal samples for taeniasis diagnosis, are described. DNA extracted from fecal specimens with phenol/chloroform/isoamilic alcohol and DNAzol® reagent had to be first purified to generate fragments of 170 pb and 600 pb by HDP2-PCR. This purification step was not necessary with the use of QIAmp DNA stool mini kit®. Best DNA extraction results were achieved after eggs disruption with glass beads, either with phenol/chloroform/isoamilic alcohol, DNAzol® reagent or QIAmp DNA stool mini kit®.

  7. A Microbial Signature Approach to Identify Fecal Pollution in the Waters Off an Urbanized Coast of Lake Michigan

    Science.gov (United States)

    Newton, Ryan J.; Bootsma, Melinda J.; Morrison, Hilary G.; Sogin, Mitchell L.

    2014-01-01

    Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee's urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to >2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint in

  8. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.

    Science.gov (United States)

    Khanna, Sahil; Vazquez-Baeza, Yoshiki; González, Antonio; Weiss, Sophie; Schmidt, Bradley; Muñiz-Pedrogo, David A; Rainey, John F; Kammer, Patricia; Nelson, Heidi; Sadowsky, Michael; Khoruts, Alexander; Farrugia, Stefan L; Knight, Rob; Pardi, Darrell S; Kashyap, Purna C

    2017-05-15

    Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD. In this study, we investigated changes in gut microbiota following FMT in 38 patients with CDI with or without underlying IBD. There was a significant change in gut microbial composition towards the donor microbiota and an overall increase in microbial diversity consistent with previous studies after FMT. FMT was successful in treating CDI using a diverse set of donors, and varying degrees of donor stool engraftment suggesting that donor type and degree of engraftment are not drivers of a successful FMT treatment of CDI. However, patients with underlying IBD experienced an increased number of CDI relapses (during a 24-month follow-up) and a decreased growth of new taxa, as compared to the subjects without IBD. Moreover, the need for IBD therapy did not change following FMT. These results underscore the importance of the existing gut microbial landscape as a decisive factor to successfully treat CDI and potentially for improvement of the underlying pathophysiology in IBD. FMT leads to a significant change in microbial diversity in patients with recurrent CDI and complete resolution of symptoms. Stool donor type (related or unrelated) and degree of engraftment are not the key for successful treatment of CDI by FMT. However, CDI patients with IBD have higher proportion of the original community after FMT and lack of improvement of their IBD symptoms and increased episodes of CDI on long-term follow-up.

  9. Enzymatic Modification of Corn Starch Influences Human Fecal Fermentation Profiles.

    Science.gov (United States)

    Dura, Angela; Rose, Devin J; Rosell, Cristina M

    2017-06-14

    Enzymatically modified starches have been widely used in food applications to develop new products, but information regarding digestion and fecal fermentation of these products is sparse. The objective of this study was to determine the fermentation properties of corn starch modified with α-amylase, amyloglucosidase, or cyclodextrin glycosyltransferase and the possible role of hydrolysis products. Samples differed in their digestibility and availability to be fermented by the microbiota, resulting in differences in microbial metabolites produced during in vitro fermentation. The presence or absence of hydrolysis products and gelatinization affected starch composition and subsequent metabolite production by the microbiota. Amyloglucosidase-treated starch led to the greatest production of short- and branched-chain fatty acid production by the microbiota. Results from this study could be taken into consideration to confirm the possible nutritional claims and potential health benefits of these starches as raw ingredients for food development.

  10. Effect of Fermented Supplementation on Growth Performance, Nutrient Digestibility, Blood Characteristics, Fecal Microbial and Fecal Noxious Gas Content in Growing Pigs

    Directory of Open Access Journals (Sweden)

    L. Yan

    2012-12-01

    Full Text Available A total of 96 growing pigs ((Landrace×Yorkshire×Duroc; BW = 26.58±1.41 kg were used in a 6-wk feeding trail to evaluate the effects of fermented chlorella (FC supplementation on growth performance, nutrient digestibility, blood characteristics, fecal microbial and fecal noxious gas content in growing pigs. Pigs were randomly allotted into 1 of 4 dietary treatments with 6 replicate pens (2 barrows and 2 gilts per treatment. Dietary treatments were: i negative control (NC, basal diet (without antibiotics; ii positive control (PC, NC+0.05% tylosin; iii (fermented chlorella 01 FC01, NC+0.1% FC, and iv fermented chlorella 02 (FC02, NC+0.2% FC. In this study, feeding pigs PC or FC01 diets led to a higher average daily gain (ADG and dry matter (DM digestibility than those fed NC diet (p0.05 was observed on the body weight, average daily feed intake (ADFI, gain:feed (G:F ratio, the apparent total tract digestibility of N and energy throughout the experiment. The inclusion of PC or FC did not affect the blood characteristics (p>0.05. Moreover, dietary FC treatment led to a higher (p<0.05 lactobacillus concentration and lower E. coli concentration than the NC treatment, whereas the antibiotic supplementation only decreased the E. coli concentration. Pigs fed FC or PC diet had reduced (p<0.05 fecal NH3 and H2S content compared with those fed NC diet. In conclusion, our results indicated that the inclusion of FC01 treatment could improve the growth performance, nutrient digestibility, fecal microbial shedding (lower E. coli and higher lactobacillus, and decrease the fecal noxious gas emission in growing pigs when compared with the group fed the basal diet. In conclusion, dietary FC could be considered as a good source of supplementation in growing pigs because of its growth promoting effect.

  11. Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease.

    Science.gov (United States)

    Robinson, Ainsley M; Gondalia, Shakuntla V; Karpe, Avinash V; Eri, Rajaraman; Beale, David J; Morrison, Paul D; Palombo, Enzo A; Nurgali, Kulmira

    2016-12-01

    Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.

  12. Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice

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    Jose F. Garcia-Mazcorro

    2016-02-01

    Full Text Available The digestive tract of mammals and other animals is colonized by trillions of metabolically-active microorganisms. Changes in the gut microbiota have been associated with obesity in both humans and laboratory animals. Dietary modifications can often modulate the obese gut microbial ecosystem towards a more healthy state. This phenomenon should preferably be studied using dietary ingredients that are relevant to human nutrition. This study was designed to evaluate the influence of whole-wheat, a food ingredient with several beneficial properties, on gut microorganisms of obese diabetic mice. Diabetic (db/db mice were fed standard (obese-control or whole-wheat isocaloric diets (WW group for eight weeks; non-obese mice were used as control (lean-control. High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools and quantitative real-time PCR were used to analyze fecal bacterial 16S rRNA gene sequences. Short-chain fatty acids were measured in caecal contents using quantitative high-performance liquid chromatography photo-diode array analysis. Results showed no statistical difference in final body weights between the obese-control and the WW group. The bacterial richness (number of Operational Taxonomic Units did not differ among the treatment groups. The abundance of Ruminococcaceae, a family containing several butyrate-producing bacteria, was found to be higher in obese (median: 6.9% and WW-supplemented mice (5.6% compared to lean (2.7%, p = 0.02, Kruskal-Wallis test. Caecal concentrations of butyrate were higher in obese (average: 2.91 mmol/mg of feces but especially in WW-supplemented mice (4.27 mmol/mg compared to lean controls (0.97 mmol/mg, while caecal succinic acid was lower in the WW group compared to obese but especially to the lean group. WW consumption was associated with ∼3 times higher abundances of Lactobacillus spp. compared to both obese and lean control mice. Analysis of weighted Uni

  13. Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water

    Science.gov (United States)

    Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

  14. Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

    Science.gov (United States)

    Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

    2013-01-01

    Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

  15. Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups▿

    Science.gov (United States)

    Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

    2009-01-01

    The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination. PMID:19525269

  16. Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups.

    Science.gov (United States)

    Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

    2009-08-01

    The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination.

  17. IDENTIFICATION OF CHICKEN-SPECIFIC FECAL MICROBIAL SEQUENCES USING A METAGENOMIC APPROACH

    Science.gov (United States)

    In this study, we applied a genome fragment enrichment (GFE) method to select for genomic regions that differ between different fecal metagenomes. Competitive DNA hybridizations were performed between chicken fecal DNA and pig fecal DNA (C-P) and between chicken fecal DNA and an ...

  18. Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

    Directory of Open Access Journals (Sweden)

    Sílvia Bofill-Mas

    2013-01-01

    Full Text Available Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking. In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples.

  19. Human-associated fecal qPCR measurements and predicted risk of gastrointestinal illness in recreational waters contaminated with raw sewage

    Science.gov (United States)

    We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

  20. Human-Associated Fecal Quantitative Polymerase Chain ReactionMeasurements and Simulated Risk of Gastrointestinal Illness in Recreational Waters Contaminated with Raw Sewage

    Science.gov (United States)

    We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

  1. Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls.

    Science.gov (United States)

    Staley, Zachery R; Grabuski, Josey; Sverko, Ed; Edge, Thomas A

    2016-11-01

    Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log 10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log 10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log 10 CFU/100 ml, and 7.65 log 10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can

  2. Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers - is it feasible?

    Science.gov (United States)

    Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated...

  3. Effects of high- and low-fiber diets on fecal fermentation and fecal microbial populations of captive chimpanzees

    Czech Academy of Sciences Publication Activity Database

    Kišidayová, S.; Váradyová, Z.; Pristaš, P.; Piknová, M.; Nigutová, K.; Petrželková, Klára Judita; Profousová, Ilona; Schovancová, Kateřina; Kamler, Jiří; Modrý, David

    2009-01-01

    Roč. 71, č. 7 (2009), s. 548-557 ISSN 0275-2565 R&D Projects: GA ČR GA524/06/0264 Grant - others:VEGA(SK) 2/0009/08; MVTS(SK) SK-CZ-0086-07 Institutional research plan: CEZ:AV0Z60930519; CEZ:AV0Z60220518 Keywords : chimpanzee * fiber * diet * in vitro fecal fermentation * DGGE * archaea * eubacteria Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.565, year: 2009

  4. Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

    Science.gov (United States)

    Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

    2012-01-01

    During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

  5. Gleaning Insights from Fecal Microbiota Transplantation and Probiotic Studies for the Rational Design of Combination Microbial Therapies

    Science.gov (United States)

    Hudson, Lauren E.; Anderson, Sarah E.; Corbett, Anita H.

    2016-01-01

    SUMMARY Beneficial microorganisms hold promise for the treatment of numerous gastrointestinal diseases. The transfer of whole microbiota via fecal transplantation has already been shown to ameliorate the severity of diseases such as Clostridium difficile infection, inflammatory bowel disease, and others. However, the exact mechanisms of fecal microbiota transplant efficacy and the particular strains conferring this benefit are still unclear. Rationally designed combinations of microbial preparations may enable more efficient and effective treatment approaches tailored to particular diseases. Here we use an infectious disease, C. difficile infection, and an inflammatory disorder, the inflammatory bowel disease ulcerative colitis, as examples to facilitate the discussion of how microbial therapy might be rationally designed for specific gastrointestinal diseases. Fecal microbiota transplantation has already shown some efficacy in the treatment of both these disorders; detailed comparisons of studies evaluating commensal and probiotic organisms in the context of these disparate gastrointestinal diseases may shed light on potential protective mechanisms and elucidate how future microbial therapies can be tailored to particular diseases. PMID:27856521

  6. Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome.

    Science.gov (United States)

    Shankar, Vijay; Reo, Nicholas V; Paliy, Oleg

    2015-12-09

    We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy age-matched controls. Here we explored whether observed fecal microbiota and metabolite differences between these two adolescent populations can be used to discriminate between IBS and health. We constructed individual microbiota- and metabolite-based sample classification models based on the partial least squares multivariate analysis and then applied a Bayesian approach to integrate individual models into a single classifier. The resulting combined classification achieved 84 % accuracy of correct sample group assignment and 86 % prediction for IBS-D in cross-validation tests. The performance of the cumulative classification model was further validated by the de novo analysis of stool samples from a small independent IBS-D cohort. High-throughput microbial and metabolite profiling of subject stool samples can be used to facilitate IBS diagnosis.

  7. Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ingmar S Middelbos

    Full Text Available BACKGROUND: Dogs suffer from many of the same maladies as humans that may be affected by the gut microbiome, but knowledge of the canine microbiome is incomplete. This work aimed to use 16S rDNA tag pyrosequencing to phylogenetically characterize hindgut microbiome in dogs and determine how consumption of dietary fiber affects community structure. PRINCIPAL FINDINGS: Six healthy adult dogs were used in a crossover design. A control diet without supplemental fiber and a beet pulp-supplemented (7.5% diet were fed. Fecal DNA was extracted and the V3 hypervariable region of the microbial 16S rDNA gene amplified using primers suitable for 454-pyrosequencing. Microbial diversity was assessed on random 2000-sequence subsamples of individual and pooled DNA samples by diet. Our dataset comprised 77,771 reads with an average length of 141 nt. Individual samples contained approximately 129 OTU, with Fusobacteria (23-40% of reads, Firmicutes (14-28% of reads and Bacteroidetes (31-34% of reads being co-dominant phyla. Feeding dietary fiber generally decreased Fusobacteria and increased Firmicutes, but these changes were not equally apparent in all dogs. UniFrac analysis revealed that structure of the gut microbiome was affected by diet and Firmicutes appeared to play a strong role in by-diet clustering. CONCLUSIONS: Our data suggest three co-dominant bacterial phyla in the canine hindgut. Furthermore, a relatively small amount of dietary fiber changed the structure of the gut microbiome detectably. Our data are among the first to characterize the healthy canine gut microbiome using pyrosequencing and provide a basis for studies focused on devising dietary interventions for microbiome-associated diseases.

  8. A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

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    Timothy R Julian

    Full Text Available Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data. Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

  9. A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

    Science.gov (United States)

    Julian, Timothy R; Pickering, Amy J

    2015-01-01

    Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food) responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data). Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing) to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci) concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

  10. In vitro fermentability of sugar beet pulp derived oligosaccharides using human and pig fecal inocula

    NARCIS (Netherlands)

    Leijdekkers, A.G.M.; Aguirre, M.; Venema, K.; Bosch, G.; Gruppen, H.; Schols, H.A.

    2014-01-01

    The in vitro fermentation characteristics of different classes of sugar beet pectic oligosaccharides (SBPOS) were studied using human and pig fecal inocula. The SBPOS consisted mainly of partially acetylated rhamnogalacturonan oligosaccharides and partially methyl-esterified/acetylated

  11. In Vitro fermentability of sugar beet pulp derived oligosaccharides using human and pig fecal inocula

    NARCIS (Netherlands)

    Leijdekkers, A.G.M.; Aguirre, M.; Venema, K.; Bosch, G.; Gruppen, H.; Schols, H.A.

    2014-01-01

    The in vitro fermentation characteristics of different classes of sugar beet pectic oligosaccharides (SBPOS) were studied using human and pig fecal inocula. The SBPOS consisted mainly of partially acetylated rhamnogalacturonan-oligosaccharides and partially methyl esterified/acetylated

  12. Effects of Resveratrol and Essential Oils on Growth Performance, Immunity, Digestibility and Fecal Microbial Shedding in Challenged Piglets

    Directory of Open Access Journals (Sweden)

    S. T. Ahmed

    2013-05-01

    Full Text Available A study was conducted to evaluate the effects of resveratrol and essential oils from medicinal plants on the growth performance, immunity, digestibility, and fecal microbial shedding of weaned piglets. A total of 48 weaned piglets (8 kg initial weight, 28-d-old were randomly allotted to four dietary treatments with 3 replications of 4 piglets each. The dietary treatments were NC (negative control; basal diet, PC (positive control; basal diet+0.002% apramycin, T1 (basal diet+0.2% resveratrol, and T2 (basal diet+0.0125% essential oil blend. All piglets were orally challenged with 5 ml culture fluid containing 2.3×108 cfu/ml of Escherichia coli KCTC 2571 and 5.9×108 cfu/ml Salmonella enterica serover Typhimurium. The PC group (p0.05. Serum IgG level was increased in the T1 group, whereas TNF-α levels was reduced in the supplemented groups compared to control (p<0.05. The PC diet improved the dry matter (DM digestibility, whereas PC and T2 diets improved nitrogen (N digestibility compared to NC and T1 diets (p<0.05. Fecal Salmonella and E. coli counts were reduced in all treatment groups compared to control (p<0.05. Fecal Lactobacillus spp. count was increased in the T2 group compared to others (p<0.05. Dietary treatments had no significant effect on fecal Bacillus spp. count throughout the entire experimental period. Based on these results, resveratrol showed strong potential as antibiotic alternatives for reversing the adverse effects of weaning stress on growth performance, immunity and microbial environment in E. coli and Salmonella-challenged piglets.

  13. Carbohydrate-free peach (Prunus persica and plum (Prunus domestica juice affects fecal microbial ecology in an obese animal model.

    Directory of Open Access Journals (Sweden)

    Giuliana D Noratto

    Full Text Available BACKGROUND: Growing evidence shows the potential of nutritional interventions to treat obesity but most investigations have utilized non-digestible carbohydrates only. Peach and plum contain high amounts of polyphenols, compounds with demonstrated anti-obesity effects. The underlying process of successfully treating obesity using polyphenols may involve an alteration of the intestinal microbiota. However, this phenomenon is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: Obese Zucker rats were assigned to three groups (peach, plum, and control, n = 10 each, wild-type group was named lean (n = 10. Carbohydrates in the fruit juices were eliminated using enzymatic hydrolysis. Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats. Several bacterial groups (e.g. Lactobacillus and members of Ruminococcacea were found to be more abundant in the peach but especially in the plum group (plum juice contained 3 times more total polyphenolics compared to peach juice. Principal coordinate analysis based on Unifrac-based unweighted distance matrices revealed a distinct separation between the microbiota of control and treatment groups. These changes in fecal microbiota occurred simultaneously with differences in fecal short-chain acids concentrations between the control and treatment groups as well as a significant decrease in body weight in the plum group. CONCLUSIONS: This study suggests that consumption of carbohydrate-free peach and plum juice has the potential to modify fecal microbial ecology in an obese animal model. The separate contribution of polyphenols and non-polyphenols compounds (vitamins and minerals to the observed changes is unknown.

  14. The fecal bacteria

    Science.gov (United States)

    Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

  15. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

    Science.gov (United States)

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  16. INFLUENCE OF EQUINE FECAL CONTAMINATION ON MICROBIAL COMMUNITY STRUCTURE IN A SUB-WATERSHED

    Science.gov (United States)

    As monitoring of watershed water quality is directly related to proposed uses, it is important for our Naton's water systems that the d4etemrination of and distinction between fecal contamination source is made. The most common water quality monitoring approach is to screen for f...

  17. Microbial indicators of fecal contamination in soils under different wastewater irrigation patterns

    International Nuclear Information System (INIS)

    Contreras-Godinez, C. A.; Palacios-Lopez, O. A.; Munoz-Castellanos, L. N.; Saucedo-Teran, R.; Rubio-Arias, H.; Nevarez-Moorillon, G. V.

    2009-01-01

    The use of wastewater to irrigate produce was a common practice in some suburban areas in Mexico. The continuous use of wastewater can increase the chance of fecal soil contamination, which can percolate in soil and finally cause groundwater contamination. A suburban area in Chihuahua, mexico, has been traditionally irradiated with wastewater for production of agriculture goods, including produce and animal foodstuffs. (Author)

  18. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    Science.gov (United States)

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  19. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

    DEFF Research Database (Denmark)

    Kumar, Jitendra; Kumar, Manoj; Gupta, Shashank

    2016-01-01

    Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obta...

  20. Evaluation on prebiotic properties of β-glucan and oligo-β-glucan from mushrooms by human fecal microbiota in fecal batch culture

    Directory of Open Access Journals (Sweden)

    Chiraphon Chaikliang

    2015-11-01

    Full Text Available Background: β-glucan is dietary fiber, a structural polysaccharide, β-linked linear chains of D-glucose polymers with variable frequency of branches. β-glucan is isolated from different sources such as cell walls of baker’s yeast (Saccharomyces cerevisiae, cereals (oat and barley and various species of mushrooms. Among 8 mushrooms in the study, Schizophylum commune Fr and Auricularia auricula Judae had the highest in β-glucan contents and the cheapest cost of mushroom per content of β-glucan, respectively. Even the function of β-glucan on immune modulation has been known however no report on interaction between β-glucan and human gut microbiota. Gut microbiota is thought to have health effects by interaction with non-digestible component particular fermentable dietary fiber. It is important to correlate the specific groups of the microbial communities associated with β-glucan fermentation and the consequential SCFA profiles. β-glucan from mushroom may has potential prebiotic function similar to those from commercial yeast (Saccharomyces cerevisiae β-glucan. Objective: To evaluate on prebiotic properties of soluble β-glucans and oligo-β-glucans from Schizophylum commune Fr and Auricularia auricula Judae by fecal fermentation in batch culture. Methods: In vitro fecal fermentation in anaerobic batch cultures under simulated conditions similar to human colon with human faecal samples from three donors were performed. Comparison on 3 β-glucans and 2 oligo-β-glucans have been studied. Sample was taken at 0 h, 24 h and 48 h to analyze the numbers of bacterial changes by fluorescent in situ hybridization (FISH technique. Short chain fatty acids (SCFA were analyzed by HPLC. The prebiotic index (PI was calculated according to the change of 5 specific bacterial genus within 48 h fermentation. Results: Soluble β-glucan from Auricularia auricula Judae increased numbers of bifidobacteria and lactobacillus significantly (P<0.05. The PI of

  1. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

    Science.gov (United States)

    Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

    2011-09-01

    Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that

  2. Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose

    DEFF Research Database (Denmark)

    Owusu-Ansah, Emmanuel de-Graft Johnson; Sampson, Angelina; Amponsah, Samuel K.

    2017-01-01

    physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study......The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10− 5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different...... attempts to fit a QMRA model to genome copies of norovirus data. The model estimates the risk of norovirus infection from the intake of vegetables irrigated with wastewater from different sources. The results were compared to the results of a corresponding model using the fecal indicator conversion ratio...

  3. PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

  4. PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

    Science.gov (United States)

    Exposure to environmental pollutants can alter gut microbial populations. Short-chain fatty acids (SCFAs), produced from gut microbial fermentation of dietary fibers such as inulin, exert numerous effects on host energy metabolism. SCFAs are also linked to health promoting effects, including a red...

  5. Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome

    OpenAIRE

    Shankar, Vijay; Reo, Nicholas V.; Paliy, Oleg

    2015-01-01

    Background We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy age-matched controls. Here we explored whether observed fecal microbiota and metabolite differences between these two adolescent populations can be used to discriminate between IBS and health. Findings We constructed individual microbiota- and metabolite-based sample classifi...

  6. Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water (ASM 2017 Presentation)

    Science.gov (United States)

    Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

  7. Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

    Science.gov (United States)

    Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial ...

  8. A human fecal contamination index for ranking impaired recreational watersusing the HF183 quantitative real-time PCR method

    Science.gov (United States)

    Human fecal pollution of surface water remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for recreational water quality risk managem...

  9. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo.

    Science.gov (United States)

    Harlow, Brittany E; Lawrence, Laurie M; Harris, Patricia A; Aiken, Glen E; Flythe, Michael D

    2017-01-01

    Cereal grains are often included in equine diets. When starch intake exceeds foregut digestion starch will reach the hindgut, impacting microbial ecology. Probiotics (e.g., lactobacilli) are reported to mitigate GI dysbioses in other species. This study was conducted to determine the effect of exogenous lactobacilli on pH and the growth of amylolytic and lactate-utilizing bacteria. Feces were collected from 3 mature geldings fed grass hay with access to pasture. Fecal microbes were harvested by differential centrifugation, washed, and re-suspended in anaerobic media containing ground corn, wheat, or oats at 1.6% (w/v) starch and one of five treatments: Control (substrate only), L. acidophilus, L. buchneri, L. reuteri, or an equal mixture of all three (107 cells/mL, final concentration). After 24 h of incubation (37°C, 160 rpm), samples were collected for pH and enumerations of total amylolytics, Group D Gram-positive cocci (GPC; Enterococci, Streptococci), lactobacilli, and lactate-utilizing bacteria. Enumeration data were log transformed prior to ANOVA (SAS, v. 9.3). Lactobacilli inhibited pH decline in corn and wheat fermentations (P Exogenous lactobacilli decreased amylolytics, while increasing lactate-utilizers in corn and wheat fermentations (P Exogenous lactobacilli decreased the initial (first 8 h) rate of starch catalysis when wheat was the substrate, but did not decrease total (24 h) starch utilization in any case. These results indicate that exogenous lactobacilli can impact the microbial community and pH of cereal grain fermentations by equine fecal microflora ex vivo. Additionally, dead (autoclaved) exogenous lactobacilli had similar effects as live lactobacilli on fermentation. This latter result indicates that the mechanism by which lactobacilli impact other amylolytic bacteria is not simple resource competition.

  10. Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans

    NARCIS (Netherlands)

    Tannock, G.W.; Munro, K.; Bibiloni, R.; Simon, M.A.; Hargreaves, P.; Gopal, P.; Harmsen, H.J.M.; Welling, Gjalt

    Human subjects consumed biscuits containing either galacto-oligosaccharides or fructo-oligosaccharides in a double-blinded, crossover study. The impact of supplementing the diet with three biscuits per day on the fecal microbiota was evaluated by selective culture of particular bacterial groups,

  11. The presence and near-shore transport of human fecal pollution in Lake Michigan beaches

    Science.gov (United States)

    Molloy, S.L.; Liu, L.B.; Phanikumar, M.S.; Jenkins, T.M.; Wong, M.V.; Rose, J.B.; Whitman, R.L.; Shively, D.A.; Nevers, M.B.

    2005-01-01

    The Great Lakes are a source of water for municipal, agricultural and industrial use, and support significant recreation, commercial and sport fishing industries. Every year millions of people visit the 500 plus recreational beaches in the Great Lakes. An increasing public health risk has been suggested with increased evidence of fecal contamination at the shoreline. To investigate the transport and fate of fecal pollution at Great Lakes beaches and the health risk associated with swimming at these beaches, the near-shore waters of Mt Baldy Beach, Lake Michigan and Trail Creek, a tributary discharging into the lake were examined for fecal pollution indicators. A model of surf zone hydrodynamics coupled with a transport model with first-order inactivation of pollutant was used to understand the relative importance of different processes operating in the surf zone (e.g. physical versus biological processes). The Enterococcus human fecal pollution marker, which targets a putative virulence factor, the enterococcal surface protein (esp) in Enterococcus faecium, was detected in 2/28 samples (7%) from the tributaries draining into Lake Michigan and in 6/30 samples (20%) from Lake Michigan beaches. Preliminary analysis suggests that the majority of fecal indicator bactateria variation and water quality changes at the beaches can be explained by inputs from the influential stream and hydrometeorological conditions. Using modeling methods to predict impaired water quality may help reduce potential health threats to recreational visitors.

  12. Origin of fecal contamination in waters from contrasted areas: Stanols as Microbial Source Tracking markers

    OpenAIRE

    Derrien, M.; Jarde, E.; Gruau, G.; Pourcher, A. M.; Gourmelon, Michele; Jadas-hecart, Alain; Wickmann, A. C. Pierson

    2012-01-01

    Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5 beta-cholestan-3 beta-ol (coprostanol), 5 beta-cholestan-3 alpha-ol (epicoprostanol), 24-methyl-5 alpha-cholestan-3 beta-ol (campestanol), 24-ethyl-5 alpha-cholestan-3 beta-ol (sitostanol), 24-ethyl-5 beta-cholestan-3 beta-ol (24-eth...

  13. Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters.

    Science.gov (United States)

    Feng, Shuchen; Bootsma, Melinda; McLellan, Sandra L

    2018-05-04

    The human microbiome contains many organisms that could potentially be used as indicators of human fecal pollution. Here we report the development of two novel human-associated genetic marker assays that target organisms within the family Lachnospiraceae Next-generation sequencing of the V6 region of the 16S rRNA gene from sewage and animal stool samples identified 40 human-associated marker candidates with a robust signal in sewage and low or no occurrence in nonhuman hosts. Two were chosen for quantitative PCR (qPCR) assay development using longer sequences (V2 to V9 regions) generated from clone libraries. Validation of these assays, designated Lachno3 and Lachno12, was performed using fecal samples (n=55) from cat, dog, pig, cow, deer, and gull sources, and compared with established host-associated assays (Lachno2, and two Human Bacteroides assays; HB and HF183/BacR287). Each of the established assays cross-reacted with at least one other animal, including animals common in urban areas. Lachno3 and Lachno12 were primarily human-associated; however, Lachno12 demonstrated low levels of cross-reactivity with select cows, and non-specific amplification in pigs. This limitation may not be problematic when testing urban waters. These novel markers resolved ambiguous results from previous investigations in stormwater-impacted waters, demonstrating their utility. The complexity of the microbiome in humans and animals suggests no single organism is strictly specific to humans, and multiple complementary markers used in combination will provide the highest resolution and specificity for assessing fecal pollution sources. IMPORTANCE Traditional fecal indicator bacteria do not distinguish animal from human fecal pollution, which is necessary to evaluate health risks and mitigate pollution sources. Assessing urban areas is challenging since water can be impacted by sewage, which has a high likelihood of carrying human pathogens, as well as pet waste and urban wildlife. We

  14. Screening for fecal carriage of MCR-producing Enterobacteriaceae in healthy humans and primary care patients

    Directory of Open Access Journals (Sweden)

    Katrin Zurfluh

    2017-03-01

    Full Text Available Abstract Background The extent of the occurrence of the plasmid-encoded colistin resistance genes mcr-1 and mcr-2 among humans is currently sparsely studied in Western Europe. Objectives To determine the occurrence of MCR-producing Enterobacteriaceae in fecal samples of healthy humans with high occupational exposure to food and primary care patients in Switzerland. Methods Stool samples from 1091 healthy individuals and fecal swabs from 53 primary care patients were screened for polymyxin-resistant Enterobacteriaceae using LB agar containing 4 mg/L colistin. Minimal inhibitory concentrations (MICs of colistin were determined for non-intrinsic colistin-resistant isolates. Isolates were screened by PCR for the presence of mcr-1 and mcr-2 genes. Results The fecal carriage rate of colistin resistant (MIC value >2 mg/l Enterobacteriaceae was 1.5% for healthy people and 3.8% for primary care patients. Isolates included Hafnia alvei (n = 9, Escherichia coli (n = 3, Enterobacter cloacae (n = 4, Klebsiella pneumoniae (n = 1 and Raoultella ornithinolytica (n = 1. None of the isolates harbored the mcr-1 or mcr-2 genes. Conclusions There is no evidence for the presence of MCR-producers in the fecal flora of healthy people or primary care patients. Therefore, the risk of transfer of mcr genes from animals, food or the environment to humans is likely to be low in Switzerland.

  15. Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong).

    Science.gov (United States)

    McKenney, Erin A; Ashwell, Melissa; Lambert, Joanna E; Fellner, Vivek

    2014-11-01

    Microbial populations in the gastrointestinal tract contribute to host health and nutrition. Although gut microbial ecology is well studied in livestock and domestic animals, little is known of the endogenous populations inhabiting primates or carnivora. We characterized microbial populations in fecal cultures from gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding strategies. Each species was fed a distinct standardized diet for 2 weeks prior to fecal collection. All diets were formulated to reflect the species' feeding strategies in situ. Fresh fecal samples were pooled within species and used to inoculate in vitro batch cultures. Acetate, propionate, butyrate and valerate were measured after 24 h of incubation. Eubacterial DNA was extracted from individual fecal samples, pooled, and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host species. Short chain fatty acids (P < 0.001) and methane (P < 0.001) were significantly different across species. Eubacterial profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber. © 2014 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  16. Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex

    NARCIS (Netherlands)

    Verschuren, Lisanne M.G.; Calus, Mario P.L.; Jansman, Aalfons J.M.; Bergsma, Rob; Knol, Egbert F.; Gilbert, Hélène; Zemb, Olivier

    2018-01-01

    Dietary fiber content and composition affect microbial composition and activity in the gut, which in turn influence energetic contribution of fermentation products to the metabolic energy supply in pigs. This may affect feed efficiency (FE) in pigs. The present study investigated the relationship

  17. Natural soil reservoirs for human pathogenic and fecal indicator bacteria

    Science.gov (United States)

    Boschiroli, Maria L; Falkinham, Joseph; Favre-Bonte, Sabine; Nazaret, Sylvie; Piveteau, Pascal; Sadowsky, Michael J.; Byappanahalli, Muruleedhara; Delaquis, Pascal; Hartmann, Alain

    2016-01-01

    Soils receive inputs of human pathogenic and indicator bacteria through land application of animal manures or sewage sludge, and inputs by wildlife. Soil is an extremely heterogeneous substrate and contains meso- and macrofauna that may be reservoirs for bacteria of human health concern. The ability to detect and quantify bacteria of human health concern is important in risk assessments and in evaluating the efficacy of agricultural soil management practices that are protective of crop quality and protective of adjacent water resources. The present chapter describes the distribution of selected Gram-positive and Gram-negative bacteria in soils. Methods for detecting and quantifying soilborne bacteria including extraction, enrichment using immunomagnetic capture, culturing, molecular detection and deep sequencing of metagenomic DNA to detect pathogens are overviewed. Methods for strain phenotypic and genotypic characterization are presented, as well as how comparison with clinical isolates can inform the potential for human health risk.

  18. Using fecal sterols to assess dynamics of sewage input in sediments along a human-impacted river-estuary system in eastern China.

    Science.gov (United States)

    He, Ding; Zhang, Kai; Tang, Jianhui; Cui, Xingqian; Sun, Yongge

    2018-05-01

    Sedimentary fecal sterols and other sterol biomarkers, combined with bulk total organic carbon (TOC) and its stable carbon isotope were applied to characterize the sewage contamination across a ca. 280 km transect from the Xiaoqing River to the Laizhou Bay, a typical river-estuary system subjected to extensive anthropogenic stress due to rapid regional urbanization and industrialization in eastern China. Two sampling events were performed in both spring and summer seasons in the Laizhou Bay adjacent to the Xiaoqing River in order to assess the potential seasonal variation. Fecal sterols such as coprostanol and epicoprostanol, which are typical indicators of anthropogenic sewage input, displayed high concentrations of up to 63.2 μg g -1 dry weight (dw) and 13.1 μg g -1 dw, respectively. Results suggested that most of the stations along the Xiaoqing River were severely contaminated by fecal inputs with a decreasing trend from the river to the estuary that was mainly explained by the increasing distance from the diffuse sewage sources and the gradual dilution by sea water. Although there was no significant difference in fecal sterol concentrations between spring and summer in the Laizhou Bay, suggestive of no significant difference in sewage abundance, significantly higher average epicoprostanol/coprostanol and lower coprostanol/epicoprostanol ratios were observed in spring than summer, indicative of different sewage sources (e.g., human vs. non-human). Seasonal discharge and land-runoff, air temperature related to microbial activity differences and different extend of animal manure irrigation during agricultural planting could be additional reasons and need further investigation. Nevertheless, fecal sterol concentrations, distributions and diagnostic ratios should all be taken into consideration to better understand sewage inputs and source dynamics in river-estuary ecosystems. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Cross-Comparison of Human Wastewater-Associated Molecular Markers in Relation to Fecal Indicator Bacteria and Enteric Viruses in Recreational Beach Waters.

    Science.gov (United States)

    Hughes, B; Beale, D J; Dennis, P G; Cook, S; Ahmed, W

    2017-04-15

    Detection of human wastewater contamination in recreational waters is of critical importance to regulators due to the risks posed to public health. To identify such risks, human wastewater-associated microbial source tracking (MST) markers have been developed. At present, however, a greater understanding of the suitability of these markers for the detection of diluted human wastewater in environmental waters is necessary to predict risk. Here, we compared the process limit of detection (PLOD) and process limit of quantification (PLOQ) of six human wastewater-associated MST markers ( Bacteroides HF183 [HF183], Escherichia coli H8 [EC H8], Methanobrevibacter smithii nifH , human adenovirus [HAdV], human polyomavirus [HPyV], and pepper mild mottle virus [PMMoV]) in relation to a fecal indicator bacterium (FIB), Enterococcus sp. 23S rRNA (ENT 23S), and three enteric viruses (human adenovirus serotypes 40/41 [HAdV 40/41], human norovirus [HNoV], and human enterovirus [EV]) in beach water samples seeded with raw and secondary-treated wastewater. Among the six MST markers tested, HF183 was the most sensitive measure of human fecal pollution and was quantifiable up to dilutions of 10 -6 and 10 -4 for beach water samples seeded with raw and secondary-treated wastewater, respectively. Other markers and enteric viruses were detected at various dilutions (10 -1 to 10 -5 ). These MST markers, FIB, and enteric viruses were then quantified in beach water ( n = 12) and sand samples ( n = 12) from South East Queensland (SEQ), Australia, to estimate the levels of human fecal pollution. Of the 12 sites examined, beach water and sand samples from several sites had quantifiable concentrations of HF183 and PMMoV markers. Overall, our results indicate that while HF183 is the most sensitive measure of human fecal pollution, it should be used in conjunction with a conferring viral marker to avoid overestimating the risk of gastrointestinal illness. IMPORTANCE MST is an effective tool to

  20. Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

    Science.gov (United States)

    Mayer, René E; Reischer, Georg H; Ixenmaier, Simone K; Derx, Julia; Blaschke, Alfred Paul; Ebdon, James E; Linke, Rita; Egle, Lukas; Ahmed, Warish; Blanch, Anicet R; Byamukama, Denis; Savill, Marion; Mushi, Douglas; Cristóbal, Héctor A; Edge, Thomas A; Schade, Margit A; Aslan, Asli; Brooks, Yolanda M; Sommer, Regina; Masago, Yoshifumi; Sato, Maria I; Taylor, Huw D; Rose, Joan B; Wuertz, Stefan; Shanks, Orin C; Piringer, Harald; Mach, Robert L; Savio, Domenico; Zessner, Matthias; Farnleitner, Andreas H

    2018-05-01

    Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log 10 7.2-8.0 marker equivalents (ME) 100 mL -1 ) and biologically treated wastewater samples (median log 10 4.6-6.0 ME 100 mL -1 ) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

  1. A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy.

    Science.gov (United States)

    AlShawaqfeh, M K; Wajid, B; Minamoto, Y; Markel, M; Lidbury, J A; Steiner, J M; Serpedin, E; Suchodolski, J S

    2017-11-01

    Recent studies have identified various bacterial groups that are altered in dogs with chronic inflammatory enteropathies (CE) compared to healthy dogs. The study aim was to use quantitative PCR (qPCR) assays to confirm these findings in a larger number of dogs, and to build a mathematical algorithm to report these microbiota changes as a dysbiosis index (DI). Fecal DNA from 95 healthy dogs and 106 dogs with histologically confirmed CE was analyzed. Samples were grouped into a training set and a validation set. Various mathematical models and combination of qPCR assays were evaluated to find a model with highest discriminatory power. The final qPCR panel consisted of eight bacterial groups: total bacteria, Faecalibacterium, Turicibacter, Escherichia coli, Streptococcus, Blautia, Fusobacterium and Clostridium hiranonis. The qPCR-based DI was built based on the nearest centroid classifier, and reports the degree of dysbiosis in a single numerical value that measures the closeness in the l2 - norm of the test sample to the mean prototype of each class. A negative DI indicates normobiosis, whereas a positive DI indicates dysbiosis. For a threshold of 0, the DI based on the combined dataset achieved 74% sensitivity and 95% specificity to separate healthy and CE dogs. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Smoking cessation alters intestinal microbiota: insights from quantitative investigations on human fecal samples using FISH.

    Science.gov (United States)

    Biedermann, Luc; Brülisauer, Karin; Zeitz, Jonas; Frei, Pascal; Scharl, Michael; Vavricka, Stephan R; Fried, Michael; Loessner, Martin J; Rogler, Gerhard; Schuppler, Markus

    2014-09-01

    There has been a dramatic increase in investigations on the potential mechanistic role of the intestinal microbiota in various diseases and factors modulating intestinal microbial composition. We recently reported on intestinal microbial shifts after smoking cessation in humans. In this study, we aimed to conduct further microbial analyses and verify our previous results obtained by pyrosequencing using a direct quantitative microbial approach. Stool samples of healthy smoking human subjects undergoing controlled smoking cessation during a 9-week observational period were analyzed and compared with 2 control groups, ongoing smoking and nonsmoking subjects. Fluorescence in situ hybridization was applied to quantify specific bacterial groups. Intestinal microbiota composition was substantially altered after smoking cessation as characterized by an increase in key representatives from the phyla of Firmicutes (Clostridium coccoides, Eubacterium rectale, and Clostridium leptum subgroup) and Actinobacteria (HGC bacteria and Bifidobacteria) as well as a decrease in Bacteroidetes (Prevotella spp. and Bacteroides spp.) and Proteobacteria (β- and γ-subgroup of Proteobacteria). As determined by fluorescence in situ hybridization, an independent direct quantitative microbial approach, we could confirm that intestinal microbiota composition in humans is influenced by smoking. The characteristics of observed microbial shifts suggest a potential mechanistic association to alterations in body weight subsequent to smoking cessation. More importantly, regarding previously described microbial hallmarks of dysbiosis in inflammatory bowel diseases, a variety of observed microbial alterations after smoking cessation deserve further consideration in view of the divergent effect of smoking on the clinical course of Crohn's disease and ulcerative colitis.

  3. Human Parvovirus 4 in Nasal and Fecal Specimens from Children, Ghana

    Science.gov (United States)

    Drexler, Jan Felix; Reber, Ulrike; Muth, Doreen; Herzog, Petra; Annan, Augustina; Ebach, Fabian; Sarpong, Nimarko; Acquah, Samuel; Adlkofer, Julia; Adu-Sarkodie, Yaw; Panning, Marcus; Tannich, Egbert; May, Jürgen; Drosten, Christian

    2012-01-01

    Nonparenteral transmission might contribute to human parvovirus 4 (PARV4) infections in sub-Saharan Africa. PARV4 DNA was detected in 8 (0.83%) of 961 nasal samples and 5 (0.53%) of 943 fecal samples from 1,904 children in Ghana. Virus concentrations ≤6–7 log10 copies/mL suggest respiratory or fecal–oral modes of PARV4 transmission. PMID:23018024

  4. Prebiotic potential of L-sorbose and xylitol in promoting the growth and metabolic activity of specific butyrate-producing bacteria in human fecal culture.

    Science.gov (United States)

    Sato, Tadashi; Kusuhara, Shiro; Yokoi, Wakae; Ito, Masahiko; Miyazaki, Kouji

    2017-01-01

    Dietary low-digestible carbohydrates (LDCs) affect gut microbial metabolism, including the production of short-chain fatty acids. The ability of various LDCs to promote butyrate production was evaluated in in vitro human fecal cultures. Fecal suspensions from five healthy males were anaerobically incubated with various LDCs. L-Sorbose and xylitol markedly promoted butyrate formation in cultures. Bacterial 16S rRNA gene-based denaturing gradient gel electrophoresis analyses of these fecal cultures revealed a marked increase in the abundance of bacteria closely related to the species Anaerostipes hadrus or A. caccae or both, during enhanced butyrate formation from L-sorbose or xylitol. By using an agar plate culture, two strains of A. hadrus that produced butyrate from each substrate were isolated from the feces of two donors. Furthermore, of 12 species of representative colonic butyrate producers, only A. hadrus and A. caccae demonstrated augmented butyrate production from L-sorbose or xylitol. These findings suggest that L-sorbose and xylitol cause prebiotic stimulation of the growth and metabolic activity of Anaerostipes spp. in the human colon. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Multi-year microbial source tracking study characterizing fecal contamination in an urban watershed

    Science.gov (United States)

    Bushon, Rebecca N.; Brady, Amie M. G.; Christensen, Eric D.; Stelzer, Erin A.

    2017-01-01

    Microbiological and hydrological data were used to rank tributary stream contributions of bacteria to the Little Blue River in Independence, Missouri. Concentrations, loadings and yields of E. coli and microbial source tracking (MST) markers, were characterized during base flow and storm events in five subbasins within Independence, as well as sources entering and leaving the city through the river. The E. coli water quality threshold was exceeded in 29% of base-flow and 89% of storm-event samples. The total contribution of E. coli and MST markers from tributaries within Independence to the Little Blue River, regardless of streamflow, did not significantly increase the median concentrations leaving the city. Daily loads and yields of E. coli and MST markers were used to rank the subbasins according to their contribution of each constituent to the river. The ranking methodology used in this study may prove useful in prioritizing remediation in the different subbasins.

  6. Optimization of Human Microbial Ecology

    Data.gov (United States)

    National Aeronautics and Space Administration — With the new tools of high-throughput sequencing providing unprecedented information about the diversity of microbes living in and on the human organism...

  7. Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment

    Directory of Open Access Journals (Sweden)

    Francis Hassard

    2017-10-01

    Full Text Available To assess fecal pollution in coastal waters, current monitoring is reliant on culture-based enumeration of bacterial indicators, which does not account for the presence of viable but non-culturable or sediment-associated micro-organisms, preventing effective quantitative microbial risk assessment (QMRA. Seasonal variability in viable but non-culturable or sediment-associated bacteria challenge the use of fecal indicator organisms (FIOs for water monitoring. We evaluated seasonal changes in FIOs and human enteric pathogen abundance in water and sediments from the Ribble and Conwy estuaries in the UK. Sediments possessed greater bacterial abundance than the overlying water column, however, key pathogenic species (Shigella spp., Campylobacter jejuni, Salmonella spp., hepatitis A virus, hepatitis E virus and norovirus GI and GII were not detected in sediments. Salmonella was detected in low levels in the Conwy water in spring/summer and norovirus GII was detected in the Ribble water in winter. The abundance of E. coli and Enterococcus spp. quantified by culture-based methods, rarely matched the abundance of these species when measured by qPCR. The discrepancy between these methods was greatest in winter at both estuaries, due to low CFU's, coupled with higher gene copies (GC. Temperature accounted for 60% the variability in bacterial abundance in water in autumn, whilst in winter salinity explained 15% of the variance. Relationships between bacterial indicators/pathogens and physicochemical variables were inconsistent in sediments, no single indicator adequately described occurrence of all bacterial indicators/pathogens. However, important variables included grain size, porosity, clay content and concentrations of Zn, K, and Al. Sediments with greater organic matter content and lower porosity harbored a greater proportion of non-culturable bacteria (including dead cells and extracellular DNA in winter. Here, we show the link between physicochemical

  8. Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose.

    Science.gov (United States)

    Owusu-Ansah, Emmanuel de-Graft Johnson; Sampson, Angelina; Amponsah, Samuel K; Abaidoo, Robert C; Dalsgaard, Anders; Hald, Tine

    2017-12-01

    The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10 -5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study attempts to fit a QMRA model to genome copies of norovirus data. The model estimates the risk of norovirus infection from the intake of vegetables irrigated with wastewater from different sources. The results were compared to the results of a corresponding model using the fecal indicator conversion ratio to estimate the norovirus count. In all scenarios of using different water sources, the application of the fecal indicator conversion ratio underestimated the norovirus disease burden, measured by the Disability Adjusted Life Years (DALYs), when compared to results using the genome copies norovirus data. In some cases the difference was >2 orders of magnitude. All scenarios using genome copies met the 10 -4 DALY per person per year for consumption of vegetables irrigated with wastewater, although these results are considered to be highly conservative risk estimates. The fecal indicator conversion ratio model of stream-water and drain-water sources of wastewater achieved the 10 -6 DALY per person per year threshold, which tends to indicate an underestimation of health risk when compared to using genome copies for estimating the dose. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. The influence of serial fecal sampling on the diagnosis of giardiasis in humans, dogs, and cats.

    Science.gov (United States)

    Uchôa, Flávia Fernandes de Mendonça; Sudré, Adriana Pittella; Macieira, Daniel de Barros; Almosny, Nádia Regina Pereira

    2017-08-24

    Giardia infection is a common clinical problem in humans and pets. The diagnosis of giardiasis is challenging as hosts intermittently excrete protozoan cysts in their feces. In the present study, we comparatively evaluated two methods of serial fecal sampling in humans, dogs, and cats from Rio de Janeiro, Brazil. The Faust et al. technique was used to examine fecal specimens collected in triplicate from 133 patients (52 humans, 60 dogs, and 21 cats). Specimens from 74 patients were received from the group assigned to carry out sampling on consecutive days - 34 humans, 35 dogs, and 5 cats, and specimens from 59 patients were received from the group assigned to carry out sampling on non-consecutive, separate days - 18 human beings, 25 dogs, and 16 cats. G. duodenalis cysts were found in stools of 30 individuals. Multiple stool sampling resulted in an increase in the number of samples that were positive for Giardia in both groups. The authors therefore conclude that multiple stool sampling increases the sensitivity of the Faust et al . technique to detect G. duodenalis cysts in samples from humans, cats and dogs.

  10. Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes

    Energy Technology Data Exchange (ETDEWEB)

    Su, Xiaoling [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Wang, Nan [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Chen, Deying [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Li, Yunong [Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Lu, Yingfeng [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Huan, Tao [Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Xu, Wei [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Li, Liang, E-mail: Liang.Li@ualberta.ca [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Li, Lanjuan, E-mail: ljli@zju.edu.cn [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China)

    2016-01-15

    Human urine and feces can be non-invasively collected for metabolomics-based disease biomarker discovery research. Because urinary and fecal metabolomes are thought to be different, analysis of both biospecimens may generate a more comprehensive metabolomic profile that can be better related to the health state of an individual. Herein we describe a method of using differential chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) for parallel metabolomic profiling of urine and feces. Dansylation labeling was used to quantify the amine/phenol submetabolome changes among different samples based on {sup 12}C-labeling of individual samples and {sup 13}C-labeling of a pooled urine or pooled feces and subsequent analysis of the {sup 13}C-/{sup 12}C-labeled mixture by LC-MS. The pooled urine and pooled feces are further differentially labeled, mixed and then analyzed by LC-MS in order to relate the metabolite concentrations of the common metabolites found in both biospecimens. This method offers a means of direct comparison of urinary and fecal submetabolomes. We evaluated the analytical performance and demonstrated the utility of this method in the analysis of urine and feces collected daily from three healthy individuals for 7 days. On average, 2534 ± 113 (n = 126) peak pairs or metabolites could be detected from a urine sample, while 2507 ± 77 (n = 63) peak pairs were detected from a fecal sample. In total, 5372 unique peak pairs were detected from all the samples combined; 3089 and 3012 pairs were found in urine and feces, respectively. These results reveal that the urine and fecal metabolomes are very different, thereby justifying the consideration of using both biospecimens to increase the probability of finding specific biomarkers of diseases. Furthermore, the CIL LC-MS method described can be used to perform parallel quantitative analysis of urine and feces, resulting in more complete coverage of the human metabolome

  11. Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes

    International Nuclear Information System (INIS)

    Su, Xiaoling; Wang, Nan; Chen, Deying; Li, Yunong; Lu, Yingfeng; Huan, Tao; Xu, Wei; Li, Liang; Li, Lanjuan

    2016-01-01

    Human urine and feces can be non-invasively collected for metabolomics-based disease biomarker discovery research. Because urinary and fecal metabolomes are thought to be different, analysis of both biospecimens may generate a more comprehensive metabolomic profile that can be better related to the health state of an individual. Herein we describe a method of using differential chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) for parallel metabolomic profiling of urine and feces. Dansylation labeling was used to quantify the amine/phenol submetabolome changes among different samples based on "1"2C-labeling of individual samples and "1"3C-labeling of a pooled urine or pooled feces and subsequent analysis of the "1"3C-/"1"2C-labeled mixture by LC-MS. The pooled urine and pooled feces are further differentially labeled, mixed and then analyzed by LC-MS in order to relate the metabolite concentrations of the common metabolites found in both biospecimens. This method offers a means of direct comparison of urinary and fecal submetabolomes. We evaluated the analytical performance and demonstrated the utility of this method in the analysis of urine and feces collected daily from three healthy individuals for 7 days. On average, 2534 ± 113 (n = 126) peak pairs or metabolites could be detected from a urine sample, while 2507 ± 77 (n = 63) peak pairs were detected from a fecal sample. In total, 5372 unique peak pairs were detected from all the samples combined; 3089 and 3012 pairs were found in urine and feces, respectively. These results reveal that the urine and fecal metabolomes are very different, thereby justifying the consideration of using both biospecimens to increase the probability of finding specific biomarkers of diseases. Furthermore, the CIL LC-MS method described can be used to perform parallel quantitative analysis of urine and feces, resulting in more complete coverage of the human metabolome. - Highlights: • A

  12. Lactulose promotes equol production and changes the microbial community during in vitro fermentation of daidzein by fecal inocula of sows.

    Science.gov (United States)

    Zheng, Weijiang; Hou, Yanjun; Su, Yong; Yao, Wen

    2014-02-01

    Equol has higher biological effects than other isoflavones. However, only about 30-50% of humans possess a microbiota capable of producing equol from dietary daidzein. In recent years, interest has grown in dietary applications to improve equol production in human and other animals. In this study, lactulose was used as a potential equol-promoting prebiotic in vitro. The effect of lactulose on transformation of daidzein into equol by sows' fecal microbiota was investigated. Results showed that lactulose treatment improved bacteria growth parameters, changing the kinetics of fermentation in vitro. Lactulose significantly increased total gas production, T1/2, Tmax, and Rmax. Furthermore, lactulose altered the microflora composition, increased equol production associated with a reduction in the population of methanogen and increased the sulfate-reducing bacteria population during 24 h of incubation. Here, we report for the first time that in a certain condition (sealing or high pressure), via a dihydrodaidzein (DHD) pathway equol might be able to reform to daidzein by further metabolism using lactulose as a substrate. This study proposes that "hydrogen-producing prebiotic" might be a novel way to promote equol production in vivo or in vitro. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Incidence of the enterococcal surface protein (esp) gene in human and animal fecal sources

    Science.gov (United States)

    Whitman, R.L.; Przybyla-Kelly, K.; Shively, D.A.; Byappanahalli, M.N.

    2007-01-01

    The occurrence of the enterococcal surface protein (esp) gene in the opportunistic pathogens Enterococcus faecalis and E. faecium is well-documented in clinical research. Recently, the esp gene has been proposed as a marker of human pollution in environmental waters; however, information on its relative incidence in various human and animal fecal sources is limited. We have determined the occurrence of the esp gene in enterococci from human (n = 64) and animal (n = 233) fecal samples by polymerase chain reaction using two primer sets: one presumably specific for E. faecium (espfm) and the other for both E. faecalis and E. faecium (espfs/fm). We believe that this research is the first to explore the use of espfs/fm for the detection of human waste in natural environmental settings. The incidence in human sources was 93.1% espfm and 100% espfs/fm in raw sewage influent; 30% for both espfm and espfs/fm in septic waste; and 0% espfm and 80% espfs/fm in active pit toilets. The overall occurrence of the gene in animal feces was 7.7% (espfs/fm) and 4.7% (espfm); animal types with positive results included dogs (9/43, all espfm), gulls (10/34, espfs/fm; 2/34, espfm), mice (3/22, all espfs/fm), and songbirds (5/55, all espfs/fm). The esp gene was not detected in cat (0/34), deer (0/4), goose (0/18), or raccoon (0/23) feces. The inconsistent occurrence, especially in septic and pit toilet sewage, suggests a low statistical power of discrimination between animal and human sources, which means a large number of replicates should be collected. Both espfm and espfs/fm were common in raw sewage, but neither one efficiently differentiated between animal and other human sources.

  14. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater.

    Science.gov (United States)

    Tran, Ngoc Han; Gin, Karina Yew-Hoong; Ngo, Huu Hao

    2015-12-15

    The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

    Science.gov (United States)

    Kageyama, A; Benno, Y

    2001-01-01

    PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

  16. Distribution of human fecal marker GB-124 bacteriophages in urban sewage and reclaimed water of São Paulo city, Brazil.

    Science.gov (United States)

    Prado, Tatiana; Bruni, Antônio de Castro; Barbosa, Mikaela Renata Funada; Bonanno, Vilma Marques Santos; Garcia, Suzi Cristina; Sato, Maria Inês Zanoli

    2018-04-01

    Bacteriophages infecting Bacteroides fragilis GB-124 have been described as potential markers of human fecal contamination in water sources. The aim of this study was to evaluate the occurrence of GB-124 phages in raw sewage, secondary effluents and reclaimed water of the São Paulo city using a low-cost microbial source tracking method. Samples were collected monthly from April 2015 to March 2016 in four municipal wastewater treatment plants that operate with activated sludge processes followed by different tertiary treatments (sand-anthracite filtration, membrane bioreactor/reverse osmosis) and final chlorination. GB-124 phages were detected in 100% of the raw sewage samples, with viral loads varying from 7.5 × 10 3 to 1.32 × 10 6 PFU/L. Virus removal efficiency in activated sludge processes ranged from 1.89 to 2.31 log 10 . Frequencies of phage detection were lower in reclaimed water samples (0-22.2%). The results indicated that GB-124 phage could be a complementary low-cost viral marker for the detection of human fecal pollution in waters impacted with urban sewage in this region. However, the datasets of tertiary effluents resulted in several samples with concentrations below the detection limit (DL ≤1 PFU/mL) suggesting the need to obtain analytical methods with lower DL for greater accuracy of negative results.

  17. A Human Fecal Contamination Score for Ranking Recreational Sites using the HF183/BacR287 Quantitative Real-Time PCR Method

    Science.gov (United States)

    Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and manag...

  18. Targeting the Sources of Fecal Contamination using Dog-, Human-, and Ruminant- Specific Markers in the Lake Herrick Watershed, Georgia.

    Science.gov (United States)

    Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Habteselassie, M.; Sowah, R.; Kannan, A.

    2016-12-01

    The Lake Herrick Watershed is about 1.5 km2 and covers portions of the University of Georgia's East campus, the Oconee Forest, residential and commercial landuse. Lake Herrick, a recreational site on the University of Georgia campus, was closed in 2002 due to fecal contamination. Subsequent monitoring confirmed persistent contamination, which led to a permanent closure to swimming, boating, and fishing. While fecal coliform abundance is a standard metric for determining human health risks, Geldreich (1970) showed that fecal abundance does not necessarily correlate with the presence of pathogens. Nor does it identify pollution sources, which are needed to mitigate health risks. Two inflow tributaries and the outlet stream were monitored for discharge, fecal coliform, forms of nitrogen and phosphorus and other water-quality data to quantify lake influent and effluent bacteria loads. Fecal sources were identified using the human HF183 genetic marker (Seurinck et al., 2005), the ruminant BacR marker (Reischer et al., 2006), and the dog mitochondrial DNA (mtDNA) marker (Tambalo et al., 2012). Preliminary results confirm high concentrations of E. coli and Enterococci, above the State's limit of 124 MPN/100 mL, in both baseflows and stormflows. The findings also suggest that the E. coli and Enterococci loads from the inlet tributaries are on average higher compared to the bacteria loads coming out of the outlet stream. The human markers were detectable at all three sites but most of the samples were not quantifiable. The ruminant markers were quantifiable at both inlets but no ruminant markers were found at the outlet. The dog markers were detectable but not quantifiable at both inlets and no dog markers were detected at the outlet. Statistical analyses will be used to establish relationships between the nutrients data, the fecal concentrations, and the gene-specific markers.

  19. Frequent detection of a human fecal indicator in the urban ocean: environmental drivers and covariation with enterococci.

    Science.gov (United States)

    Jennings, Wiley C; Chern, Eunice C; O'Donohue, Diane; Kellogg, Michael G; Boehm, Alexandria B

    2018-03-01

    Fecal pollution of surface waters presents a global human health threat. New molecular indicators of fecal pollution have been developed to address shortcomings of traditional culturable fecal indicators. However, there is still little information on their fate and transport in the environment. The present study uses spatially and temporally extensive data on traditional (culturable enterococci, cENT) and molecular (qPCR-enterococci, qENT and human-associated marker, HF183/BacR287) indicator concentrations in marine water surrounding highly-urbanized San Francisco, California, USA to investigate environmental and anthropogenic processes that impact fecal pollution. We constructed multivariable regression models for fecal indicator bacteria at 14 sampling stations. The human marker was detected more frequently in our study than in many other published studies, with detection frequency at some stations as high as 97%. The odds of cENT, qENT, and HF183/BacR287 exceeding health-relevant thresholds were statistically elevated immediately following discharges of partially treated combined sewage, and cENT levels dissipated after approximately 1 day. However, combined sewer discharges were not important predictors of indicator levels typically measured in weekly monitoring samples. Instead, precipitation and solar insolation were important predictors of cENT in weekly samples, while precipitation and water temperature were important predictors of HF183/BacR287 and qENT. The importance of precipitation highlights the significance of untreated storm water as a source of fecal pollution to the urban ocean, even for a city served by a combined sewage system. Sunlight and water temperature likely control persistence of the indicators via photoinactivation and dark decay processes, respectively.

  20. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

    Science.gov (United States)

    There is a growing interest in the application of human-associated fecal sourceidentification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data q...

  1. Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

    Science.gov (United States)

    A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing. Here, we evaluated ten of these methods (BacH, BacHum-UCD, B. thetaiotaomic...

  2. Fecal microbiota transplantation in metabolic syndrome: History, present and future

    NARCIS (Netherlands)

    de Groot, P. F.; Frissen, M. N.; de Clercq, N. C.; Nieuwdorp, M.

    2017-01-01

    The history of fecal microbiota transplantation (FMT) dates back even to ancient China. Recently, scientific studies have been looking into FMT as a promising treatment of various diseases, while in the process teaching us about the interaction between the human host and its resident microbial

  3. Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution.

    Science.gov (United States)

    Peed, Lindsay A; Nietch, Christopher T; Kelty, Catherine A; Meckes, Mark; Mooney, Thomas; Sivaganesan, Mano; Shanks, Orin C

    2011-07-01

    Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.

  4. Development of high-performance chemical isotope labeling LC-MS for profiling the human fecal metabolome.

    Science.gov (United States)

    Xu, Wei; Chen, Deying; Wang, Nan; Zhang, Ting; Zhou, Ruokun; Huan, Tao; Lu, Yingfeng; Su, Xiaoling; Xie, Qing; Li, Liang; Li, Lanjuan

    2015-01-20

    Human fecal samples contain endogenous human metabolites, gut microbiota metabolites, and other compounds. Profiling the fecal metabolome can produce metabolic information that may be used not only for disease biomarker discovery, but also for providing an insight about the relationship of the gut microbiome and human health. In this work, we report a chemical isotope labeling liquid chromatography-mass spectrometry (LC-MS) method for comprehensive and quantitative analysis of the amine- and phenol-containing metabolites in fecal samples. Differential (13)C2/(12)C2-dansyl labeling of the amines and phenols was used to improve LC separation efficiency and MS detection sensitivity. Water, methanol, and acetonitrile were examined as an extraction solvent, and a sequential water-acetonitrile extraction method was found to be optimal. A step-gradient LC-UV setup and a fast LC-MS method were evaluated for measuring the total concentration of dansyl labeled metabolites that could be used for normalizing the sample amounts of individual samples for quantitative metabolomics. Knowing the total concentration was also useful for optimizing the sample injection amount into LC-MS to maximize the number of metabolites detectable while avoiding sample overloading. For the first time, dansylation isotope labeling LC-MS was performed in a simple time-of-flight mass spectrometer, instead of high-end equipment, demonstrating the feasibility of using a low-cost instrument for chemical isotope labeling metabolomics. The developed method was applied for profiling the amine/phenol submetabolome of fecal samples collected from three families. An average of 1785 peak pairs or putative metabolites were found from a 30 min LC-MS run. From 243 LC-MS runs of all the fecal samples, a total of 6200 peak pairs were detected. Among them, 67 could be positively identified based on the mass and retention time match to a dansyl standard library, while 581 and 3197 peak pairs could be putatively

  5. Changes in the composition of the human fecal microbiome following bacteriotherapy for recurrent Clostridium difficile-associated diarrhea

    Energy Technology Data Exchange (ETDEWEB)

    Khoruts, A.; Dicksved, J.; Jansson, J.K.; Sadowsky, M.J.

    2009-08-15

    CDAD is the major known cause of antibiotic-induced diarrhea and colitis, and the disease is thought to result from persistent disruption of commensal gut microbiota. Bacteriotherapy by way of fecal transplantation can be used to treat recurrent CDAD and is thought to re-establish the normal colonic microflora. However, limitations of conventional microbiologic techniques have until recently precluded testing of this idea. In this study we used T-RFLP and 16S rRNA gene sequencing approaches to characterize the bacterial composition of the colonic microflora in a patient suffering from recurrent CDAD, before and after treatment by fecal transplantation from a healthy donor. While the patient's residual colonic microbiota, prior to therapy, was deficient in members of the bacterial divisions-Firmicutes and Bacteriodetes, transplantation had a dramatic impact on the composition of the patient's gut microbiota. By 14 days post transplantation, the fecal bacterial composition of the recipient was highly similar to the donor and was dominated by Bacteroides spp. strains and an uncharacterized butyrate producing bacterium. The change in bacterial composition was accompanied by resolution of the patient's symptoms. The striking similarity of the recipient's and donor's intestinal microbiota following bacteriotherapy suggests that the donor's bacteria quickly occupied their requisite niches, resulting in restoration of both the structure and function of the microbial communities present.

  6. Fluoroquinolones and qnr genes in sediment, water, soil, and human fecal flora in an environment polluted by manufacturing discharges.

    Science.gov (United States)

    Rutgersson, Carolin; Fick, Jerker; Marathe, Nachiket; Kristiansson, Erik; Janzon, Anders; Angelin, Martin; Johansson, Anders; Shouche, Yogesh; Flach, Carl-Fredrik; Larsson, D G Joakim

    2014-07-15

    There is increasing concern that environmental antibiotic pollution promotes transfer of resistance genes to the human microbiota. Here, fluoroquinolone-polluted river sediment, well water, irrigated farmland, and human fecal flora of local villagers within a pharmaceutical industrial region in India were analyzed for quinolone resistance (qnr) genes by quantitative PCR. Similar samples from Indian villages farther away from industrial areas, as well as fecal samples from Swedish study participants and river sediment from Sweden, were included for comparison. Fluoroquinolones were detected by MS/MS in well water and soil from all villages located within three km from industrially polluted waterways. Quinolone resistance genes were detected in 42% of well water, 7% of soil samples and in 100% and 18% of Indian and Swedish river sediments, respectively. High antibiotic concentrations in Indian sediment coincided with high abundances of qnr, whereas lower fluoroquinolone levels in well water and soil did not. We could not find support for an enrichment of qnr in fecal samples from people living in the fluoroquinolone-contaminated villages. However, as qnr was detected in 91% of all Indian fecal samples (24% of the Swedish) it suggests that the spread of qnr between people is currently a dominating transmission route.

  7. Comparison of DNA extraction methods for human gut microbial community profiling.

    Science.gov (United States)

    Lim, Mi Young; Song, Eun-Ji; Kim, Sang Ho; Lee, Jangwon; Nam, Young-Do

    2018-03-01

    The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  8. Dietary whole-grain wheat increases intestinal levels of bifidobacteria in humans and bifidobacterial abundance is negatively correlated with the effect of fecal water on trans-epithelial resistance in vitro

    DEFF Research Database (Denmark)

    Christensen, Ellen Gerd; Licht, Tine Rask; Kristensen, M.

    Consumption of whole grain products are considered to have beneficial effects on human health including decreased risk of cardiovascular disease. However, effects on gut microbial composition have only been studied limitedly. We used quantitative PCR to determine changes in the gut bacterial...... composition in post-menopausal women following a 12-week energy restricted intervention with whole-grain wheat (WW, n=37) or refined wheat (RW, n=33). The WW intervention significantly increased the relative abundance of Bifidobacterium. Caco-2 cells were exposed to fecal water to determine effects...... of the bacterial community metabolites on the trans-epithelial resistance (TER). Fecal water increased TER independent of diet, indicating that commensal bacteria provide metabolites facilitating an increase in intestinal integrity. TER was unexpectedly found to be negatively correlated to the relative abundance...

  9. Metabolic fate of dietary carnitine in human adults: Identification and quantification of urinary and fecal metabolites

    International Nuclear Information System (INIS)

    Rebouche, C.J.; Chenard, C.A.

    1991-01-01

    Results of kinetic and pharmacokinetic studies have suggested that dietary carnitine is not totally absorbed and is in part degraded in the gastrointestinal tract of humans. To determine the metabolic fate of dietary carnitine in humans, we administered orally a tracer dose of methyl- 3 H L-carnitine with a meal to subjects who had been adapted to a low-carnitine diet or a high-carnitine diet. Urinary and fecal excretion of radiolabeled carnitine and metabolites was monitored for 5 to 11 d following administration of the test dose. Total radioactive metabolites excreted ranged from 13 to 34% (low carnitine diet) and 27 to 46% (high carnitine diet) of the ingested tracer. Major metabolites found were [ 3 H]trimethylamine N-oxide (8 to 39% of the administered dose; excreted primarily in urine) and [ 3 H]gamma-butyrobetaine (0.09 to 8% of the administered dose; excreted primarily in feces). Urinary excretion of total carnitine was 42 to 95% (high carnitine diet) and 190 to 364% (low carnitine diet) of intake. These results indicate that oral carnitine is 54 to 87% bioavailable from normal Western diets; the percentage of intake absorbed is related to the quantity ingested

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

    Science.gov (United States)

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

    2015-02-01

    The genetically modified (GM) rice expressing human serum albumin (HSA) is used for non-food purposes; however, its food safety assessment should be conducted due to the probability of accidental mixture with conventional food. In this research, Sprague Dawley rats were fed diets containing 50% (wt/wt) GM rice expressing HSA or non-GM rice for 90 days. Urine metabolites were detected by (1)H NMR to examine the changes of the metabolites in the dynamic process of metabolism. Fecal bacterial profiles were detected by denaturing gradient gel electrophoresis to reflect intestinal health. Additionally, short chain fatty acids and fecal enzymes were investigated. The results showed that compared with rats fed the non-GM rice, some significant differences were observed in rats fed with the GM rice; however, these changes were not significantly different from the control diet group. Additionally, the gut microbiota was associated with blood indexes and urine metabolites. In conclusion, the GM rice diet is as safe as the traditional daily diet. Furthermore, urine metabonomics and fecal bacterial profiles provide a non-invasive food safety assessment rat model for genetically modified crops that are used for non-food/feed purposes. Fecal bacterial profiles have the potential for predicting the change of blood indexes in future. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Effects of Cereal, Fruit and Vegetable Fibers on Human Fecal Weight and Transit Time: A Comprehensive Review of Intervention Trials

    Directory of Open Access Journals (Sweden)

    Jan de Vries

    2016-03-01

    Full Text Available Cereal fibers are known to increase fecal weight and speed transit time, but far less data are available on the effects of fruits and vegetable fibers on regularity. This study provides a comprehensive review of the impact of these three fiber sources on regularity in healthy humans. We identified English-language intervention studies on dietary fibers and regularity and performed weighted linear regression analyses for fecal weight and transit time. Cereal and vegetable fiber groups had comparable effects on fecal weight; both contributed to it more than fruit fibers. Less fermentable fibers increased fecal weight to a greater degree than more fermentable fibers. Dietary fiber did not change transit time in those with an initial time of <48 h. In those with an initial transit time ≥48 h, transit time was reduced by approximately 30 min per gram of cereal, fruit or vegetable fibers, regardless of fermentability. Cereal fibers have been studied more than any other kind in relation to regularity. This is the first comprehensive review comparing the effects of the three major food sources of fiber on bowel function and regularity since 1993.

  12. Effects of Cereal, Fruit and Vegetable Fibers on Human Fecal Weight and Transit Time: A Comprehensive Review of Intervention Trials.

    Science.gov (United States)

    de Vries, Jan; Birkett, Anne; Hulshof, Toine; Verbeke, Kristin; Gibes, Kernon

    2016-03-02

    Cereal fibers are known to increase fecal weight and speed transit time, but far less data are available on the effects of fruits and vegetable fibers on regularity. This study provides a comprehensive review of the impact of these three fiber sources on regularity in healthy humans. We identified English-language intervention studies on dietary fibers and regularity and performed weighted linear regression analyses for fecal weight and transit time. Cereal and vegetable fiber groups had comparable effects on fecal weight; both contributed to it more than fruit fibers. Less fermentable fibers increased fecal weight to a greater degree than more fermentable fibers. Dietary fiber did not change transit time in those with an initial time of <48 h. In those with an initial transit time ≥48 h, transit time was reduced by approximately 30 min per gram of cereal, fruit or vegetable fibers, regardless of fermentability. Cereal fibers have been studied more than any other kind in relation to regularity. This is the first comprehensive review comparing the effects of the three major food sources of fiber on bowel function and regularity since 1993.

  13. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    Energy Technology Data Exchange (ETDEWEB)

    White, G.J.

    1996-08-01

    Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

  14. Dietary fibers from mushroom sclerotia: 3. In vitro fermentability using human fecal microflora.

    Science.gov (United States)

    Wong, Ka-Hing; Wong, King-Yee; Kwan, Hoi-Shan; Cheung, Peter C K

    2005-11-30

    The in vitro fermentability of three novel dietary fibers (DFs) prepared from mushroom sclerotia, namely, Pleurotus tuber-regium, Polyporous rhinocerus, and Wolfiporia cocos, was investigated and compared with that of the cellulose control. All DF samples (0.5 g each) were fermented in vitro with a human fecal homogenate (10 mL) in a batch system (total volume, 50 mL) under strictly anaerobic conditions (using oxygen reducing enzyme and under argon atmosphere) at 37 degrees C for 24 h. All three novel sclerotial DFs exhibited notably higher dry matter disappearance (P. tuber-regium, 8.56%; P. rhinocerus, 13.5%; and W. cocos, 53.4%) and organic matter disappearance (P. tuber-regium, 9.82%; P. rhinocerus, 14.6%; and W. cocos, 57.4%) when compared with those of the cellulose control. Nevertheless, only the W. cocos DF was remarkably degraded to produce considerable amounts of total short chain fatty acids (SCFAs) (5.23 mmol/g DF on organic matter basis, with a relatively higher molar ratio of propionate) that lowered the pH of its nonfermented residue to a slightly acidic level (5.89). Variations on the in vitro fermentability among the three sclerotial DFs might mainly be attributed to their different amounts of interwoven hyphae present (different amounts of enzyme inaccessible cell wall components) as well as the possible different structural arrangement (linkage and degree of branching) of their beta-glucans.

  15. Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Edward Alain B. Pajarillo

    2015-04-01

    Full Text Available This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level. Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

  16. Microbial genome-wide association studies: lessons from human GWAS.

    Science.gov (United States)

    Power, Robert A; Parkhill, Julian; de Oliveira, Tulio

    2017-01-01

    The reduced costs of sequencing have led to whole-genome sequences for a large number of microorganisms, enabling the application of microbial genome-wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS are likely to further advance our understanding of infectious diseases. These advances include insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this Review, we outline the methodologies of GWAS, the current state of the field of microbial GWAS, and how lessons from human GWAS can direct the future of the field.

  17. Effect of adding herbs (Ziziphora clinopodioides, Mentha spicata and Mentha pulegium in milk on performance, blood metabolites and fecal microbial population on Holstein calves

    Directory of Open Access Journals (Sweden)

    narges ghahhari

    2016-08-01

    Full Text Available Introduction Many herbal products (herbs and essential oils are currently used as feed additives by the feed industry in the European Union and elsewhere. These phytogenic substances which increase feed aroma or palatability of feeds are classified as sensory additives by European Council. However, several publications show that some essential oils may have beneficial effects on animal performance and health status because of other properties except their sensory characteristics. These claimed properties are stimulation of digestive secretions; antimicrobial, coccidiostat, anthelmintic, and anti-inflammatory activities; and antioxidant properties. Most research revealed that supplementing herbal essential oils to diets resulted in reducing blood cholesterol, increasing palatability of feed and stimulating the immune system in poultry, while different results obtained by ruminants because of rumen microbial population and ruminal fermentation conditions. The use of large and repeated quantities of antibiotics in animal feed may cause to eliminate beneficial intestinal microflora and innate immune system and subsequently cause to antibiotic resistance and remains antibiotics in animal products. Recently, many herbal products because having flavoring and antimicrobial properties as introduced as good alternatives for antibiotics. The aim of the present investigation was to study of effect of Ziziphora clinopodioies, Mentha spicata and Mentha pulegium on the performance of suckling calves, dry matter digestibility, blood parameters and the immune system, the effect on the incidence of diarrhea and fecal microbial population (Escherichia coli, lactobacillus and total aerobic bacteria. Materials and Methods In the present study, extraction of essential oils from three plant species (Ziziphora clinopodioies, Mentha spicata and Mentha pulegium by means of gas chromatography coupled to mass spectrometry (GC–MS were analyzed. In order to determine the

  18. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo

    Science.gov (United States)

    Cereal grains are often included in equine diets. When starch intake exceeds foregut digestion starch will reach the hindgut, impacting microbial ecology. Probiotics (e.g., lactobacilli) are reported to mitigate GI dysbioses in other species. This study was conducted to determine the effect of star...

  19. Quantification of human-associated fecal indicators reveal sewage from urban watersheds as a source of pollution to Lake Michigan

    Science.gov (United States)

    Olds, Hayley T.; Dila, Deborah K.; Bootsma, Melinda J.; Corsi, Steven; McLellan, Sandra L.

    2016-01-01

    Sewage contamination of urban waterways from sewer overflows and failing infrastructure is a major environmental and public health concern. Fecal coliforms (FC) are commonly employed as fecal indicator bacteria, but do not distinguish between human and non-human sources of fecal contamination. Human Bacteroides and humanLachnospiraceae, two genetic markers for human-associated indicator bacteria, were used to identify sewage signals in two urban rivers and the estuary that drains to Lake Michigan. Grab samples were collected from the rivers throughout 2012 and 2013 and hourly samples were collected in the estuary across the hydrograph during summer 2013. Human Bacteroides and human Lachnospiraceae were highly correlated with each other in river samples (Pearson’s r = 0.86), with average concentrations at most sites elevated during wet weather. These human indicators were found during baseflow, indicating that sewage contamination is chronic in these waterways. FC are used for determining total maximum daily loads (TMDLs) in management plans; however, FC concentrations alone failed to prioritize river reaches with potential health risks. While 84% of samples with >1000 CFU/100 ml FC had sewage contamination, 52% of samples with moderate (200–1000 CFU/100 ml) and 46% of samples with low (events and was highest during an event with a short duration of intense rain. This work demonstrates urban areas have unrecognized sewage inputs that may not be adequately prioritized for remediation by the TMDL process. Further analysis using these approaches could determine relationships between land use, storm characteristics, and other factors that drive sewage contamination in urban waterways.

  20. Microbial communities and fecal indicator bacteria associated with Cladophora mats on beach sites along Lake Michigan shores.

    Science.gov (United States)

    Olapade, Ola A; Depas, Morgan M; Jensen, Erika T; McLellan, Sandra L

    2006-03-01

    A high biomasses of Cladophora, a filamentous green alga, is found mainly during the summer along the shores of Lake Michigan. In this study, the abundance and persistence of the fecal indicator bacterium Escherichia coli and sulfate-reducing bacteria (SRB) on Cladophora mats collected at Lake Michigan beaches were evaluated using both culture-based and molecular analyses. Additionally, 16S rRNA gene cloning and sequencing were used to examine the bacterial community composition. Overall, E. coli was detected in all 63 samples obtained from 11 sites, and the average levels at most beaches ranged from 2,700 CFU/100 g (wet weight) of Cladophora to 7,500 CFU/100 g of Cladophora. However, three beaches were found to have site average E. coli densities of 12,800, 21,130, and 27,950 CFU/100 g of Cladophora. The E. coli levels in the lake water collected at the same time from these three sites were less than the recommended U.S. Environmental Protection Agency limit, 235 CFU/100 ml. E. coli also persisted on Cladophora mats in microcosms at room temperature for more than 7 days, and in some experiments it persisted for as long as 28 days. The SRB densities on Cladophora mats were relatively high, ranging from 4.4x10(6) cells/g (6.64 log CFU/g) to 5.73x10(6) cells/g (6.76 log CFU/g) and accounting for between 20% and 27% of the total bacterial counts. Partial sequences of the 16S rRNA gene clones revealed a phylogenetically diverse community, in which the Cytophaga-Flavobacterium-Bacteroides cluster and the low-G+C-content gram-positive bacteria were the dominant organisms, accounting for 40% and 12.8%, respectively, of the total clone library. These results further reveal the potential public health and ecological significance of Cladophora mats that are commonly found along the shoreline of Lake Michigan, especially with regard to the potential to harbor microorganisms associated with fecal pollution and odor-causing bacteria.

  1. Exposure to human-associated fecal indicators and self-reported illness among swimmers at recreational beaches: a cohort study.

    Science.gov (United States)

    Napier, Melanie D; Haugland, Richard; Poole, Charles; Dufour, Alfred P; Stewart, Jill R; Weber, David J; Varma, Manju; Lavender, Jennifer S; Wade, Timothy J

    2017-10-02

    Fecal indicator bacteria used to assess illness risks in recreational waters (e.g., Escherichia coli, Enterococci) cannot discriminate among pollution sources. To address this limitation, human-associated Bacteroides markers have been proposed, but the risk of illness associated with the presence of these markers in recreational waters is unclear. Our objective was to estimate associations between human-associated Bacteroides markers in water and self-reported illness among swimmers at 6 U.S. beaches spanning 2003-2007. We used data from a prospectively-enrolled cohort of 12,060 swimmers surveyed about beach activities and water exposure on the day of their beach visit. Ten to twelve days later, participants reported gastroinestinal, diarrheal, and respiratory illnesses experienced since the visit. Daily water samples were analyzed for the presence of human-associated Bacteroides genetic markers: HF183, BsteriF1, BuniF2, HumM2. We used model-based standardization to estimate risk differences (RD) and 95% confidence intervals (CI). We assessed whether the presence of Bacteroides markers were modifiers of the association between general Enterococcus and illness among swimmers using interaction contrast. Overall we observed inconsistent associations between the presence of Bacteroides markers and illness. There was a pattern of increased risks of gastrointestinal (RD = 1.9%; 95% CI: 0.1%, 3.7%), diarrheal (RD = 1.3%; 95% CI: -0.2%, 2.7%), and respiratory illnesses (RD = 1.1%; 95% CI: -0.2%, 2.5%) associated with BsteriF1. There was no evidence that Bacteroides markers acted as modifiers of Enterococcus and illness. Patterns were similar when stratified by water matrix. Quantitative measures of fecal pollution using Bacteroides, rather than presence-absence indicators, may be necessary to accurately assess human risk specific to the presence of human fecal pollution.

  2. Caffeine as an indicator of human fecal contamination in the Sinos River: a preliminary study

    Directory of Open Access Journals (Sweden)

    R Linden

    Full Text Available The preservation of hydric resources is directly related to fecal contamination monitoring, in order to allow the development of strategies for the management of polluting sources. In the present study, twenty-five water samples from six water public supply collection sites were used for the evaluation of the presence of caffeine, total and fecal coliforms. Caffeine was detected in all samples, with concentrations ranging from 0.15 ng mL–1 to 16.72 ng mL–1. Total coliforms were detected in all samples, with concentrations in the range of 52 NMP/100 mL to higher than 24196 NMP/100 mL, whether the concentration range for fecal coliforms was in the range of below 1 NMP/100 mL to 7800 NMP/100 mL. No significant correlation was found between total coliforms and caffeine concentrations (rs = 0.35, p = 0.09. However, a moderate correlation between fecal coliforms and caffeine concentrations was found (rs = 0.412, p

  3. Potential of fecal waste for the production of biomethane, bioethanol and biodiesel.

    Science.gov (United States)

    Gomaa, Mohamed A; Abed, Raeid M M

    2017-07-10

    Fecal waste is an environmental burden that requires proper disposal, which ultimately becomes also an economic burden. Because fecal waste is nutrient-rich and contains a diverse methanogenic community, it has been utilized to produce biomethane via anaerobic digestion. Carbohydrates and lipids in fecal waste could reach up to 50% of the dry weight, which also suggests a potential as a feedstock for bioethanol and biodiesel production. We measured biomethane production from fecal waste of cows, chickens, goats and humans and compared the microbial community composition before and after anaerobic digestion. We also compared the fecal waste for cellulase production, saccharification and fermentation to produce bioethanol and for lipid content and fatty acid profiles to produce biodiesel. All fecal waste produced biomethane, with the highest yield of 433.4±77.1ml CH 4 /g VS from cow fecal waste. Production of bioethanol was achieved from all samples, with chicken fecal waste yielding as high as 1.6±0.25g/l. Sludge samples exhibited the highest extractable portion of lipids (20.9±0.08wt%) and conversion to fatty acid methyl esters (11.94wt%). Utilization of fecal waste for the production of biofuels is environmentally and economically beneficial. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn's disease and healthy individuals

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Wang, Yulan; Hao, Fuhua

    2015-01-01

    This study employs spectroscopy-based metabolic profiling of fecal extracts from healthy subjects and patients with active or inactive ulcerative colitis (UC) and Crohn's disease (CD) to substantiate the potential use of spectroscopy as a non-invasive diagnostic tool and to characterize the fecal......-projection to latent structure-discriminant analysis using SIMCA-P + 12 and MATLAB. Significant differences were found in the metabolic profiles making it possible to differentiate between active IBD and controls and between UC and CD. The metabolites holding differential power primarily belonged to a range of amino...... acids, microbiota-related short chain fatty acids, and lactate suggestive of an inflammation-driven malabsorption and dysbiosis of the normal bacterial ecology. However, removal of patients with intestinal surgery and anti-TNF-α antibody treatment eliminated the discriminative power regarding UC versus...

  5. A human gut microbial gene catalogue established by metagenomic sequencing

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn

    2010-01-01

    To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence...

  6. Changes in the fecal profile of inflammatory markers after moderate consumption of red wine: a human trial study

    Directory of Open Access Journals (Sweden)

    Irene Muñoz-González

    2014-12-01

    Full Text Available The aim of this work was to evaluate the potential of moderate consumption of red wine to modulate the intestinal inflammation response on healthy humans. Fecal samples from a human intervention study (n=34 were collected before and after consumption of red wine for 4 weeks, and 24 immune markers including immunoglobulins, cytokines, chemokines and growth factors, were analysed. When considering the whole group of case volunteers, almost no statistically significant differences were found in the immune markers after wine consumption. However, a detailed exploration of the values differentiated a 6-volunteer subgroup that showed unusually high values of cytokines before wine consumption. For this subgroup, wine consumption significantly reduced the content of 16 out of 24 markers down to usual values, especially noticeable for cytokines related to the promotion of initial inflammation (tumor necrosis factor-alpha, interleukin 6 and interferon-gamma. This study reveals, for the first time, changes in the fecal profile of inflammatory markers after moderate consumption of red wine.

  7. Next generation sequencing reveals distinct fecal pollution signatures in aquatic sediments across gradients of anthropogenic influence

    Directory of Open Access Journals (Sweden)

    Gian Marco Luna

    2016-11-01

    Full Text Available Aquatic sediments are the repository of a variety of anthropogenic pollutants, including bacteria of fecal origin, that reach the aquatic environment from a variety of sources. Although fecal bacteria can survive for long periods of time in aquatic sediments, the microbiological quality of sediments is almost entirely neglected when performing quality assessments of aquatic ecosystems. Here we investigated the relative abundance, patterns and diversity of fecal bacterial populations in two coastal areas in the Northern Adriatic Sea (Italy: the Po river prodelta (PRP, an estuarine area receiving significant contaminant discharge from one of the largest European rivers and the Lagoon of Venice (LV, a transitional environment impacted by a multitude of anthropogenic stressors. From both areas, several indicators of fecal and sewage contamination were determined in the sediments using Next Generation Sequencing (NGS of 16S rDNA amplicons. At both areas, fecal contamination was high, with fecal bacteria accounting for up to 3.96% and 1.12% of the sediment bacterial assemblages in PRP and LV, respectively. The magnitude of the fecal signature was highest in the PRP site, highlighting the major role of the Po river in spreading microbial contaminants into the adjacent coastal area. In the LV site, fecal pollution was highest in the urban area, and almost disappeared when moving to the open sea. Our analysis revealed a large number of fecal Operational Taxonomic Units (OTU, 960 and 181 in PRP and LV, respectively and showed a different fecal signature in the two areas, suggesting a diverse contribution of human and non-human sources of contamination. These results highlight the potential of NGS techniques to gain insights into the origin and fate of different fecal bacteria populations in aquatic sediments.

  8. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

    Science.gov (United States)

    Džunková, Mária; D'Auria, Giuseppe; Pérez-Villarroya, David; Moya, Andrés

    2012-01-01

    Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

  9. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

    Directory of Open Access Journals (Sweden)

    Mária Džunková

    Full Text Available Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

  10. Influence of Sterilized Human Fecal Extract on the Sensitivity of Salmonella enterica ATCC 13076 and Listeria monocytogenes ATCC 15313 to Enrofloxacin.

    Science.gov (United States)

    Ahn, Youngbeom; Stuckey, Ryan; Sung, Kidon; Rafii, Fatemeh; Cerniglia, Carl E

    2013-12-02

    There is much debate on whether continuous exposure of commensal bacteria and potential pathogens residing in the human intestinal tract to low levels of antimicrobial agents from treated food animals pose a public health concern. To investigate antimicrobial effects on bacteria under colonic conditions, we studied resistance development in Salmonella enterica and Listeria monocytogenes exposed to enrofloxacin in the presence of fecal extract. The bacteria were incubated at 37 °C in Mueller-Hinton broth, with and without 0.01~0.5 μg/mL enrofloxacin, in the presence and absence of sucrose, and with 1% or 2.5% filter-sterilized fecal extract, for three passages. In the second and third passages, only the bacteria incubated in the media containing sterilized fecal extract grew in 0.5 μg/mL of enrofloxacin. Fecal extract (1% and 2.5%) decreased the sensitivity of S. enterica to enrofloxacin in the medium containing the efflux pump inhibitors reserpine and carbonyl cyanide-m-chlorophenylhydrazone (CCCP) and affected the accumulation of ethidium bromide (EtBr) in this bacterium. Enrofloxacin (0.06 µg/mL) and fecal extract altered the composition of fatty acids in S. enterica and L. monocytogenes. We conclude that fecal extract decreased the susceptibilities of S. enterica and L. monocytogenes to concentrations of enrofloxacin higher than the MIC and resulted in rapid resistance selection.

  11. Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam

    NARCIS (Netherlands)

    Oude Munnink, Bas B.; Phan, My V. T.; Simmonds, Peter; Koopmans, Marion P. G.; Kellam, Paul; van der Hoek, Lia; Cotten, Matthew

    2017-01-01

    Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus

  12. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks.

    Science.gov (United States)

    Hale, Vanessa L; Tan, Chia L; Knight, Rob; Amato, Katherine R

    2015-06-01

    Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Effects of environmental conditions, human activity, reproduction, antler cycle and grouping on fecal glucocorticoids of free-ranging Pampas deer stags (Ozotoceros bezoarticus bezoarticus).

    Science.gov (United States)

    Garcia Pereira, Ricardo José; Barbanti Duarte, José Maurício; Negrão, João Alberto

    2006-01-01

    In this study, a commercial enzyme immunoassay (EIA) was validated in detecting glucocorticoids in Pampas deer feces, in order to investigate the influence of several factors on the adrenocortical function. Fecal samples, behavioral data and information concerning male grouping and antlers status were collected at a monthly basis during a 1 year period from free-ranging stags living at Emas National Park, Brazil (18 degrees S/52 degrees W). The results revealed that concentrations of fecal glucocorticoids in winter were significantly higher than those corresponding to spring and summer. In addition, dry season data presented higher levels than during the wet season. Significant difference was found between fecal levels of breeding stags in summer and nonbreeding stags, whereas no difference was observed between breeding stags in winter and nonbreeding stags. On the other hand, males from areas with frequent human disturbance exhibited higher glucocorticoid concentrations and flight distances than individuals from areas of lower human activity. Males with antlers in velvet had elevated levels compared with animals in hard antler or antler casting. Also, we found that glucocorticoid levels were higher in groups with three or more males than in groups with only one male. The flight distances showed positive correlation with fecal glucocorticoid. These data indicate that fecal glucocorticoid provides a useful approach in the evaluation of physiological effects of environment, inter-individuals relationship and human-induced stressors on free-ranging Pampas deer stags.

  14. Lactic acid bacteria affect serum cholesterol levels, harmful fecal enzyme activity, and fecal water content

    Directory of Open Access Journals (Sweden)

    Chung Myung

    2009-06-01

    Full Text Available Abstract Background Lactic acid bacteria (LAB are beneficial probiotic organisms that contribute to improved nutrition, microbial balance, and immuno-enhancement of the intestinal tract, as well as lower cholesterol. Although present in many foods, most trials have been in spreads or dairy products. Here we tested whether Bifidobacteria isolates could lower cholesterol, inhibit harmful enzyme activities, and control fecal water content. Methods In vitro culture experiments were performed to evaluate the ability of Bifidobacterium spp. isolated from healthy Koreans (20~30 years old to reduce cholesterol-levels in MRS broth containing polyoxyethanylcholesterol sebacate. Animal experiments were performed to investigate the effects on lowering cholesterol, inhibiting harmful enzyme activities, and controlling fecal water content. For animal studies, 0.2 ml of the selected strain cultures (108~109 CFU/ml were orally administered to SD rats (fed a high-cholesterol diet every day for 2 weeks. Results B. longum SPM1207 reduced serum total cholesterol and LDL levels significantly (p B. longum SPM1207 also increased fecal LAB levels and fecal water content, and reduced body weight and harmful intestinal enzyme activities. Conclusion Daily consumption of B. longum SPM1207 can help in managing mild to moderate hypercholesterolemia, with potential to improve human health by helping to prevent colon cancer and constipation.

  15. Differential effects of whisky brands on human gut microbiome and fecal metabolome

    Directory of Open Access Journals (Sweden)

    Priyanka Sarkar

    2017-10-01

    Full Text Available The gut bacteria have significant impact on human physiology and are influenced by dietary habit [1]. Apart from normal diet, alcoholic beverages have also been shown to influence gut microbial makeup. The wine polyphenols have been linked to increase the beneficial bacteria in the gut after 4 weeks of consumption [2]. Consumption of alcoholic beverages for longer period (>10 years has also been correlated to detrimental gut bacterial dysbiosis [3]. The contrasting effects of alcoholic beverages in these two studies necessitate further research. Globally, 45.7% of alcoholic drinkers are spirit drinkers with India having the highest (71% [4]. In India whisky is preferred by most of the drinkers and 1400 million liters of whisky was consumed in India in the year 2012 [5]. Till date, no study has been reported to understand the effect of long-term consumption of different types of whisky on gut bacterial profile (GBP. In this purview apilot study of gut bacterial and metabolite profile was performed between the whisky drinker (n=18 and non-drinker (n=8 along with rice beer drinkers (n=3. PCR-denaturing gradient gel electrophoresis (PCR-DGGE coupled with next generation sequencing (NGS analysis on illumina miseq platform revealed decrease in gut bacterial diversity in the drinkers compared to the non-drinkers. The whisky types have differential effects on the GBP. The GBP of whisky type 1 drinkers had higher abundance of Clostridiaceae and Enterobacteriaceae (fold change log 2: 3.33 & 3.1537, respectively; p< 0.002 in comparison to the non-drinker group, while the type 2 whisky drinkers had increased abundance of Lactococcus and Streptococcus (fold change log 2: 9.1827 & 4.2986; p< 0.002 compared to the non-drinker group. The butyric acid producing genera, Ruminococcaceae was found to be decreased in both the whisky drinking cohorts (fold change log 2: -1.5449 & -2.7327, respectively; p<0.002. Short-chain fatty acids (SCFA, mainly butyric acid

  16. Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders.

    Science.gov (United States)

    Swidsinski, Alexander; Loening-Baucke, Vera; Schulz, Stefan; Manowsky, Julia; Verstraelen, Hans; Swidsinski, Sonja

    2016-02-01

    Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N=20 each) treated for bacterial vaginosis with ciprofloxacin+metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A_Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group A_Sb. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30μm broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

  17. A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method.

    Science.gov (United States)

    Cao, Yiping; Sivaganesan, Mano; Kelty, Catherine A; Wang, Dan; Boehm, Alexandria B; Griffith, John F; Weisberg, Stephen B; Shanks, Orin C

    2018-01-01

    Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance. Published by Elsevier Ltd.

  18. Canine scent detection and microbial source tracking of human waste contamination in storm drains.

    Science.gov (United States)

    Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

    2014-06-01

    Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

  19. Microbial co-occurrence relationships in the human microbiome.

    Directory of Open Access Journals (Sweden)

    Karoline Faust

    Full Text Available The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs to taxonomic marker (16S rRNA gene profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut often compete, while potential pathogens (e.g. Treponema and

  20. Microbial Co-occurrence Relationships in the Human Microbiome

    Science.gov (United States)

    Izard, Jacques; Segata, Nicola; Gevers, Dirk

    2012-01-01

    The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the

  1. Gut microbial metabolites of polyunsaturated fatty acids correlate with specific fecal bacteria and serum markers of metabolic syndrome in obese women.

    Science.gov (United States)

    Druart, Céline; Dewulf, Evelyne M; Cani, Patrice D; Neyrinck, Audrey M; Thissen, Jean-Paul; Delzenne, Nathalie M

    2014-04-01

    The aim of this human study was to assess the influence of prebiotic-induced gut microbiota modulation on PUFA-derived bacterial metabolites production. Therefore, we analyzed the circulating fatty acid profile including CLA/CLnA in obese women treated during 3 months with inulin-type fructan prebiotics. In these patients, we had already determined gut microbiota composition by phylogenetic microarray and qPCR analysis of 16S rDNA. Some PUFA-derived bacterial metabolites were detected in the serum of obese patients. Despite the prebiotic-induced modulation of gut microbiota, including changes in CLA/CLnA-producing bacteria, the treatment did not impact significantly on the circulating level of these metabolites. However, some PUFA-derived bacterial metabolites were positively correlated with specific fecal bacteria (Bifidobacterium spp., Eubacterium ventriosum and Lactobacillus spp.) and inversely correlated with serum cholesterol (total, LDL, HDL). These correlations suggest a potential beneficial effect of some of these metabolites but this remains to be confirmed by further investigation.

  2. In vitro fermentation of mulberry fruit polysaccharides by human fecal inocula and impact on microbiota.

    Science.gov (United States)

    Chen, Chun; Huang, Qiang; Fu, Xiong; Liu, Rui Hai

    2016-11-09

    This study investigated the in vitro fermentation of polysaccharides from Morus alba L., the contribution of its carbohydrates to the fermentation, and the effect on the composition of gut microbiota. Over 48 h of fermentation, the pH value in the fecal culture decreased from 7.12 to 6.14, and the total short chain fatty acids (SCFA) and acetic, propionic, and butyric acids all significantly increased. After 48 h of fermentation, 45.36 ± 1.36% of the total carbohydrates in the polysaccharide, including 35.72 ± 1.51% of arabinose, 23.1 ± 1.19% of galactose, 41.43 ± 1.52% of glucose, 26.36 ± 1.93% of rhamnose and 65.57 ± 1.07% of galacturic acid, were consumed. The increase in acetic and butyric acids was primarily due to the fermentation of galactose and galacturonic acid in the polysaccharide, while the increase in propionic acid resulted mainly from the fermentation of arabinose and glucose. In addition, the polysaccharide could modulate the gut microbiota composition by increasing the Bacteroidetes population and decreasing the Firmicutes population. The results may facilitate the development of food products known as prebiotics, aimed at improving gastrointestinal health.

  3. Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting the groEL Gene

    Science.gov (United States)

    Junick, Jana

    2012-01-01

    Quantitative real-time PCR assays targeting the groEL gene for the specific enumeration of 12 human fecal Bifidobacterium species were developed. The housekeeping gene groEL (HSP60 in eukaryotes) was used as a discriminative marker for the differentiation of Bifidobacterium adolescentis, B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. gallicum, B. longum, B. pseudocatenulatum, B. pseudolongum, and B. thermophilum. The bifidobacterial chromosome contains a single copy of the groEL gene, allowing the determination of the cell number by quantification of the groEL copy number. Real-time PCR assays were validated by comparing fecal samples spiked with known numbers of a given Bifidobacterium species. Independent of the Bifidobacterium species tested, the proportion of groEL copies recovered from fecal samples spiked with 5 to 9 log10 cells/g feces was approximately 50%. The quantification limit was 5 to 6 log10 groEL copies/g feces. The interassay variability was less than 10%, and variability between different DNA extractions was less than 23%. The method developed was applied to fecal samples from healthy adults and full-term breast-fed infants. Bifidobacterial diversity in both adults and infants was low, with mostly ≤3 Bifidobacterium species and B. longum frequently detected. The predominant species in infant and adult fecal samples were B. breve and B. adolescentis, respectively. It was possible to distinguish B. catenulatum and B. pseudocatenulatum. We conclude that the groEL gene is a suitable molecular marker for the specific and accurate quantification of human fecal Bifidobacterium species by real-time PCR. PMID:22307308

  4. Rapid detection of Opisthorchis viverrini and Strongyloides stercoralis in human fecal samples using a duplex real-time PCR and melting curve analysis.

    Science.gov (United States)

    Janwan, Penchom; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

    2011-12-01

    Human opisthorchiasis caused by the liver fluke Opisthorchis viverrini is an endemic disease in Southeast Asian countries including the Lao People's Democratic Republic, Cambodia, Vietnam, and Thailand. Infection with the soil-transmitted roundworm Strongyloides stercoralis is an important problem worldwide. In some areas, both parasitic infections are reported as co-infections. A duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis was developed for the rapid detection of O. viverrini and S. stercoralis in human fecal samples. Duplex real-time FRET PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two genera of DNA elements: the 162 bp pOV-A6 DNA sequence specific to O. viverrini and the 244 bp 18S rRNA sequence specific to S. stercoralis, and two pairs of specific fluorophore-labeled probes. Both O. viverrini and S. stercoralis can be differentially detected in infected human fecal samples by this process through their different fluorescence channels and melting temperatures. Detection limit of the method was as little as two O. viverrini eggs and four S. stercoralis larvae in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasite materials, as well as from the DNA of human leukocytes and other control parasites. The technique showed 100% sensitivity and specificity. The introduced duplex real-time FRET PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The method is important for simultaneous detection especially in areas where both parasites overlap incidence and is useful as the screening tool in the returning travelers and immigrants to industrialized countries where number of samples in the diagnostic units will become increasing.

  5. Marine and Freshwater Fecal Indicators and Source Identification

    Science.gov (United States)

    Fecal indicators are organisms or chemical constituents found in fecal material or wastewater that can be measured to demonstrate the presence of fecal pollution. Fecal waste from humans and other animals can contaminant surface waters and pose a serious threat to the environmen...

  6. Detection of Giardia duodenalis antigen in human fecal eluates by enzyme-linked immunosorbent assay using polyclonal antibodies

    Directory of Open Access Journals (Sweden)

    Sofía Duque-Beltrán

    2002-12-01

    Full Text Available The present study developed and standardized an enzime-linked immunosorbent assay (ELISA to detect Giardia antigen in feces using rabbit polyclonal antibodies. Giardia cysts were purified from human fecal samples by sucrose and percoll gradients. Gerbils (Meriones unguiculatus were infected to obtain trophozoites. Rabbits were inoculated with either cyst or trophozoite antigens of 14 Colombian Giardia isolates to develop antibodies against the respective stages. The IgG anti-Giardia were purified by sequential caprylic acid and ammonium sulfate precipitation. A portion of these polyclonal antibodies was linked to alkaline phosphatase (conjugate. One hundred and ninety six samples of human feces, from different patients, were tested by parasitologic diagnosis: 69 were positive for Giardia cysts, 56 had no Giardia parasites, and 71 revealed parasites other than Giardia. The optimal concentration of polyclonal antibodies for antigen capture was 40 µg/ml and the optimal conjugate dilution was 1:100. The absorbance cut-off value was 0.24. The parameters of the ELISA test for Giardia antigen detection were: sensitivity, 100% (95% CI: 93.4-100%; specificity, 95% (95% CI: 88.6-97.6%; positive predictive value, 91% (95% CI: 81.4-95.9%; and negative predictive value, 100% (95% CI: 96.1-100%. This ELISA will improve the diagnosis of Giardia infections in Colombia and will be useful in following patients after treatment.

  7. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

    NARCIS (Netherlands)

    Gigliucci, Federica; von Meijenfeldt, F A Bastiaan; Knijn, Arnold; Michelacci, Valeria; Scavia, Gaia; Minelli, Fabio; Dutilh, Bas E|info:eu-repo/dai/nl/304546313; Ahmad, Hamideh M; Raangs, Gerwin C; Friedrich, Alex W; Rossen, John W A; Morabito, Stefano

    2018-01-01

    The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic

  8. Molecular Monitoring of the Fecal Microbiota of Healthy Human Subjects during Administration of Lactulose and Saccharomyces boulardii

    Science.gov (United States)

    Vanhoutte, Tom; De Preter, Vicky; De Brandt, Evie; Verbeke, Kristin; Swings, Jean; Huys, Geert

    2006-01-01

    Diet is a major factor in maintaining a healthy human gastrointestinal tract, and this has triggered the development of functional foods containing a probiotic and/or prebiotic component intended to improve the host's health via modulation of the intestinal microbiota. In this study, a long-term placebo-controlled crossover feeding study in which each subject received several treatments was performed to monitor the effect of a prebiotic substrate (i.e., lactulose), a probiotic organism (i.e., Saccharomyces boulardii), and their synbiotic combination on the fecal microbiota of three groups of 10 healthy human subjects differing in prebiotic dose and/or intake of placebo versus synbiotic. For this purpose, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was used to detect possible changes in the overall bacterial composition using the universal V3 primer and to detect possible changes at the subpopulation level using group-specific primers targeting the Bacteroides fragilis subgroup, the genus Bifidobacterium, the Clostridium lituseburense group (cluster XI), and the Clostridium coccoides-Eubacterium rectale group (cluster XIVa). Although these populations remained fairly stable based on DGGE profiling, one pronounced change was observed in the universal fingerprint profiles after lactulose ingestion. Band position analysis and band sequencing revealed that a band appearing or intensifying following lactulose administration could be assigned to the species Bifidobacterium adolescentis. Subsequent analysis with real-time PCR (RT-PCR) indicated a statistically significant increase (P < 0.05) in total bifidobacteria in one of the three subject groups after lactulose administration, whereas a similar but nonsignificant trend was observed in the other two groups. Combined RT-PCR results from two subject groups indicated a borderline significant increase (P = 0.074) of B. adolescentis following lactulose intake. The probiotic yeast S

  9. Correlation of crAssphage-based qPCR markers with culturable and molecular indicators of human fecal pollution in an impacted urban watershed.

    Science.gov (United States)

    Stachler, Elyse; Akyon, Benay; Aquino de Carvalho, Nathalia; Ference, Christian; Bibby, Kyle

    2018-06-06

    Environmental waters are monitored for fecal pollution to protect public health. Many previously developed human-specific fecal pollution indicators lack adequate sensitivity to be reliably detected in environmental waters or do not correlate well with viral pathogens. Recently, two novel human sewage-associated source tracking qPCR markers were developed based on the bacteriophage crAssphage, CPQ_056 and CPQ_064. These assays are highly human specific, abundant in sewage, and are viral-based, suggesting great promise for environmental application as human fecal pollution indicators. A 30-day sampling study was conducted in an urban stream impacted by combined sewer overflows to evaluate the crAssphage markers' performance in an environmental system. The crAssphage markers were present at concentrations of 4.02-6.04 log10 copies/100 mL throughout the study period, indicating their high abundance and ease of detection in polluted environmental waters. In addition, the crAssphage assays were correlated with rain events, molecular markers for human polyomavirus and HF183, as well as culturable E. coli, enterococci, and somatic coliphage. The CPQ_064 assay correlated strongly to a greater number of biological indicators than the CPQ_056 assay. This study is the first to evaluate both crAssphage qPCR assays in an extended environmental application of crAssphage markers for monitoring of environmental waters. It is also the first study to compare crAssphage marker concentration with other viral-based indicators.

  10. Comparison of bile acid synthesis determined by isotope dilution versus fecal acidic sterol output in human subjects

    International Nuclear Information System (INIS)

    Duane, W.C.; Holloway, D.E.; Hutton, S.W.; Corcoran, P.J.; Haas, N.A.

    1982-01-01

    Fecal acidic sterol output has been found to be much lower than bile acid synthesis determined by isotope dilution. Because of this confusing discrepancy, we compared these 2 measurements done simultaneously on 13 occasions in 5 normal volunteers. In contrast to previous findings, bile acid synthesis by the Lindstedt isotope dilution method averaged 16.3% lower than synthesis simultaneously determined by fecal acidic sterol output (95% confidence limit for the difference - 22.2 to -10.4%). When one-sample determinations of bile acid pools were substituted for Lindstedt pools, bile acid synthesis by isotope dilution averaged 5.6% higher than synthesis by fecal acidic sterol output (95% confidence limits -4.9 to 16.1%). These data indicate that the 2 methods yield values in reasonably close agreement with one another. If anything, fecal acidic sterol outputs are slightly higher than synthesis by isotope dilution

  11. USE OF COMPETITIVE GENOMIC HYBRIDIZATION TO ENRICH FOR GENOME-SPECIFIC DIFFERENCES BETWEEN TWO CLOSELY RELATED HUMAN FECAL INDICATOR BACTERIA

    Science.gov (United States)

    Enterococci are frequently used as indicators of fecal pollution in surface waters. To accelerate the identification of Enterococcus faecalis-specific DNA sequences, we employed a comparative genomic strategy utilizing a positive selection process to compare E. faec...

  12. 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

  13. Influence of manure age and sunlight on the community structure of cattle fecal bacteria as revealed by Illumina sequencing

    Science.gov (United States)

    Wong, K.; Shaw, T. I.; Oladeinde, A.; Molina, M.

    2013-12-01

    Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. Stream and river impairment due to fecal pollution is largely the result of agricultural activities in the United States. In the last few years, numerous metagenomic studies utilized next generation sequencing to develop microbial community profiles by massively sequencing the 16sRNA hypervariable region. This technology supports the application of water quality assessment such as pathogen detection and fecal source tracking. The bacteria communities of samples in these studies were determined when they were freshly collected; therefore, little is known about how feces age or how environmental stress influences the microbial ecology of fecal materials. In this study we monitored bacteria community changes in cattle feces for 57 days after excretion (day 0, 2, 4 8, 15, 22, 29, 43, 57) by sequencing the 16s variable region 4, using Illumnia MiSeq. Twelve cattle feces were studied; half of the samples were directly exposed to sunlight (unshaded) and half were shaded. Results indicate that the relative abundance (RA) profile in both shaded and unshaded samples rapidly changed from day 0 to 15, but stabilized from day 22 to 57. Firmcutes were the most abundant phylum (~40%) at day 0, but were reduced to rarefaction curve analysis, richness of bacteria diversity in feces decreased as time progressed. Some pathogens such as Campylobacter were detected only at the beginning, meaning they substantially decayed during the course of our study. Overall, this study indicated: (1) sunlight can influence the community structure and (2) after excretion the fecal bacteria diversity can be significantly changed over time. Future studies should therefore use not only the microbial signature of fresh but also moderately aged fecal samples to develop more accurate community profiles for fecal source tracking.

  14. Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

    OpenAIRE

    Schwiertz, Andreas; Le Blay, Gwenaelle; Blaut, Michael

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none...

  15. Correlation between discharged worms and fecal egg counts in human clonorchiasis.

    Directory of Open Access Journals (Sweden)

    Jae-Hwan Kim

    2011-10-01

    Full Text Available BACKGROUND: Stool examination by counting eggs per gram of feces (EPGs is the best method to estimate worm burden of Clonorchis sinensis in infected humans. The present study investigated a correlation between EPGs and worm burden in human clonorchiasis. METHODS AND FINDINGS: A total of 60 residents, 50 egg-positive and 10 egg-negative, in Sancheong-gun, Korea, participated in this worm collection trial in 2006-2009. They were diagnosed by egg positivity in feces using the Kato-Katz method. After administration of praziquantel, they were purged with cathartics on the next day, and then discharged adult worms were collected from their feces. Their EPGs ranged from 0 to 65,544. Adult worms of C. sinensis were collected from 17 egg-positive cases, and the number of worms ranged from 1 to 114 in each individual. A positive correlation between EPGs and numbers of worms was demonstrated (r = 0.681, P<0.001. Worm recovery rates were 9.7% in cases of EPGs 1-1,000 and 73.7% in those of EPGs over 1,000. No worms were detected from egg-negative subjects. Maximum egg count per worm per day was roughly estimated 3,770 in a subject with EPGs 2,664 and 106 collected worms. CONCLUSIONS: The numbers of the worms are significantly correlated with the egg counts in human clonorchiasis. It is estimated that at least 110 worms are infected in a human body with EPGs around 3,000, and egg productivity of a worm per day is around 4,000.

  16. Towards the Fecal Metabolome Derived from Moderate Red Wine Intake

    Directory of Open Access Journals (Sweden)

    Ana Jiménez-Girón

    2014-12-01

    Full Text Available Dietary polyphenols, including red wine phenolic compounds, are extensively metabolized during their passage through the gastrointestinal tract; and their biological effects at the gut level (i.e., anti-inflammatory activity, microbiota modulation, interaction with cells, among others seem to be due more to their microbial-derived metabolites rather than to the original forms found in food. In an effort to improve our understanding of the biological effects that phenolic compounds exert at the gut level, this paper summarizes the changes observed in the human fecal metabolome after an intervention study consisting of a daily consumption of 250 mL of wine during four weeks by healthy volunteers (n = 33. It assembles data from two analytical approaches: (1 UPLC-ESI-MS/MS analysis of phenolic metabolites in fecal solutions (targeted analysis; and (2 UHPLC-TOF MS analysis of the fecal solutions (non-targeted analysis. Both approaches revealed statistically-significant changes in the concentration of several metabolites as a consequence of the wine intake. Similarity and complementarity between targeted and non-targeted approaches in the analysis of the fecal metabolome are discussed. Both strategies allowed the definition of a complex metabolic profile derived from wine intake. Likewise, the identification of endogenous markers could lead to new hypotheses to unravel the relationship between moderate wine consumption and the metabolic functionality of gut microbiota.

  17. Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.

    Science.gov (United States)

    Van den Abbeele, Pieter; Taminiau, Bernard; Pinheiro, Iris; Duysburgh, Cindy; Jacobs, Heidi; Pijls, Loek; Marzorati, Massimo

    2018-02-07

    Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.

  18. [Microbial "friend-foe" identification in human intestine microsymbiocenosis].

    Science.gov (United States)

    Bukharin, O V; Petrunova, N B

    2011-01-01

    Development of methodical approach of evaluation of microbial "friend-foe" identification in human intestine microsymbiocenosis. 9 bifidobacteria cultures (dominants) and 18 opportunistic microorganism strains (associants) isolated from patients during examination for intestine dysbiosis and identified by conventional methods were used. Evaluation of microbial "friend-foe" identification in microsymbiocenosis was performed by author developed technique that is based on determination of growth factors (GF), anti-lysozyme activity (ALA) and formation of biofilms (BFF) of associants co-incubated with exometabolites of dominants. GF, ALA, BFF were studied photometrically (Bukharin O.V., 1999, 2009; O'Toole G.A., 2000). The data were statistically analyzed by Fisher-Student criteria. The detected opposite (increase/reduction) phenomenon of the "dominant-associant" pair allowed realization of the "friend-foe" identification in microsymbiocenosis. Associants (E. coli and Enterococcus faecium) were "friend" species, in which bifidobacteria exometabolites did not change growth properties and stimulated ALA (by 17,5--32%) and BFF (by 25 - 39%). Associants (Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Candida albicans) were "foe" microsymbiont species, in which bifidoflora exometabolites decreased GF (by 20,7--68%), ALA (by 22,7--54%) and BFF (by 22,5 --39%). Indigenous microflora during microsymbiocenosis formation can participate in "friend-foe" identification, the basis of which is determined by microsymbiont exometabolites. The data obtained open a perspective of understanding mechanisms of intramicrobial interactions and can be used for both diagnostics and optimal selection of "candidates" during creation of new probiotics and synbiotics.

  19. A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides).

    Science.gov (United States)

    Phan, Tung G; Dreno, Brigitte; da Costa, Antonio Charlys; Li, Linlin; Orlandi, Patricia; Deng, Xutao; Kapusinszky, Beatrix; Siqueira, Juliana; Knol, Anne-Chantal; Halary, Franck; Dantal, Jacques; Alexander, Kathleen A; Pesavento, Patricia A; Delwart, Eric

    2016-09-01

    We genetically characterized seven nearly complete genomes in the protoparvovirus genus from the feces of children with diarrhea. The viruses, provisionally named cutaviruses (CutaV), varied by 1-6% nucleotides and shared ~76% and ~82% amino acid identity with the NS1 and VP1 of human bufaviruses, their closest relatives. Using PCR, cutavirus DNA was found in 1.6% (4/245) and 1% (1/100) of diarrhea samples from Brazil and Botswana respectively. In silico analysis of pre-existing metagenomics datasets then revealed closely related parvovirus genomes in skin biopsies from patients with epidermotropic cutaneous T-cell lymphoma (CTCL or mycosis fungoides). PCR of skin biopsies yielded cutavirus DNA in 4/17 CTCL, 0/10 skin carcinoma, and 0/21 normal or noncancerous skin biopsies. In situ hybridization of CTCL skin biopsies detected viral genome within rare individual cells in regions of neoplastic infiltrations. The influence of cutavirus infection on human enteric functions and possible oncolytic role in CTCL progression remain to be determined. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. A radioimmunoassay for human antibody specific for microbial antigens

    International Nuclear Information System (INIS)

    Tew, J.G.; Burmeister, J.; Greene, E.J.; Pflaumer, S.K.; Goldstein, J.

    1977-01-01

    A simple and sensitive method for detecting and quantitating antibody specific or microbial antigens is described. Bacterial, fungal, parasitic or viral antigens attached to bromoacetyl cellulose or the intact cells themselves were added to a series of two-fold dilutions of human serum. After a short incubation period, which allowed human antibody to attach to the antigens, the complex was thoroughly washed and carbon-14 labeled anti-human light chain antibody was added to each dilution. The resulting complex was washed, collected on a filter pad, placed in a scintillation vial and radioassayed. The relationship between radioactivity bound and -log 2 of the serum dilution was linear. The endpoint for each assay and a confidence interval was calculated by doing inverse prediction from simple linear regression. Results obtained using this assay indicated the presence of antibody in a pool of normal human sera specific for herpes virus and for both cell surface and intracellular antigens of Streptococcus mutans, Naegleria fowleri and Cryptococcus neoformans. In general the dominant response was against the intracellular antigens rather than cell surface antigens

  1. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

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    Federica Gigliucci

    2018-02-01

    Full Text Available The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.

  2. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

    Science.gov (United States)

    Gigliucci, Federica; von Meijenfeldt, F. A. Bastiaan; Knijn, Arnold; Michelacci, Valeria; Scavia, Gaia; Minelli, Fabio; Dutilh, Bas E.; Ahmad, Hamideh M.; Raangs, Gerwin C.; Friedrich, Alex W.; Rossen, John W. A.; Morabito, Stefano

    2018-01-01

    The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection. PMID:29468143

  3. Prospective study on human fecal carriage of Enterobacteriaceae possessing mcr-1 and mcr-2 genes in a regional hospital in Hong Kong.

    Science.gov (United States)

    Chan, Wai-Sing; Au, Chun-Hang; Ho, Dona N; Chan, Tsun-Leung; Ma, Edmond Shiu-Kwan; Tang, Bone Siu-Fai

    2018-02-13

    Human fecal carriage of Enterobacteriaceae possessing mobilized colistin resistance genes (mcr-1 and mcr-2) remains obscure in Hong Kong. As part of routine surveillance on emerging antibiotic resistance, we conducted a prospective study on this topic in a regional hospital in Hong Kong. From October 31 to November 25, 2016, all fecal specimens submitted for routine analysis were included in this surveillance study. These comprised 672 consecutive routine fecal specimens collected from 616 individuals. Fecal specimens were screened for colistin-resistant Enterobacteriaceae by culture-based method, and the presence of mcr-1 and mcr-2 genes in resistant isolates was identified by polymerase chain reaction and Sanger sequencing. Whole genome sequencing (WGS) of mcr-1-possessing Escherichia coli strains was facilitated using Illumina® MiSeq® followed by sequence analysis with appropriate bioinformatics tools. Fourteen mcr-1-positive E. coli strains were isolated from 14 separate individuals (2.08% of total fecal specimens), with 9 of them being asymptomatic, healthy clients coming for health assessment. No mcr-2-possessing Enterobacteriaceae was identified. Colistin minimum inhibitory concentrations of these mcr-1-positive isolates ranged from 2 to 4 μg/mL. All these isolates were susceptible to carbapenems with 2 being extended spectrum β-lactamase producers. WGS data revealed that these isolates belonged to at least 12 different sequence types (STs) and possessed diversified plasmid replicons, virulence and acquired antibiotic resistance genes. Further study on an E. coli ST201 strain (Pasteur scheme) revealed coexistence of 47,818-bp IncP-1 and 33,309-bp IncX4 types of mcr-1 plasmids, which was a combination of stability and high transmissibility. To the best of our knowledge, this is the first study on human fecal carriage of Enterobacteriaceae possessing mcr-1 and mcr-2 genes in Hong Kong. Our data further revealed asymptomatic carriage of mcr-1-possessing

  4. Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

    Science.gov (United States)

    2013-01-01

    Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods. PMID:23755882

  5. Molecular Detection and Identification of Zoonotic Microspor-idia Spore in Fecal Samples of Some Animals with Close-Con-tact to Human

    Directory of Open Access Journals (Sweden)

    Zeinab ASKARI

    2015-10-01

    Full Text Available Background: Microsporidia species are obligatory intracellular agents that can in­fect all major animal groups including mammals, birds, fishes and insects. Whereas world­wide human infection reports are increasing, the cognition of sources of infec­tion particularly zoonotic transmission could be helpful. We aimed to detect zoono­tic microsporidia spore in fecal samples from some animals with close – contact to human.Methods: Overall, 142 fecal samples were collected from animals with closed-con­tact to human, during 2012-2013. Trichrome – blue staining were performed and DNA was then extracted from samples, identified positive, microscopically. Nested PCR was also carried out with primers targeting SSU rRNA gene and PCR products were sequenced.Results: From 142 stool samples, microsporidia spores have been observed microscopi­cally in 15 (10.56% samples. En. cuniculi was found in the faces of 3 (15% small white mice and 1 (10% laboratory rabbits(totally 2.81%. Moreover, E. bieneusi was detected in 3 (10% samples of sheep, 2 (5.12% cattle, 1 (10% rabbit, 3 (11.53% cats and 2 (11.76% ownership dogs (totally 7.74%. Phylogenetic analysis showed interesting data. This is the first study in Iran, which identified E. bieneusi and En. Cuniculi in fecal samples of laboratory animals with close – contact to human as well as domesticated animal and analyzed them in phylogenetic tree. Conclusion: E. bieneusi is the most prevalent microsporidia species in animals. Our results can also alert us about potentially zoonotic transmission of microsporidiosis.

  6. Fecal bacteria source characterization and sensitivity analysis of SWAT 2005

    Science.gov (United States)

    The Soil and Water Assessment Tool (SWAT) version 2005 includes a microbial sub-model to simulate fecal bacteria transport at the watershed scale. The objectives of this study were to demonstrate methods to characterize fecal coliform bacteria (FCB) source loads and to assess the model sensitivity t...

  7. 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.

  8. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  9. Sequence-based Methods in Human Microbial Ecology: A The 2nd HumanGenome Comes of Age

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-06-01

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  10. The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples.

    Science.gov (United States)

    Maukonen, Johanna; Simões, Catarina; Saarela, Maria

    2012-03-01

    Recently several human health-related microbiota studies have had partly contradictory results. As some differences may be explained by methodologies applied, we evaluated how different storage conditions and commonly used DNA-extraction kits affect bacterial composition, diversity, and numbers of human fecal microbiota. According to our results, the DNA-extraction did not affect the diversity, composition, or quantity of Bacteroides spp., whereas after a week's storage at -20 °C, the numbers of Bacteroides spp. were 1.6-2.5 log units lower (P Eubacterium rectale (Erec)-group, Clostridium leptum group, bifidobacteria, and Atopobium group were 0.5-4 log units higher (P < 0.05) after mechanical DNA-extraction as detected with qPCR, regardless of storage. Furthermore, the bacterial composition of Erec-group differed significantly after different DNA-extractions; after enzymatic DNA-extraction, the most prevalent genera detected were Roseburia (39% of clones) and Coprococcus (10%), whereas after mechanical DNA-extraction, the most prevalent genera were Blautia (30%), Coprococcus (13%), and Dorea (10%). According to our results, rigorous mechanical lysis enables detection of higher bacterial numbers and diversity from human fecal samples. As it was shown that the results of clostridial and actinobacterial populations are highly dependent on the DNA-extraction methods applied, the use of different DNA-extraction protocols may explain the contradictory results previously obtained. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  11. Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers

    Science.gov (United States)

    In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

  12. Fecal microbiota transplant

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/007703.htm Fecal microbiota transplant To use the sharing features on this page, please enable JavaScript. Fecal microbiota transplantation (FMT) helps to replace some of the " ...

  13. Extended-spectrum beta-lactamase-producing bacteria are not detected in supragingival plaque samples from human fecal carriers of ESBL-producing Enterobacteriaceae

    Directory of Open Access Journals (Sweden)

    Arne Søraas

    2014-08-01

    Full Text Available Background: The prevalence of infections caused by Cefotaximase-Munich (CTX-M-type extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E has rapidly increased during the past 15 years. Enterobacteriaceae are commonly found in the gastrointestinal tract and long-term intestinal carriage is considered important for the spread of ESBL and as a source of clinical infections. Oral biofilm such as supragingival plaque is known to contain numerous antibiotic resistance determinants and may also represent a poorly investigated site for ESBL carriage and further spread. Objective: To investigate possible carriage of ESBL-producing bacteria in supragingival plaque of known fecal carriers of these bacteria. Design: We screened for the presence of aerobic and anaerobic ESBL-producing bacteria and blaCTX-M in supragingival plaque samples from healthy human adults with culture-verified fecal carriage of CTX-M-producing Escherichia coli. The presence or absence of Enterobacteriaceae and ESBL-producing bacteria in plaque samples was evaluated using culture-based methods and consensus CTX-M PCR. Results: Oral samples were obtained from 17 participants with known previous carriage of ESBL-producing E. coli. No ESBL-producing bacteria or ESBL genes were detected using culture-based and molecular methods. One colony of Rahnella aquatilis harboring the class A ESBL gene bla RAHN-1/2 was identified in an oral sample from one of the participants. Conclusion: This pilot study supports the notion that the presence of CTX-M-producing bacteria is uncommon in oral plaque of healthy human adult fecal carriers. Due to the limited number of persons tested, a low prevalence of oral ESBL-carriage in healthy adults or carriage in selected groups of patients cannot be excluded. To our knowledge, this is the first description of an R. aquatilis with the RAHN-1/2 gene in the oral cavity.

  14. Comparative fecal metagenomics unveils unique functional capacity of the swine gut

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    Martinson John

    2011-05-01

    Full Text Available Abstract Background Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results Analysis of 637, 722 pyrosequencing reads (130 megabases generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes. Other abundant proteins unique to the distal swine gut shared high sequence homology to putative carbohydrate membrane transporters. Conclusions The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices.

  15. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

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    Marcus J Claesson

    Full Text Available BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. METHODS AND FINDINGS: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400-1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. CONCLUSIONS: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genus-level with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate

  16. Lactic acid bacteria affect serum cholesterol levels, harmful fecal enzyme activity, and fecal water content.

    Science.gov (United States)

    Lee, Do Kyung; Jang, Seok; Baek, Eun Hye; Kim, Mi Jin; Lee, Kyung Soon; Shin, Hea Soon; Chung, Myung Jun; Kim, Jin Eung; Lee, Kang Oh; Ha, Nam Joo

    2009-06-11

    Lactic acid bacteria (LAB) are beneficial probiotic organisms that contribute to improved nutrition, microbial balance, and immuno-enhancement of the intestinal tract, as well as lower cholesterol. Although present in many foods, most trials have been in spreads or dairy products. Here we tested whether Bifidobacteria isolates could lower cholesterol, inhibit harmful enzyme activities, and control fecal water content. In vitro culture experiments were performed to evaluate the ability of Bifidobacterium spp. isolated from healthy Koreans (20 approximately 30 years old) to reduce cholesterol-levels in MRS broth containing polyoxyethanylcholesterol sebacate. Animal experiments were performed to investigate the effects on lowering cholesterol, inhibiting harmful enzyme activities, and controlling fecal water content. For animal studies, 0.2 ml of the selected strain cultures (108 approximately 109 CFU/ml) were orally administered to SD rats (fed a high-cholesterol diet) every day for 2 weeks. B. longum SPM1207 reduced serum total cholesterol and LDL levels significantly (p water content, and reduced body weight and harmful intestinal enzyme activities. Daily consumption of B. longum SPM1207 can help in managing mild to moderate hypercholesterolemia, with potential to improve human health by helping to prevent colon cancer and constipation.

  17. Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection.

    Science.gov (United States)

    Peer, Xavier; An, Gary

    2014-10-01

    Agent-based modeling is a computational modeling method that represents system-level behavior as arising from multiple interactions between the multiple components that make up a system. Biological systems are thus readily described using agent-based models (ABMs), as multi-cellular organisms can be viewed as populations of interacting cells, and microbial systems manifest as colonies of individual microbes. Intersections between these two domains underlie an increasing number of pathophysiological processes, and the intestinal tract represents one of the most significant locations for these inter-domain interactions, so much so that it can be considered an internal ecology of varying robustness and function. Intestinal infections represent significant disturbances of this internal ecology, and one of the most clinically relevant intestinal infections is Clostridium difficile infection (CDI). CDI is precipitated by the use of broad-spectrum antibiotics, involves the depletion of commensal microbiota, and alterations in bile acid composition in the intestinal lumen. We present an example ABM of CDI (the C. difficile Infection ABM, or CDIABM) to examine fundamental dynamics of the pathogenesis of CDI and its response to treatment with anti-CDI antibiotics and a newer treatment therapy, fecal microbial transplant. The CDIABM focuses on one specific mechanism of potential CDI suppression: commensal modulation of bile acid composition. Even given its abstraction, the CDIABM reproduces essential dynamics of CDI and its response to therapy, and identifies a paradoxical zone of behavior that provides insight into the role of intestinal nutritional status and the efficacy of anti-CDI therapies. It is hoped that this use case example of the CDIABM can demonstrate the usefulness of both agent-based modeling and the application of abstract functional representation as the biomedical community seeks to address the challenges of increasingly complex diseases with the goal of

  18. A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen

    Science.gov (United States)

    Pilotte, Nils; Baumer, Ben; Grant, Jessica; Asbjornsdottir, Kristjana; Schaer, Fabian; Hu, Yan; Aroian, Raffi; Walson, Judd; Williams, Steven A.

    2018-01-01

    Background Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. Methodology Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against “no preservative” controls and the “gold standard” of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. Conclusions At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity

  19. Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease

    Science.gov (United States)

    Wang, Zi-Kai; Yang, Yun-Sheng; Chen, Ye; Yuan, Jing; Sun, Gang; Peng, Li-Hua

    2014-01-01

    The intestinal microbiota plays an important role in inflammatory bowel disease (IBD). The pathogenesis of IBD involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. However, there are still no definitive microbial pathogens linked to the onset of IBD. The composition and function of the intestinal microbiota and their metabolites are indeed disturbed in IBD patients. The special alterations of gut microbiota associated with IBD remain to be evaluated. The microbial interactions and host-microbe immune interactions are still not clarified. Limitations of present probiotic products in IBD are mainly due to modest clinical efficacy, few available strains and no standardized administration. Fecal microbiota transplantation (FMT) may restore intestinal microbial homeostasis, and preliminary data have shown the clinical efficacy of FMT on refractory IBD or IBD combined with Clostridium difficile infection. Additionally, synthetic microbiota transplantation with the defined composition of fecal microbiota is also a promising therapeutic approach for IBD. However, FMT-related barriers, including the mechanism of restoring gut microbiota, standardized donor screening, fecal material preparation and administration, and long-term safety should be resolved. The role of intestinal microbiota and FMT in IBD should be further investigated by metagenomic and metatranscriptomic analyses combined with germ-free/human flora-associated animals and chemostat gut models. PMID:25356041

  20. Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.

    Science.gov (United States)

    van Baarlen, Peter; van Belkum, Alex; Thomma, Bart P H J

    2007-02-01

    Relatively simple eukaryotic model organisms such as the genetic model weed plant Arabidopsis thaliana possess an innate immune system that shares important similarities with its mammalian counterpart. In fact, some human pathogens infect Arabidopsis and cause overt disease with human symptomology. In such cases, decisive elements of the plant's immune system are likely to be targeted by the same microbial factors that are necessary for causing disease in humans. These similarities can be exploited to identify elementary microbial pathogenicity factors and their corresponding targets in a green host. This circumvents important cost aspects that often frustrate studies in humans or animal models and, in addition, results in facile ethical clearance.

  1. Identification and determination of the viability of Giardia lamblia cysts and Cryptosporidium parvum and Cryptosporidium hominis oocysts in human fecal and water supply samples by fluorescent in situ hybridization (FISH) and monoclonal antibodies.

    Science.gov (United States)

    Lemos, Vanessa; Graczyk, Thaddeus K; Alves, Margarida; Lobo, Maria Luísa; Sousa, Maria C; Antunes, Francisco; Matos, Olga

    2005-12-01

    In the present study, fluorescent in situ hybridization (FISH) and monoclonal antibodies (MAbs) were evaluated for species-specific detection and viability determination of Giardia lamblia, Cryptosporidium parvum, and Cryptosporidium hominis in human fecal and water supply samples. A total of 50 fecal human samples positive for G. lamblia cysts, 38 positive for C. parvum, and 23 positive for C. hominis were studied. Also, 18 water supply samples positive for Giardia spp. and Cryptosporidium spp. by the United States Environmental Protection Agency (USEPA) Method 1623 were studied by FISH and fluorescein isothiocyanate (FITC)-conjugated MAbs. Eighteen percent of the fecal samples parasitologically positive for G. lamblia presented viable and nonviable cysts, and 5% of those positive for Cryptosporidium spp. presented viable and nonviable oocysts. Of the 18 water supply samples analyzed, 6 (33%) presented Giardia spp. viable and nonviable cysts and 2 (11%) presented viable and nonviable Cryptosporidium spp. oocysts. G. lamblia identification was confirmed by polymerase chain reaction (PCR) and sequencing of the beta-giardin gene in the fecal and water samples found positive by FISH and FITC-conjugated MAbs. C. parvum and Cryptosporidium muris were identified, by PCR and sequencing of the small subunit of ribosomal RNA gene, in seven and one water samples, respectively. Our results confirm that this technique enables simultaneous visualization, species-specific identification, and viability determination of the organisms present in human fecal and water supply samples.

  2. Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.

    Science.gov (United States)

    Schwiertz, A; Le Blay, G; Blaut, M

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.

  3. A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer.

    Science.gov (United States)

    Wang, QuanQiu; Li, Li; Xu, Rong

    2018-04-18

    Colorectal cancer (CRC) is the second leading cause of cancer-related deaths. It is estimated that about half the cases of CRC occurring today are preventable. Recent studies showed that human gut microbiota and their collective metabolic outputs play important roles in CRC. However, the mechanisms by which human gut microbial metabolites interact with host genetics in contributing CRC remain largely unknown. We hypothesize that computational approaches that integrate and analyze vast amounts of publicly available biomedical data have great potential in better understanding how human gut microbial metabolites are mechanistically involved in CRC. Leveraging vast amount of publicly available data, we developed a computational algorithm to predict human gut microbial metabolites for CRC. We validated the prediction algorithm by showing that previously known CRC-associated gut microbial metabolites ranked highly (mean ranking: top 10.52%; median ranking: 6.29%; p-value: 3.85E-16). Moreover, we identified new gut microbial metabolites likely associated with CRC. Through computational analysis, we propose potential roles for tartaric acid, the top one ranked metabolite, in CRC etiology. In summary, our data-driven computation-based study generated a large amount of associations that could serve as a starting point for further experiments to refute or validate these microbial metabolite associations in CRC cancer.

  4. Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

    Science.gov (United States)

    Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

    2000-01-01

    A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

  5. Impact of microbial count distributions on human health risk estimates

    DEFF Research Database (Denmark)

    Ribeiro Duarte, Ana Sofia; Nauta, Maarten

    2015-01-01

    Quantitative microbiological risk assessment (QMRA) is influenced by the choice of the probability distribution used to describe pathogen concentrations, as this may eventually have a large effect on the distribution of doses at exposure. When fitting a probability distribution to microbial...... enumeration data, several factors may have an impact on the accuracy of that fit. Analysis of the best statistical fits of different distributions alone does not provide a clear indication of the impact in terms of risk estimates. Thus, in this study we focus on the impact of fitting microbial distributions...... on risk estimates, at two different concentration scenarios and at a range of prevalence levels. By using five different parametric distributions, we investigate whether different characteristics of a good fit are crucial for an accurate risk estimate. Among the factors studied are the importance...

  6. Application of a loop-mediated isothermal amplification (LAMP) assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples.

    Science.gov (United States)

    Rahman, S M Mazidur; Song, Hyun Beom; Jin, Yan; Oh, Jin-Kyoung; Lim, Min Kyung; Hong, Sung-Tae; Choi, Min-Ho

    2017-10-01

    Clonorchiasis is prevalent in the Far East, and a major health problem in endemic areas. Infected persons may experience, if not treated, serious complications such as bile stone formation, pyogenic cholangitis, and even cholangiocarcinoma. Early diagnosis and treatment are important to prevent serious complications and, therefore, the simple and reliable diagnostic method is necessary to control clonorchiasis in endemic areas, where resources for the diagnosis are limited. The loop-mediated isothermal amplification (LAMP) assay has been applied for the detection of Clonorchis sinensis DNA. Six primers targeting eight locations on the cytochrome c oxidase subunit 1 gene of C. sinensis were designed for species-specific amplification using the LAMP assay. The LAMP assay was sensitive enough to detect as little as 100 fg of C. sinensis genomic DNA and the detection limit in 100 mg of stool was as low as one egg. The assay was highly specific because no cross-reactivity was observed with the DNA of other helminths, protozoa or Escherichia coli. Then, LAMP assay was applied to human fecal samples collected from an endemic area of clonorchiasis in Korea. Using samples showing consistent results by both Kato-Katz method and real-time PCR as reference standards, the LAMP assay showed 97.1% (95% CI, 90.1-99.2) of sensitivity and 100% (95% CI, 92.9-100) of specificity. In stool samples with more than 100 eggs per gram of feces, the sensitivity achieved 100%. To detect C. sinensis in human fecal samples, the LAMP assay was applied and achieved high sensitivity and specificity. The LAMP assay can be utilized in field laboratories as a powerful tool for diagnosis and epidemiological survey of clonorchiasis.

  7. Application of a loop-mediated isothermal amplification (LAMP assay targeting cox1 gene for the detection of Clonorchis sinensis in human fecal samples.

    Directory of Open Access Journals (Sweden)

    S M Mazidur Rahman

    2017-10-01

    Full Text Available Clonorchiasis is prevalent in the Far East, and a major health problem in endemic areas. Infected persons may experience, if not treated, serious complications such as bile stone formation, pyogenic cholangitis, and even cholangiocarcinoma. Early diagnosis and treatment are important to prevent serious complications and, therefore, the simple and reliable diagnostic method is necessary to control clonorchiasis in endemic areas, where resources for the diagnosis are limited.The loop-mediated isothermal amplification (LAMP assay has been applied for the detection of Clonorchis sinensis DNA. Six primers targeting eight locations on the cytochrome c oxidase subunit 1 gene of C. sinensis were designed for species-specific amplification using the LAMP assay. The LAMP assay was sensitive enough to detect as little as 100 fg of C. sinensis genomic DNA and the detection limit in 100 mg of stool was as low as one egg. The assay was highly specific because no cross-reactivity was observed with the DNA of other helminths, protozoa or Escherichia coli. Then, LAMP assay was applied to human fecal samples collected from an endemic area of clonorchiasis in Korea. Using samples showing consistent results by both Kato-Katz method and real-time PCR as reference standards, the LAMP assay showed 97.1% (95% CI, 90.1-99.2 of sensitivity and 100% (95% CI, 92.9-100 of specificity. In stool samples with more than 100 eggs per gram of feces, the sensitivity achieved 100%.To detect C. sinensis in human fecal samples, the LAMP assay was applied and achieved high sensitivity and specificity. The LAMP assay can be utilized in field laboratories as a powerful tool for diagnosis and epidemiological survey of clonorchiasis.

  8. Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

    Directory of Open Access Journals (Sweden)

    Isabelle Laforest-Lapointe

    2017-07-01

    Full Text Available Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease.

  9. Antibody against Microbial Neuraminidases Recognizes Human Sialidase 3 (NEU3: the Neuraminidase/Sialidase Superfamily Revisited

    Directory of Open Access Journals (Sweden)

    Chiguang Feng

    2017-06-01

    Full Text Available Neuraminidases (NAs are critical virulence factors for several microbial pathogens. With a highly conserved catalytic domain, a microbial NA “superfamily” has been proposed. We previously reported that murine polymorphonuclear leukocyte (PMN sialidase activity was important in leukocyte trafficking to inflamed sites and that antibodies to Clostridium perfringens NA recognized a cell surface molecule(s, presumed to be a sialidase of eukaryotic origin on interleukin-8-stimulated human and murine PMNs. These antibodies also inhibited cell sialidase activity both in vitro and, in the latter instance, in vivo. We therefore hypothesized that mammalian sialidases share structural homology and epitopes with microbial NAs. We now report that antibodies to one of the isoforms of C. perfringens NA, as well as anti-influenza virus NA serum, recognize human NEU3 but not NEU1 and that antibodies to C. perfringens NA inhibit NEU3 enzymatic activity. We conclude that the previously described microbial NA superfamily extends to human sialidases. Strategies designed to therapeutically inhibit microbial NA may need to consider potential compromising effects on human sialidases, particularly those expressed in cells of the immune system.

  10. Understanding and Modulating Mammalian-Microbial Communication for Improved Human Health

    OpenAIRE

    Mani, Sridhar; Boelsterli, Urs A.; Redinbo, Matthew R.

    2013-01-01

    The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. De...

  11. Retrospective Species Identification of Microsporidian Spores in Diarrheic Fecal Samples from Human Immunodeficiency Virus/AIDS Patients by Multiplexed Fluorescence In Situ Hybridization▿

    Science.gov (United States)

    Graczyk, Thaddeus K.; Johansson, Michael A.; Tamang, Leena; Visvesvara, Govinda S.; Moura, Laci S.; DaSilva, Alexandre J.; Girouard, Autumn S.; Matos, Olga

    2007-01-01

    In order to assess the applicability of multiplexed fluorescence in situ hybridization (FISH) assay for the clinical setting, we conducted retrospective analysis of 110 formalin-stored diarrheic stool samples from human immunodeficiency virus (HIV)/AIDS patients with intestinal microsporidiosis collected between 1992 and 2003. The multiplexed FISH assay identified microsporidian spores in 94 of 110 (85.5%) samples: 49 (52.1%) were positive for Enterocytozoon bieneusi, 43 (45.8%) were positive for Encephalitozoon intestinalis, 2 (2.1%) were positive for Encephalitozoon hellem, and 9 samples (9.6%) contained both E. bieneusi and E. intestinalis spores. Quantitative spore counts per ml of stool yielded concentration values from 3.5 × 103 to 4.4 × 105 for E. bieneusi (mean, 8.8 × 104/ml), 2.3 × 102 to 7.8 × 104 (mean, 1.5 × 104/ml) for E. intestinalis, and 1.8 × 102 to 3.6 × 102 for E. hellem (mean, 2.7 × 102/ml). Identification of microsporidian spores by multiplex FISH assay was more sensitive than both Chromotrope-2R and CalcoFluor White M2R stains; 85.5% versus 72.7 and 70.9%, respectively. The study demonstrated that microsporidian coinfection in HIV/AIDS patients with intestinal microsporidiosis is not uncommon and that formalin-stored fecal samples older than 10 years may not be suitable for retrospective analysis by techniques targeting rRNA. Multiplexed FISH assay is a reliable, quantitative fluorescence microscopy method for the simultaneous identification of E. bieneusi, E. intestinalis, and E. hellem, as well as Encephalitozoon cuniculi, spores in fecal samples and is a useful tool for assessing spore shedding intensity in intestinal microsporidiosis. The method can be used for epidemiological investigations and applied in clinical settings. PMID:17287331

  12. Microbial DNA fingerprinting of human fingerprints: dynamic colonization of fingertip microflora challenges human host inferences for forensic purposes.

    Science.gov (United States)

    Tims, Sebastian; van Wamel, Willem; Endtz, Hubert P; van Belkum, Alex; Kayser, Manfred

    2010-09-01

    Human fingertip microflora is transferred to touched objects and may provide forensically relevant information on individual hosts, such as on geographic origins, if endogenous microbial skin species/strains would be retrievable from physical fingerprints and would carry geographically restricted DNA diversity. We tested the suitability of physical fingerprints for revealing human host information, with geographic inference as example, via microbial DNA fingerprinting. We showed that the transient exogenous fingertip microflora is frequently different from the resident endogenous bacteria of the same individuals. In only 54% of the experiments, the DNA analysis of the transient fingertip microflora allowed the detection of defined, but often not the major, elements of the resident microflora. Although we found microbial persistency in certain individuals, time-wise variation of transient and resident microflora within individuals was also observed when resampling fingerprints after 3 weeks. While microbial species differed considerably in their frequency spectrum between fingerprint samples from volunteers in Europe and southern Asia, there was no clear geographic distinction between Staphylococcus strains in a cluster analysis, although bacterial genotypes did not overlap between both continental regions. Our results, though limited in quantity, clearly demonstrate that the dynamic fingerprint microflora challenges human host inferences for forensic purposes including geographic ones. Overall, our results suggest that human fingerprint microflora is too dynamic to allow for forensic marker developments for retrieving human information.

  13. Valorization of Brewer's spent grain to prebiotic oligosaccharide: Production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model.

    Science.gov (United States)

    Sajib, Mursalin; Falck, Peter; Sardari, Roya R R; Mathew, Sindhu; Grey, Carl; Karlsson, Eva Nordberg; Adlercreutz, Patrick

    2018-02-20

    Brewer's spent grain (BSG) accounts for around 85% of the solid by-products from beer production. BSG was first extracted to obtain water-soluble arabinoxylan (AX). Using subsequent alkali extraction (0.5 M KOH) it was possible to dissolve additional AX. In total, about 57% of the AX in BSG was extracted with the purity of 45-55%. After comparison of nine xylanases, Pentopan mono BG, a GH11 enzyme, was selected for hydrolysis of the extracts to oligosaccharides with minimal formation of monosaccharides. Growth of Bifidobacterium adolescentis (ATCC 15703) was promoted by the enzymatic hydrolysis to arabinoxylooligosaccharides, while Lactobacillus brevis (DSMZ 1264) utilized only unsubstituted xylooligosaccharides. Furthermore, utilization of the hydrolysates by human gut microbiota was also assessed in a batch human fecal fermentation model. Results revealed that the rates of fermentation of the BSG hydrolysates by human gut microbiota were similar to that of commercial prebiotic fructooligosaccharides, while inulin was fermented at a slower rate. In summary, a sustainable process to valorize BSG to functional food ingredients has been proposed. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Identification of fecal contamination sources in water using host-associated markers.

    Science.gov (United States)

    Krentz, Corinne A; Prystajecky, Natalie; Isaac-Renton, Judith

    2013-03-01

    In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.

  15. Microbial Eco-Physiology of the human intestinal tract: a flow cytometric approach

    NARCIS (Netherlands)

    Amor, Ben K.

    2004-01-01

    This thesis describes a multifaceted approach to further enhance our view of the complex human intestinal microbial ecosystem. This approach combines me advantages of flow cyrometry (FCM), a single cell and high-throughput technology, and molecular techniques that have proven themselves to be

  16. Microbial DNA fingerprinting of human fingerprints: dynamic colonization of fingertip microflora challenges human host inferences for forensic purposes

    NARCIS (Netherlands)

    S. Tims (Sebastian); W.J.B. van Wamel (Willem); H.P. Endtz (Hubert); A.F. van Belkum (Alex); M.H. Kayser (Manfred)

    2009-01-01

    textabstractHuman fingertip microflora is transferred to touched objects and may provide forensically relevant information on individual hosts, such as on geographic origins, if endogenous microbial skin species/strains would be retrievable from physical fingerprints and would carry geographically

  17. Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment.

    Science.gov (United States)

    Hsu, Tiffany; Joice, Regina; Vallarino, Jose; Abu-Ali, Galeb; Hartmann, Erica M; Shafquat, Afrah; DuLong, Casey; Baranowski, Catherine; Gevers, Dirk; Green, Jessica L; Morgan, Xochitl C; Spengler, John D; Huttenhower, Curtis

    2016-01-01

    Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium , Corynebacterium , Staphylococcus , and Streptococcus . The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa . Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we

  18. Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

    OpenAIRE

    Hasan, Nur A.; Young, Brian A.; Minard-Smith, Angela T.; Saeed, Kelly; Li, Huai; Heizer, Esley M.; McMillan, Nancy J.; Isom, Richard; Abdullah, Abdul Shakur; Bornman, Daniel M.; Faith, Seth A.; Choi, Seon Young; Dickens, Michael L.; Cebula, Thomas A.; Colwell, Rita R.

    2014-01-01

    Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify ba...

  19. Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes

    Science.gov (United States)

    Oliveira, Ryan D.; Mousel, Michelle R.; Pabilonia, Kristy L.; Highland, Margaret A.; Taylor, J. Bret; Knowles, Donald P.

    2017-01-01

    Coxiella burnetii is a globally distributed zoonotic bacterial pathogen that causes abortions in ruminant livestock. In humans, an influenza-like illness results with the potential for hospitalization, chronic infection, abortion, and fatal endocarditis. Ruminant livestock, particularly small ruminants, are hypothesized to be the primary transmission source to humans. A recent Netherlands outbreak from 2007–2010 traced to dairy goats resulted in over 4,100 human cases with estimated costs of more than 300 million euros. Smaller human Q fever outbreaks of small ruminant origin have occurred in the United States, and characterizing shedding is important to understand the risk of future outbreaks. In this study, we assessed bacterial shedding and seroprevalence in 100 sheep from an Idaho location associated with a 1984 human Q fever outbreak. We observed 5% seropositivity, which was not significantly different from the national average of 2.7% for the U.S. (P>0.05). Furthermore, C. burnetii was not detected by quantitative PCR from placentas, vaginal swabs, or fecal samples. Specifically, a three-target quantitative PCR of placenta identified 0.0% shedding (exact 95% confidence interval: 0.0%-2.9%). While presence of seropositive individuals demonstrates some historical C. burnetii exposure, the placental sample confidence interval suggests 2016 shedding events were rare or absent. The location maintained the flock with little or no depopulation in 1984 and without C. burnetii vaccination during or since 1984. It is not clear how a zero-shedding rate was achieved in these sheep beyond natural immunity, and more work is required to discover and assess possible factors that may contribute towards achieving zero-shedding status. We provide the first U.S. sheep placental C. burnetii shedding update in over 60 years and demonstrate potential for C. burnetii shedding to reach undetectable levels after an outbreak event even in the absence of targeted interventions, such

  20. Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes.

    Directory of Open Access Journals (Sweden)

    Ryan D Oliveira

    Full Text Available Coxiella burnetii is a globally distributed zoonotic bacterial pathogen that causes abortions in ruminant livestock. In humans, an influenza-like illness results with the potential for hospitalization, chronic infection, abortion, and fatal endocarditis. Ruminant livestock, particularly small ruminants, are hypothesized to be the primary transmission source to humans. A recent Netherlands outbreak from 2007-2010 traced to dairy goats resulted in over 4,100 human cases with estimated costs of more than 300 million euros. Smaller human Q fever outbreaks of small ruminant origin have occurred in the United States, and characterizing shedding is important to understand the risk of future outbreaks. In this study, we assessed bacterial shedding and seroprevalence in 100 sheep from an Idaho location associated with a 1984 human Q fever outbreak. We observed 5% seropositivity, which was not significantly different from the national average of 2.7% for the U.S. (P>0.05. Furthermore, C. burnetii was not detected by quantitative PCR from placentas, vaginal swabs, or fecal samples. Specifically, a three-target quantitative PCR of placenta identified 0.0% shedding (exact 95% confidence interval: 0.0%-2.9%. While presence of seropositive individuals demonstrates some historical C. burnetii exposure, the placental sample confidence interval suggests 2016 shedding events were rare or absent. The location maintained the flock with little or no depopulation in 1984 and without C. burnetii vaccination during or since 1984. It is not clear how a zero-shedding rate was achieved in these sheep beyond natural immunity, and more work is required to discover and assess possible factors that may contribute towards achieving zero-shedding status. We provide the first U.S. sheep placental C. burnetii shedding update in over 60 years and demonstrate potential for C. burnetii shedding to reach undetectable levels after an outbreak event even in the absence of targeted

  1. Fecal microbiota transplantation in metabolic syndrome: History, present and future.

    Science.gov (United States)

    de Groot, P F; Frissen, M N; de Clercq, N C; Nieuwdorp, M

    2017-05-04

    The history of fecal microbiota transplantation (FMT) dates back even to ancient China. Recently, scientific studies have been looking into FMT as a promising treatment of various diseases, while in the process teaching us about the interaction between the human host and its resident microbial communities. Current research focuses mainly on Clostridium difficile infections, however interest is rising in other areas such as inflammatory bowel disease (IBD) and the metabolic syndrome. With regard to the latter, the intestinal microbiota might be causally related to the progression of insulin resistance and diabetes. FMT in metabolic syndrome has proven to be an intriguing method to study the role of the gut microbiota and open the way to new therapies by dissecting in whom insulin resistance is driven by microbiota. In this article we review the history of FMT, the present evidence on its role in the pathophysiology of metabolic syndrome and its efficacy, limitations and future prospects.

  2. Automated Annotation of Microbial and Human Flavonoid-Derived Metabolites

    NARCIS (Netherlands)

    Mihaleva, V.V.; Ünlü, F.; Vervoort, J.J.M.; Ridder, L.O.

    2015-01-01

    Flavonoids are a class of natural compounds essentially produced by plants that are part of animal and human diets and have assumed health-promoting benefits. Upon human consumption, these flavonoids are to a modest extent absorbed in the small intestines. The major part arrives in the colon where

  3. The Low-Diversity Fecal Microbiota of the Critically Endangered Kākāpō Is Robust to Anthropogenic Dietary and Geographic Influences

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    Elena K. Perry

    2017-10-01

    Full Text Available The critically endangered kākāpō, an herbivorous parrot endemic to New Zealand, is subject to intensive management to increase its population size. Key aspects of the management program include supplementary feeding and translocation of kākāpō between different predator-free islands to optimize the genetic composition of the breeding populations. While these practices have helped boost the kākāpō population, their impact on the kākāpō fecal microbiota is uncertain. Previous studies have found that the kākāpō possesses a low-diversity fecal microbiota, typically dominated by Escherichia/Shigella spp. However, the question of whether the low diversity of the kākāpō fecal microbiota is an inadvertent consequence of human interventions has yet to be investigated. To that end, we used high-throughput Illumina sequencing of 16S rRNA gene amplicons obtained from fecal material of 63 kākāpō representing different diets, islands, and ages. Remarkably, neither supplementary feeding nor geographic location were associated with significant differences in the overall fecal microbial community structures of adult kākāpō, suggesting that the kākāpō's low-diversity fecal microbiota is both inherent to this species and robust to these external influences.

  4. Search for microbial signatures within human and microbial calcifications using soft x-ray spectromicroscopy.

    Science.gov (United States)

    Benzerara, Karim; Miller, Virginia M; Barell, Gerard; Kumar, Vivek; Miot, Jennyfer; Brown, Gordon E; Lieske, John C

    2006-11-01

    The origin of advanced arterial and renal calcification remains poorly understood. Self-replicating, calcifying entities have been detected and isolated from calcified human tissues, including blood vessels and kidney stones, and are referred to as nanobacteria. However, the microbiologic nature of putative nanobacteria continues to be debated, in part because of the difficulty in discriminating biomineralized microbes from minerals nucleated on anything else (eg, macromolecules, cell membranes). To address this controversy, the use of techniques capable of characterizing the organic and mineral content of these self-replicated structures at the submicrometer scale would be beneficial. Calcifying gram-negative bacteria (Caulobacter crescentus, Ramlibacter tataouinensis) used as references and self-replicating calcified nanoparticles cultured from human samples of calcified aneurysms were examined using a scanning transmission x-ray microscope (STXM) at the Advanced Light Source at Lawrence Berkeley National Laboratory. This microscope uses a monochromated and focused synchrotron x-ray beam (80-2,200 eV) to yield microscopic and spectroscopic information on both organic compounds and minerals at the 25 nm scale. High-spatial and energy resolution near-edge x-ray absorption fine structure (NEXAFS) spectra indicative of elemental speciation acquired at the C K-edge, N K-edge, and Ca L(2,3)-edge on a single-cell scale from calcified C. crescentus and R. tataouinensis displayed unique spectral signatures different from that of nonbiologic hydroxyapatite (Ca(10)(PO(4))(6)(OH)(2)). Further, preliminary NEXAFS measurements of calcium, carbon, and nitrogen functional groups of cultured calcified nanoparticles from humans revealed evidence of organics, likely peptides or proteins, specifically associated with hydroxyapatite minerals. Using NEXAFS at the 25 nm spatial scale, it is possible to define a biochemical signature for cultured calcified bacteria, including proteins

  5. REVIEW OF INTERNATIONAL PROJECTS IN А FIELD OF HUMAN MICROBIAL ECOLOGY AND CONSTRUCTION OF PROBIOTICS

    Directory of Open Access Journals (Sweden)

    S. A. Starovoitova

    2013-06-01

    Full Text Available Modern huge and world-wide known projects concerning studying of human microbial ecology and construction of probiotics, particularly: Society for Microbial Ecology and Disease, Probiotics & Health Targeted Initiative of International Science and Technology Center (TI PROBIO ISTC, Human Microbiome Project of National Institutes of Health, MetaHIT Project (Metagenomics of the Human Intestinal Tract of European Commission, Human Metabolome Project of Canadian University of Alberta and some more else were characterized in the article. Brief historical information and reference to official sites of every discussed project were given. Main goals and tasks of every project were described. Short characteristic of discussed projects and also modern accessible results of researches were given. Importance of every examined project for widening scientific knowledge in the field of human microbial ecology and also for improvement and/or for construction of modern effective probiotics on basis of human normal intestinal microflora were paid attention. Close interaction of scientific data received by realization of every discussed project was shown.

  6. Characterization of the human predominant fecal microbiota - With special focus on the Clostridial clusters IV and XIVa

    OpenAIRE

    Maukonen, Johanna

    2012-01-01

    The human gut microbiota is considered to be a complex fermentor with a metabolic potential rivaling that of the liver. In addition to its primary function in digestion, it affects the human host in numerous ways: maturation and modulation of the immune system, production of short-chain fatty acids and gases, transformation of bile acids, formation of vitamins, and also potential formation of mutagenic, toxic, and carcinogenic substances. Commensal bacteria are able to modulate the expression...

  7. Microbial dynamics during production of lesser mealworms (Alphitobius diaperinus) for human consumption at industrial scale.

    Science.gov (United States)

    Wynants, E; Crauwels, S; Verreth, C; Gianotten, N; Lievens, B; Claes, J; Van Campenhout, L

    2018-04-01

    In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Microbial community profiling of human saliva using shotgun metagenomic sequencing.

    Directory of Open Access Journals (Sweden)

    Nur A Hasan

    Full Text Available Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

  9. Meta genome-wide network from functional linkages of genes in human gut microbial ecosystems.

    Science.gov (United States)

    Ji, Yan; Shi, Yixiang; Wang, Chuan; Dai, Jianliang; Li, Yixue

    2013-03-01

    The human gut microbial ecosystem (HGME) exerts an important influence on the human health. In recent researches, meta-genomics provided deep insights into the HGME in terms of gene contents, metabolic processes and genome constitutions of meta-genome. Here we present a novel methodology to investigate the HGME on the basis of a set of functionally coupled genes regardless of their genome origins when considering the co-evolution properties of genes. By analyzing these coupled genes, we showed some basic properties of HGME significantly associated with each other, and further constructed a protein interaction map of human gut meta-genome to discover some functional modules that may relate with essential metabolic processes. Compared with other studies, our method provides a new idea to extract basic function elements from meta-genome systems and investigate complex microbial environment by associating its biological traits with co-evolutionary fingerprints encoded in it.

  10. Microbe Profile: Mycobacterium tuberculosis: Humanity's deadly microbial foe.

    Science.gov (United States)

    Gordon, Stephen V; Parish, Tanya

    2018-04-01

    Mycobacterium tuberculosis is an expert and deadly pathogen, causing the disease tuberculosis (TB) in humans. It has several notable features: the ability to enter non-replicating states for long periods and cause latent infection; metabolic remodelling during chronic infection; a thick, waxy cell wall; slow growth rate in culture; and intrinsic drug resistance and antibiotic tolerance. As a pathogen, M. tuberculosis has a complex relationship with its host, is able to replicate inside macrophages, and expresses diverse immunomodulatory molecules. M. tuberculosis currently causes over 1.8 million deaths a year, making it the world's most deadly human pathogen.

  11. The first microbial colonizers of the human gut

    NARCIS (Netherlands)

    Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Palacio, Susana Delgado; Montes, Silvia Arboleya; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; Vos, De Willem; Gueimonde, Miguel; Margolles, Abelardo; Sinderen, Van Douwe; Ventura, Marco

    2017-01-01

    The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially)

  12. Human gut microbiome viewed across age and geography

    Science.gov (United States)

    Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, we characterized bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy child...

  13. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

    Science.gov (United States)

    Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

    2015-01-01

    The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

  14. MOLECULAR EVALUATION OF CHANGES IN PLANKTONIC BACTERIAL POPULATION RESULTING FROM EQUINE FECAL CONTAMINATION IN A SUB-WATERSHED

    Science.gov (United States)

    Contamination of watersheds by fecal bacteria is a frequent cause for surface waters to be placed on the national impaired waters list. However, since the presence of fecal bacteria does not always indicate human fecal input, it is necessary to distinguish between fecal sources. ...

  15. Appraisal of Microbial Evolution to Commensalism and Pathogenicity in Humans

    Directory of Open Access Journals (Sweden)

    Asit Ranjan Ghosh

    2013-01-01

    Full Text Available The human body is host to a number of microbes occurring in various forms of host-microbe associations, such as commensals, mutualists, pathogens and opportunistic symbionts. While this association with microbes in certain cases is beneficial to the host, in many other cases it seems to offer no evident benefit or motive. The emergence and re-emergence of newer varieties of infectious diseases with causative agents being strains that were once living in the human system makes it necessary to study the environment and the dynamics under which this host microbe relationship thrives. The present discussion examines this interaction while tracing the origins of this association, and attempts to hypothesize a possible framework of selective pressures that could have lead microbes to inhabit mammalian host systems.

  16. Theoretical and Numerical Modeling of Transport of Land Use-Specific Fecal Source Identifiers

    Science.gov (United States)

    Bombardelli, F. A.; Sirikanchana, K. J.; Bae, S.; Wuertz, S.

    2008-12-01

    Microbial contamination in coastal and estuarine waters is of particular concern to public health officials. In this work, we advocate that well-formulated and developed mathematical and numerical transport models can be combined with modern molecular techniques in order to predict continuous concentrations of microbial indicators under diverse scenarios of interest, and that they can help in source identification of fecal pollution. As a proof of concept, we present initially the theory, numerical implementation and validation of one- and two-dimensional numerical models aimed at computing the distribution of fecal source identifiers in water bodies (based on Bacteroidales marker DNA sequences) coming from different land uses such as wildlife, livestock, humans, dogs or cats. These models have been developed to allow for source identification of fecal contamination in large bodies of water. We test the model predictions using diverse velocity fields and boundary conditions. Then, we present some preliminary results of an application of a three-dimensional water quality model to address the source of fecal contamination in the San Pablo Bay (SPB), United States, which constitutes an important sub-embayment of the San Francisco Bay. The transport equations for Bacteroidales include the processes of advection, diffusion, and decay of Bacteroidales. We discuss the validation of the developed models through comparisons of numerical results with field campaigns developed in the SPB. We determine the extent and importance of the contamination in the bay for two decay rates obtained from field observations, corresponding to total host-specific Bacteroidales DNA and host-specific viable Bacteroidales cells, respectively. Finally, we infer transport conditions in the SPB based on the numerical results, characterizing the fate of outflows coming from the Napa, Petaluma and Sonoma rivers.

  17. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.

    Science.gov (United States)

    Xiong, Weili; Abraham, Paul E; Li, Zhou; Pan, Chongle; Hettich, Robert L

    2015-10-01

    The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Multiplex quantification of 16S rDNA of predominant bacteria group within human fecal samples by polymerase chain reaction--ligase detection reaction (PCR-LDR).

    Science.gov (United States)

    Li, Kai; Chen, Bei; Zhou, Yuxun; Huang, Rui; Liang, Yinming; Wang, Qinxi; Xiao, Zhenxian; Xiao, Junhua

    2009-03-01

    A new method, based on ligase detection reaction (LDR), was developed for quantitative detection of multiplex PCR amplicons of 16S rRNA genes present in complex mixtures (specifically feces). LDR has been widely used in single nucleotide polymorphism (SNP) assay but never applied for quantification of multiplex PCR products. This method employs one pair of DNA probes, one of which is labeled with fluorescence for signal capture, complementary to the target sequence. For multiple target sequence analysis, probes were modified with different lengths of polyT at the 5' end and 3' end. Using a DNA sequencer, these ligated probes were separated and identified by size and dye color. Then, relative abundance of target DNA were normalized and quantified based on the fluorescence intensities and exterior size standards. 16S rRNA gene of three preponderant bacteria groups in human feces: Clostridium coccoides, Bacteroides and related genera, and Clostridium leptum group, were amplified and cloned into plasmid DNA so as to make standard curves. After PCR-LDR analysis, a strong linear relationship was found between the florescence intensity and the diluted plasmid DNA concentrations. Furthermore, based on this method, 100 human fecal samples were quantified for the relative abundance of the three bacterial groups. Relative abundance of C. coccoides was significantly higher in elderly people in comparison with young adults, without gender differences. Relative abundance of Bacteroides and related genera and C. leptum group were significantly higher in young and middle aged than in the elderly. Regarding the whole set of sample, C. coccoides showed the highest relative abundance, followed by decreasing groups Bacteroides and related genera, and C. leptum. These results imply that PCR-LDR can be feasible and flexible applied to large scale epidemiological studies.

  19. Lactic acid bacteria affect serum cholesterol levels, harmful fecal enzyme activity, and fecal water content

    OpenAIRE

    Chung Myung; Shin Hea; Lee Kyung; Kim Mi; Baek Eun; Jang Seok; Lee Do; Kim Jin; Lee Kang; Ha Nam

    2009-01-01

    Abstract Background Lactic acid bacteria (LAB) are beneficial probiotic organisms that contribute to improved nutrition, microbial balance, and immuno-enhancement of the intestinal tract, as well as lower cholesterol. Although present in many foods, most trials have been in spreads or dairy products. Here we tested whether Bifidobacteria isolates could lower cholesterol, inhibit harmful enzyme activities, and control fecal water content. Methods In vitro culture experiments were performed to ...

  20. Durable coexistence of donor and recipient strains after fecal microbiota transplantation

    NARCIS (Netherlands)

    Li, Simone S.; Zhu, Ana; Benes, Vladimir; Costea, Paul I.; Hercog, Rajna; Hildebrand, Falk; Huerta-Cepas, Jaime; Nieuwdorp, Max; Salojärvi, Jarkko; Voigt, Anita Y.; Zeller, Georg; Sunagawa, Shinichi; de Vos, Willem M.; Bork, Peer

    2016-01-01

    Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor

  1. The Impact of Human Activities on Microbial Quality of Rivers in the Vhembe District, South Africa

    Directory of Open Access Journals (Sweden)

    Afsatou N. Traoré

    2016-08-01

    Full Text Available Background: Water quality testing is dictated by microbial agents found at the time of sampling in reference to their acceptable risk levels. Human activities might contaminate valuable water resources and add to the microbial load present in water bodies. Therefore, the effects of human activities on the microbial quality of rivers collected from twelve catchments in the Vhembe District in South Africa were investigated, with samples analyzed for total coliform (TC and Eschericha coli (E. coli contents. Methods: Physical parameters and various human activities were recorded for each sampling site. The Quanti-Tray® method was adopted for the assessment of TC and E. coli contents in the rivers over a two-year period. A multiplex polymerase chain (PCR method was used to characterize the strains of E. coli found. Results: The microbial quality of the rivers was poor with both TC and E. coli contents found to be over acceptable limits set by the South African Department of Water and Sanitation (DWS. No significant difference (p > 0.05 was detected between TC and E. coli risks in dry and wet seasons. All six pathogenic E. coli strains were identified and Enteroaggregative E. coli (EAEC, atypical Enteropathogenic E. coli (a-EPEC and Enterotoxigenic E. coli (ETEC were the most prevalent E. coli strains detected (respectively, 87%, 86% and 83%. Conclusions: The study indicated that contamination in the majority of sampling sites, due to human activities such as car wash, animal grazing and farming, poses health risks to communities using the rivers for various domestic chores. It is therefore recommended that more education by the respective departments is done to avert pollution of rivers and prevent health risks to the communities in the Vhembe District.

  2. Nucleic acid probes in the diagnosis of human microbial pathogens

    International Nuclear Information System (INIS)

    Hyypia, T.; Huovinen, P.; Holmberg, M.; Pettersson, U.

    1989-01-01

    The development of effective vaccines and antimicrobial drugs against infectious diseases has been among the most successful achievements in modern medicine. The control of these diseases requires efficient diagnostic methods for the evaluation of the prevalence of diseases and for initiation of specific treatment. Virtually all known microbes can be specifically identified today but in many cases further development is needed for more accurate, rapid, easy-to-use, and inexpensive diagnostic assays. Cell culture facilities are needed for the isolation of viruses in clinical specimens. Any gene of any known microorganism can be cloned in a vector and produced in large amounts economically and then used in diagnostic assays for the identification of the pathogen. The application of the nucleic acid hybridization methods in detection of human pathogens has received considerable attention during the past few years. This paper presents examples of this application of gene technology

  3. Profiles of microbial fatty acids in the human metabolome are disease-specific

    Directory of Open Access Journals (Sweden)

    Zhanna A Ktsoyan

    2011-01-01

    Full Text Available The human gastrointestinal tract is inhabited by a diverse and dense symbiotic microbiota, the composition of which is the result of host-microbe co-evolution and co-adaptation. This tight integration creates intense crosstalk and signalling between the host and microbiota at the cellular and metabolic levels. In many genetic or infectious diseases the balance between host and microbiota may be compromised resulting in erroneous communication. Consequently, the composition of the human metabolome, which includes the gut metabolome, may be different in health and disease states in terms of microbial products and metabolites entering systemic circulation. To test this hypothesis, we measured the level of hydroxy, branched, cyclopropyl and unsaturated fatty acids, aldehydes, and phenyl derivatives in blood of patients with a hereditary autoinflammatory disorder, familial Mediterranean fever (FMF, and in patients with peptic ulceration (PU resulting from Helicobacter pylori infection. Discriminant function analysis of a data matrix consisting of 94 cases as statistical units (37 FMF patients, 14 PU patients, and 43 healthy controls and the concentration of 35 microbial products in the blood as statistical variables revealed a high accuracy of the proposed model (all cases were correctly classified. This suggests that the profile of microbial products and metabolites in the human metabolome is specific for a given disease and may potentially serve as a biomarker for disease.

  4. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine

    NARCIS (Netherlands)

    Claesson, M.J.; O'Sullivan, O.; Wang, Q.; Nikkilä, J.; Marchesi, J.R.; Smidt, H.; Vos, de W.M.; Ross, R.P.; O'Toole, P.W.

    2009-01-01

    BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such

  5. Antibiotic, Pesticide, and Microbial Contaminants of Honey: Human Health Hazards

    Directory of Open Access Journals (Sweden)

    Noori Al-Waili

    2012-01-01

    Full Text Available Agricultural contamination with pesticides and antibiotics is a challenging problem that needs to be fully addressed. Bee products, such as honey, are widely consumed as food and medicine and their contamination may carry serious health hazards. Honey and other bee products are polluted by pesticides, heavy metals, bacteria and radioactive materials. Pesticide residues cause genetic mutations and cellular degradation and presence of antibiotics might increase resistant human or animal's pathogens. Many cases of infant botulisms have been attributed to contaminated honey. Honey may be very toxic when produced from certain plants. Ingestion of honey without knowing its source and safety might be problematic. Honey should be labeled to explore its origin, composition, and clear statement that it is free from contaminants. Honey that is not subjected for analysis and sterilization should not be used in infants, and should not be applied to wounds or used for medicinal purposes. This article reviews the extent and health impact of honey contamination and stresses on the introduction of a strict monitoring system and validation of acceptable minimal concentrations of pollutants or identifying maximum residue limits for bee products, in particular, honey.

  6. 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

  7. Relationships among bather density, levels of human waterborne pathogens, and fecal coliform counts in marine recreational beach water.

    Science.gov (United States)

    Graczyk, Thaddeus K; Sunderland, Deirdre; Awantang, Grace N; Mashinski, Yessika; Lucy, Frances E; Graczyk, Zofi; Chomicz, Lidia; Breysse, Patrick N

    2010-04-01

    During summer months, samples of marine beach water were tested weekly for human waterborne pathogens in association with high and low bather numbers during weekends and weekdays, respectively. The numbers of bathers on weekends were significantly higher than on weekdays (P turbidity. The proportion of water samples containing Cryptosporidium parvum, Giardia duodenalis, and Enterocytozoon bieneusi was significantly higher (P marine beach water; (c) water should be tested for enterococci during times when bather numbers are high; (d) re-suspension of bottom sediments by bathers caused elevated levels of enterococci and waterborne parasites, thus bathers themselves can create a non-point source for water contamination; and (e) exposure to recreational bathing waters can play a role in epidemiology of microsporidiosis. In order to protect public health, it is recommended to: (a) prevent diapered children from entering beach water; (b) introduce bather number limits to recreational areas; (c) advise people with gastroenteritis to avoid bathing; and (d) use showers prior to and after bathing.

  8. Current and future trends in fecal source tracking and deployment in the Lake Taihu Region of China

    Science.gov (United States)

    Hagedorn, Charles; Liang, Xinqiang

    The emerging discipline of microbial and/or chemical source tracking (collectively termed fecal source tracking (FST)) is being used to identify origins of fecal contamination in polluted waters in many countries around the world. FST has developed rapidly because standard methods of measuring contamination in water by enumerating fecal indicator bacteria (FIB) such as fecal coliforms and enterococci do not identify the sources of the contamination. FST is an active area of research and development in both the academic and private sectors and includes: Developing and testing new microbial and chemical FST methods. Determining the geographic application and animal host ranges of existing and emerging FST techniques. Conducting experimental comparisons of FST techniques. Combining direct monitoring of human pathogens associated with waterborne outbreaks and zoonotic pathogens responsible for infections among people, wildlife, or domesticated animals with the use of FST techniques. Applying FST to watershed analysis and coastal environments. Designing appropriate statistical and probability analysis of FST data and developing models for mass loadings of host-specific fecal contamination. This paper includes a critical review of FST with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), which methods are applicable to different situations, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper addresses the broader question of whether FST and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many FST methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the “real” answer is not known, so their comparative performance and accuracy cannot be assessed. For FST to be

  9. Moisture content during extrusion of oats impacts the initial fermentation metabolites and probiotic bacteria during extended fermentation by human fecal microbiota.

    Science.gov (United States)

    Brahma, Sandrayee; Weier, Steven A; Rose, Devin J

    2017-07-01

    Extrusion exposes flour components to high pressure and shear during processing, which may affect the dietary fiber fermentability by human fecal microbiota. The objective of this study was to determine the effect of flour moisture content during extrusion on in vitro fermentation properties of whole grain oats. Extrudates were processed at three moisture levels (15%, 18%, and 21%) at fixed screw speed (300rpm) and temperature (130°C). The extrudates were then subjected to in vitro digestion and fermentation. Extrusion moisture significantly affected water-extractable β-glucan (WE-BG) in the extrudates, with samples processed at 15% moisture (lowest) and 21% moisture (highest) having the highest concentration of WE-BG. After the first 8h of fermentation, more WE-BG remained in fermentation media in samples processed at 15% moisture compared with the other conditions. Also, extrusion moisture significantly affected the production of acetate, butyrate, and total SCFA by the microbiota during the first 8h of fermentation. Microbiota grown on extrudates processed at 18% moisture had the highest production of acetate and total SCFA, whereas bacteria grown on extrudates processed at 15% and 18% moisture had the highest butyrate production. After 24h of fermentation, samples processed at 15% moisture supported lower Bifidobacterium counts than those produced at other conditions, but had among the highest Lactobacillus counts. Thus, moisture content during extrusion significantly affects production of fermentation metabolites by the gut microbiota during the initial stages of fermentation, while also affecting probiotic bacteria counts during extended fermentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area.

    Science.gov (United States)

    Sinigalliano, C D; Gidley, M L; Shibata, T; Whitman, D; Dixon, T H; Laws, E; Hou, A; Bachoon, D; Brand, L; Amaral-Zettler, L; Gast, R J; Steward, G F; Nigro, O D; Fujioka, R; Betancourt, W Q; Vithanage, G; Mathews, J; Fleming, L E; Solo-Gabriele, H M

    2007-05-22

    Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes. Vibrio and Legionella species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; no evidence of a long-term hurricane-induced algal bloom was observed. Giardia and Cryptosporidium were detected in canal waters. Elevated levels of fecal indicator bacteria observed in sediment could not be solely attributed to impacts from floodwaters, as both flooded and nonflooded areas exhibited elevated levels of fecal indicator bacteria. Evidence from measurements of Bifidobacterium and bacterial diversity analysis suggest that the fecal indicator bacteria observed in the sediment were from human fecal sources. Epidemiologic studies are highly recommended to evaluate the human health effects of the sediments deposited by the floodwaters.

  11. Microbial Degradation of Forensic Samples of Biological Origin: Potential Threat to Human DNA Typing.

    Science.gov (United States)

    Dash, Hirak Ranjan; Das, Surajit

    2018-02-01

    Forensic biology is a sub-discipline of biological science with an amalgam of other branches of science used in the criminal justice system. Any nucleated cell/tissue harbouring DNA, either live or dead, can be used as forensic exhibits, a source of investigation through DNA typing. These biological materials of human origin are rich source of proteins, carbohydrates, lipids, trace elements as well as water and, thus, provide a virtuous milieu for the growth of microbes. The obstinate microbial growth augments the degradation process and is amplified with the passage of time and improper storage of the biological materials. Degradation of these biological materials carriages a huge challenge in the downstream processes of forensic DNA typing technique, such as short tandem repeats (STR) DNA typing. Microbial degradation yields improper or no PCR amplification, heterozygous peak imbalance, DNA contamination from non-human sources, degradation of DNA by microbial by-products, etc. Consequently, the most precise STR DNA typing technique is nullified and definite opinion can be hardly given with degraded forensic exhibits. Thus, suitable precautionary measures should be taken for proper storage and processing of the biological exhibits to minimize their decaying process by micro-organisms.

  12. Influence of Novel Highly Pathogenic Avian Influenza A (H5N1 Virus Infection on Migrating Whooper Swans Fecal Microbiota

    Directory of Open Access Journals (Sweden)

    Na Zhao

    2018-02-01

    Full Text Available The migration of wild birds plays an important role in the transmission and spread of H5 highly pathogenic avian influenza (HPAI virus, posing a severe risk to animal and human health. Substantial evidence suggests that altered gut microbial community is implicated in the infection of respiratory influenza virus. However, the influence of H5N1 infection in gut microbiota of migratory birds remains unknown. In January 2015, a novel recombinant H5N1 virus emerged and killed about 100 migratory birds, mainly including whooper swans in Sanmenxia Reservoir Area of China. Here, we describe the first fecal microbiome diversity study of H5N1-infected migratory birds. By investigating the influence of H5N1 infection on fecal bacterial communities in infected and uninfected individuals, we found that H5N1 infection shaped the gut microbiota composition by a difference in the dominance of some genera, such as Aeromonas and Lactobacillus. We also found a decreased α diversity and increased β diversity in infectious individuals. Our results highlight that increases in changes in pathogen-containing gut communities occur when individuals become infected with H5N1. Our study may provide the first evidence that there are statistical association among H5N1 presence and fecal microbiota compositional shifts, and properties of the fecal microbiota may serve as the risk of gut-linked disease in migrates with H5N1 and further aggravate the disease transmission.

  13. Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota.

    Science.gov (United States)

    Zhao, Na; Wang, Supen; Li, Hongyi; Liu, Shelan; Li, Meng; Luo, Jing; Su, Wen; He, Hongxuan

    2018-01-01

    The migration of wild birds plays an important role in the transmission and spread of H5 highly pathogenic avian influenza (HPAI) virus, posing a severe risk to animal and human health. Substantial evidence suggests that altered gut microbial community is implicated in the infection of respiratory influenza virus. However, the influence of H5N1 infection in gut microbiota of migratory birds remains unknown. In January 2015, a novel recombinant H5N1 virus emerged and killed about 100 migratory birds, mainly including whooper swans in Sanmenxia Reservoir Area of China. Here, we describe the first fecal microbiome diversity study of H5N1-infected migratory birds. By investigating the influence of H5N1 infection on fecal bacterial communities in infected and uninfected individuals, we found that H5N1 infection shaped the gut microbiota composition by a difference in the dominance of some genera, such as Aeromonas and Lactobacillus . We also found a decreased α diversity and increased β diversity in infectious individuals. Our results highlight that increases in changes in pathogen-containing gut communities occur when individuals become infected with H5N1. Our study may provide the first evidence that there are statistical association among H5N1 presence and fecal microbiota compositional shifts, and properties of the fecal microbiota may serve as the risk of gut-linked disease in migrates with H5N1 and further aggravate the disease transmission.

  14. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats.

    Science.gov (United States)

    Vientós-Plotts, Aida I; Ericsson, Aaron C; Rindt, Hansjorg; Grobman, Megan E; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A; Reinero, Carol R

    2017-01-01

    Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial

  15. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats

    Science.gov (United States)

    Rindt, Hansjorg; Grobman, Megan E.; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A.; Reinero, Carol R.

    2017-01-01

    Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial

  16. The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

    Directory of Open Access Journals (Sweden)

    Shoshanit eOhad

    2016-02-01

    Full Text Available The emerging Microbial Source Tracking (MST methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes High Throughput Sequencing (HTS to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU analysis was then performed, from which sequences were retained for downstream qPCR marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae and other bacteria. Two assays (Av4143 and Av163 identified most of the avian fecal samples and demonstrated sensitivity values of 91% and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216 identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

  17. Fecal Transplants: What Is Being Transferred?

    Directory of Open Access Journals (Sweden)

    Diana P Bojanova

    2016-07-01

    Full Text Available Fecal transplants are increasingly utilized for treatment of recurrent infections (i.e., Clostridium difficile in the human gut and as a general research tool for gain-of-function experiments (i.e., gavage of fecal pellets in animal models. Changes observed in the recipient's biology are routinely attributed to bacterial cells in the donor feces (~1011 per gram of human wet stool. Here, we examine the literature and summarize findings on the composition of fecal matter in order to raise cautiously the profile of its multipart nature. In addition to viable bacteria, which may make up a small fraction of total fecal matter, other components in unprocessed human feces include colonocytes (~107 per gram of wet stool, archaea (~108 per gram of wet stool, viruses (~108 per gram of wet stool, fungi (~106 per gram of wet stool, protists, and metabolites. Thus, while speculative at this point and contingent on the transplant procedure and study system, nonbacterial matter could contribute to changes in the recipient's biology. There is a cautious need for continued reductionism to separate out the effects and interactions of each component.

  18. The human microbiota: the role of microbial communities in health and disease

    Directory of Open Access Journals (Sweden)

    Luz Elena Botero Palacio

    2016-01-01

    Full Text Available During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. The microbiota varies with age, with features that depend on the body site, host lifestyle and health status. The challenge is therefore to identify and characterize these microbial communities and use this information to learn how they function and how they can influence the host in terms of health and well-being. Here we provide an overview of some of the recent studies involving the human microbiota and about how these communities might affect host health and disease. A special emphasis is given to studies related to tuberculosis, a disease that claims over one million lives each year worldwide and still represents a challenge for control in many countries, including Colombia.

  19. Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa).

    Science.gov (United States)

    Huang, Qianqian; Holman, Devin B; Alexander, Trevor; Hu, Tianming; Jin, Long; Xu, Zhongjun; McAllister, Tim A; Acharya, Surya; Zhao, Guoqi; Wang, Yuxi

    2018-01-01

    The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing. Regardless of diet, the bacterial community was dominated by Firmicutes and Bacteroidetes with many sequences unclassified at the genus level. Forage type and CT had no effect on the fecal microbial composition at the phylum level or on α-diversity. Compared to the Alf diet, the Mix diet reduced the relative abundance of Akkermansia (P = 0.03) and Asteroleplasma (P = 0.05). Fecal microbial populations in Alf and Mix-P clustered separately from each other when assessed using unweighted UniFrac (P < 0.05). These results indicate that PPC CT up to 36 g/kg DM in the diet had no major effect on fecal microbial flora at the phyla level and exerted only minor effects on the genera composition of fecal microbiota in lambs.

  20. Molecular characterization of bacteriophages for microbial source tracking in Korea.

    Science.gov (United States)

    Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo

    2009-11-01

    We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

  1. Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

    Science.gov (United States)

    Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

    2017-05-01

    Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

  2. [Tracing the Fecal Contamination Sources Based on Bacteroides 16S rRNA PCR- DGGE in Karst Groundwater: Taking Laolongdong Underground River System, Nanshan, Chongqing as an Example].

    Science.gov (United States)

    Zhang, Hong; Jiang, Yong-jun; Zhang, Yuan-zhu; Duan, Yi-fan; Lü, Xian-fu; He, Qiu-fang

    2016-05-15

    Microbial contamination in karst groundwater continually increases and tracing the source researches has become a hot topic for international researchers. In this study, Laolongdong underground river at Nanshan, Chongqing was chosen as an example to adopt filter membrane methods to monitor the fecal microbial contaminations including the total bacterial concentration (TB), the total E. coli concentration (TE), the total fecal coliform (FC) and the total fecal Streptocoocci (FS). Bacteriodes was used as an indicator and PCR-DGGE analysis was used to trace fecal contamination sources in karst groundwater. The results suggested that groundwater in this area was seriously polluted by microbes from feces. The concentrations of microbial parameters exceeded limited levels greatly and the total bacterial amounts ranged 10-2.9 x 10⁷ CFU · mL⁻¹, the concentrations of E. coli were between 4.3-4.0 x 10⁵ CFU · mL⁻¹, the max concentration of FC was 1.1 x 10⁶ CFU · (100 mL)⁻¹ and the max concentration of FS was 1.1 x 10⁵ CFU · (100 mL)⁻¹. The FC/FS ratios were mostly over 2 which suggested that the main fecal source in groundwater was human feces. In addition, PCR-DGGE contrastive analysis of Bacteroides communities showed that the similarities between groundwater samples and human feces were in range of 7. 1% -69. 1% , and the similarity of the groundwater sample from Laolongdong underground river outlet was 69.1% . Bacteroides community similarities between groundwater samples and swine feces were in range of 1.1%-53.4%, and the similarity of Laolongdong underground river outlet was merely 1.5%. The similarity data implied that groundwater contamination resulted mainly from human feces, swine feces contamination composed part of animals' fecal contamination, and other animals' feces participated too. Furthermore, sequencing results of PCR-DGGE products revealed that most Bacteroides in groundwater originated from human intestinal tract and human feces.

  3. Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River.

    Science.gov (United States)

    Sun, Haohao; He, Xiwei; Ye, Lin; Zhang, Xu-Xiang; Wu, Bing; Ren, Hongqiang

    2017-03-01

    The fecal bacteria in natural waters may pose serious risks on human health. Although many source tracking methods have been developed and used to determine the possible sources of the fecal pollution, little is known about the overall diversity and abundance of fecal bacterial community in natural waters. In this study, a method based on fecal bacterial sequence library was introduced to evaluate the fecal bacterial profile in the Yangtze River (Nanjing section). Our results suggested that the Yangtze River water harbors diverse fecal bacteria. Fifty-eight fecal operational taxonomic units (97% identity level) were detected in the Yangtze River water samples and the relative abundance of fecal bacteria in these samples ranged from 0.1 to 8%. It was also found that the relative abundances of the fecal bacteria in locations near to the downstream of wastewater treatment plants were obviously higher than those in other locations. However, the high abundance of fecal bacteria could decrease to the normal level in 2~4 km in the river due to degradation or dilution, and the overall fecal bacteria level changed little when the Yangtze River flew through the Nanjing City. Moreover, the fecal bacteria in the Yangtze River water were found to be highly associated (Spearman rho = 0.804, P Yangtze River and advance our understandings of the fecal bacteria community in the natural waters.

  4. Sewage Reflects the Microbiomes of Human Populations

    Science.gov (United States)

    Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

    2015-01-01

    ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

  5. Microbial communities associated with human decomposition and their potential use as postmortem clocks.

    Science.gov (United States)

    Finley, Sheree J; Benbow, M Eric; Javan, Gulnaz T

    2015-05-01

    Most forensic research that is used to better understand how to estimate the postmortem interval (PMI) entails the study of the physiochemical characteristics of decomposition and the effects that environmental factors have on the decomposition process. Forensic entomology exploits the life cycles of arthropods like Diptera (blow flies or flesh flies) and Coleoptera (beetles) deposited on the decaying carcass to determine PMI. Forensic taphonomy, from the Greek word taphos meaning burial, studies the creation of the fossils of decomposed cadavers to ascertain information as to the nature and time of death. Compared to other areas of taphonomy, there have been relatively few forensic science studies that have investigated the impact of human decomposition on the microbial changes occurring on or in a corpse or in the soil communities underneath a body. Such research may facilitate the critical determination of PMI. Therefore, the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.

  6. Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

    NARCIS (Netherlands)

    Rajilic-Stojanovic, M.; Maathuis, A.; Heilig, G.H.J.; Venema, K.; Vos, de W.M.; Smidt, H.

    2010-01-01

    A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large

  7. Rainfall-induced fecal indicator organisms transport from animal waste applied fields: model sensitivity analysis

    Science.gov (United States)

    The microbial quality of surface waters warrants attention because of associated food- and waterborne-disease outbreaks, and fecal indicator organisms (FIOs) are commonly used to evaluate levels of microbial pollution. Models that predict the fate and transport of FIOs are required for designing and...

  8. Effects of the photodynamic therapy on microbial reduction of diabetic ulcers in humans

    Science.gov (United States)

    Carrinho Aureliano, Patrícia Michelassi; Andreani, Dora Inés. Kozusny; Morete, Vislaine de Aguiar; Iseri Giraldeli, Shizumi; Baptista, Alessandra; Navarro, Ricardo Scarparo; Villaverde, Antonio Balbin

    2018-02-01

    Diabetes Mellitus is a chronic disease that can lead to lower-limb ulceration. The photodynamic therapy (PDT) is based on light interaction with a photosensitizer capable to promote bacterial death and tissue repair acceleration. This study analyzed the effects of PDT in the repair of human diabetic ulcers, by means of microbiological assessment. The clinical study was composed of 12 patients of both sexes with diabetic ulcers in lower limbs that were divided into two groups, control group (n=6) and PDT group (n=6). All patients were treated with collagenase/chloramphenicol during the experimental period, in which 6 of them have received PDT with methylene blue dye (0.01%) associated with laser therapy (660 nm), dose of 6 J/cm2¨ and 30 mW laser power. PDT group received ten treatment sessions. Wounds were evaluated for micro-organisms analysis. It was found a reduction in the occurrence of Staphylococcus aureus in both groups, being that reduction more pronounced in the PDT group. Microbial count was performed on PDT group, showing a statistical difference reduction (p<0.05) when compared before and after the treatment. It is concluded that PDT seems to be effective in microbial reduction of human diabetic wounds, promoting acceleration and improvement of tissue repair quality.ty.

  9. Estimating true human and animal host source contribution in quantitative microbial source tracking using the Monte Carlo method.

    Science.gov (United States)

    Wang, Dan; Silkie, Sarah S; Nelson, Kara L; Wuertz, Stefan

    2010-09-01

    Cultivation- and library-independent, quantitative PCR-based methods have become the method of choice in microbial source tracking. However, these qPCR assays are not 100% specific and sensitive for the target sequence in their respective hosts' genome. The factors that can lead to false positive and false negative information in qPCR results are well defined. It is highly desirable to have a way of removing such false information to estimate the true concentration of host-specific genetic markers and help guide the interpretation of environmental monitoring studies. Here we propose a statistical model based on the Law of Total Probability to predict the true concentration of these markers. The distributions of the probabilities of obtaining false information are estimated from representative fecal samples of known origin. Measurement error is derived from the sample precision error of replicated qPCR reactions. Then, the Monte Carlo method is applied to sample from these distributions of probabilities and measurement error. The set of equations given by the Law of Total Probability allows one to calculate the distribution of true concentrations, from which their expected value, confidence interval and other statistical characteristics can be easily evaluated. The output distributions of predicted true concentrations can then be used as input to watershed-wide total maximum daily load determinations, quantitative microbial risk assessment and other environmental models. This model was validated by both statistical simulations and real world samples. It was able to correct the intrinsic false information associated with qPCR assays and output the distribution of true concentrations of Bacteroidales for each animal host group. Model performance was strongly affected by the precision error. It could perform reliably and precisely when the standard deviation of the precision error was small (≤ 0.1). Further improvement on the precision of sample processing and q

  10. Incontinencia fecal del adulto

    OpenAIRE

    Vergara A,M. Teresa; Suárez M,Juan; Orellana G,Hernán; Cofré L,Pamela; Germain P,Fernando; Stanley E,William; Sivori H,Javiera; Cruz M,Cecilia

    2011-01-01

    El propósito de esta revisión es actualizar los conocimientos sobre esta patología, destacando su evolución clínica, estudio y tratamiento, aspectos que ameritan un enfoque multidisciplinario, ya que, además de su compleja fisiopatología, puede asociarse a incontinencia urinaria y prolapso de los tres compartimentos de la pelvis. La incontinencia fecal (IF) constituye una patología altamente prevalente que afecta al menos un 2% de la población y hasta el 45% de los pacientes en casas de repos...

  11. Denitrification on internal carbon sources in RAS is limited by fibers in fecal waste of rainbow trout

    NARCIS (Netherlands)

    Meriac, A.; Eding, E.H.; Kamstra, A.; Busscher, J.P.; Schrama, J.W.; Verreth, J.A.J.

    2014-01-01

    Denitrification on internal carbon sources offers the advantage to control nitrate levels in recirculating aquaculture systems (RAS) by using the fecal carbon produced within the husbandry system. However, it is not clear to which extent fecal carbon can be utilized by the microbial community within

  12. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

    Science.gov (United States)

    Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

    2018-01-01

    The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

  13. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

    Directory of Open Access Journals (Sweden)

    Melissa R. Ingala

    2018-05-01

    Full Text Available The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

  14. Fecal Microbiota-based Therapeutics for Recurrent Clostridium difficile Infection, Ulcerative Colitis and Obesity

    Directory of Open Access Journals (Sweden)

    Christian Carlucci

    2016-11-01

    Full Text Available The human gut microbiome is a complex ecosystem of fundamental importance to human health. Our increased understanding of gut microbial composition and functional interactions in health and disease states has spurred research efforts examining the gut microbiome as a valuable target for therapeutic intervention. This review provides updated insight into the state of the gut microbiome in recurrent Clostridium difficile infection (CDI, ulcerative colitis (UC, and obesity while addressing the rationale for the modulation of the gut microbiome using fecal microbiota transplant (FMT-based therapies. Current microbiome-based therapeutics in pre-clinical or clinical development are discussed. We end by putting this within the context of the current regulatory framework surrounding FMT and related therapies.

  15. Can QMRA be used to Discount Pathogen Risk to Swimmers from Animal Fecal Contamination? Doheny Beach, CA Case Study

    Science.gov (United States)

    Estimated health risks to swimmers from seagull and bather sources of fecal contamination at Doheny Beach, California were compared using quantitative microbial risk assessment (QMRA) with a view to aiding beach closure decisions. Surfzone pathogens from seagulls were thought to...

  16. Genetic characterization of fecal impacts of seagull migration on an urban scenery lake.

    Science.gov (United States)

    Wu, Baolei; Wang, Xiaochang C; Dzakpasu, Mawuli

    2017-06-15

    A microbial source tracking scheme was devised to differentiate fecal impacts of seagulls from that of human activities on an urban scenery lake in southern China, which is a major wintering ground for the black-headed seagull. Fecal contamination of seagulls was characterized by quantifying a novel genetic marker targeting Catellicoccus marimamalium. Quantification of this marker was combined with those of Escherichia coli, human-associated Bacteroidales, thermophilic Campylobacter and Helicobacter. Findings of a year-round study indicate that C. marimamalium levels correlated strongly, both spatially and temporally, with seagull migration. A steady increase in C. marimammalium concentrations was recorded between October 2014 and March 2015, which peaked at about 5-log copies/100 mL in January. However, a background level of about 2.1-log copies/100 mL was noticeable from April through September when seagulls were absent, probably due to other host sources or secondary habitats for C. marimammalium. Seagull migration also caused an apparent elevation of E. coli concentrations (86% and 60%, respectively for qPCR and culture method; p seagull-absent season, indicating a limited influence of human activities, compared with seagull migration, on the seasonal variations in microbial water quality of the lake. The elevated levels of FIB, Campylobacter and Helicobacter along with C. marimammalium may imply human health risk of the lake water due to seasonal seagull migration, which requires further investigation for risk assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Quantitative Microbial Risk Assessment in Occupational Settings Applied to the Airborne Human Adenovirus Infection

    Directory of Open Access Journals (Sweden)

    Annalaura Carducci

    2016-07-01

    Full Text Available Quantitative Microbial Risk Assessment (QMRA methodology, which has already been applied to drinking water and food safety, may also be applied to risk assessment and management at the workplace. The present study developed a preliminary QMRA model to assess microbial risk that is associated with inhaling bioaerosols that are contaminated with human adenovirus (HAdV. This model has been applied to air contamination data from different occupational settings, including wastewater systems, solid waste landfills, and toilets in healthcare settings and offices, with different exposure times. Virological monitoring showed the presence of HAdVs in all the evaluated settings, thus confirming that HAdV is widespread, but with different average concentrations of the virus. The QMRA results, based on these concentrations, showed that toilets had the highest probability of viral infection, followed by wastewater treatment plants and municipal solid waste landfills. Our QMRA approach in occupational settings is novel, and certain caveats should be considered. Nonetheless, we believe it is worthy of further discussions and investigations.

  18. Epitopes of microbial and human heat shock protein 60 and their recognition in myalgic encephalomyelitis.

    Directory of Open Access Journals (Sweden)

    Amal Elfaitouri

    Full Text Available Myalgic encephalomyelitis (ME, also called Chronic Fatigue Syndrome, a common disease with chronic fatigability, cognitive dysfunction and myalgia of unknown etiology, often starts with an infection. The chaperonin human heat shock protein 60 (HSP60 occurs in mitochondria and in bacteria, is highly conserved, antigenic and a major autoantigen. The anti-HSP60 humoral (IgG and IgM immune response was studied in 69 ME patients and 76 blood donors (BD (the Training set with recombinant human and E coli HSP60, and 136 30-mer overlapping and targeted peptides from HSP60 of humans, Chlamydia, Mycoplasma and 26 other species in a multiplex suspension array. Peptides from HSP60 helix I had a chaperonin-like activity, but these and other HSP60 peptides also bound IgG and IgM with an ME preference, theoretically indicating a competition between HSP60 function and antibody binding. A HSP60-based panel of 25 antigens was selected. When evaluated with 61 other ME and 399 non-ME samples (331 BD, 20 Multiple Sclerosis and 48 Systemic Lupus Erythematosus patients, a peptide from Chlamydia pneumoniae HSP60 detected IgM in 15 of 61 (24% of ME, and in 1 of 399 non-ME at a high cutoff (p<0.0001. IgM to specific cross-reactive epitopes of human and microbial HSP60 occurs in a subset of ME, compatible with infection-induced autoimmunity.

  19. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine.

    Science.gov (United States)

    Louis, Petra; Flint, Harry J

    2009-05-01

    Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

  20. Pathophysiology of pediatric fecal incontinence

    NARCIS (Netherlands)

    Di Lorenzo, Carlo; Benninga, Marc A.

    2004-01-01

    This article addresses the diagnosis and treatment of pediatric fecal incontinence in 4 main categories: (1) Functional fecal retention, the withholding of feces because of fear of painful defecation, results in constipation and overflow soiling. Treatment includes dietary changes, use of laxatives,

  1. Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

    Science.gov (United States)

    Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

    2017-12-01

    New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

  2. Microbial hitchhikers on marine plastic debris: Human exposure risks at bathing waters and beach environments.

    Science.gov (United States)

    Keswani, Anisha; Oliver, David M; Gutierrez, Tony; Quilliam, Richard S

    2016-07-01

    Marine plastic debris is well characterized in terms of its ability to negatively impact terrestrial and marine environments, endanger coastal wildlife, and interfere with navigation, tourism and commercial fisheries. However, the impacts of potentially harmful microorganisms and pathogens colonising plastic litter are not well understood. The hard surface of plastics provides an ideal environment for opportunistic microbial colonisers to form biofilms and might offer a protective niche capable of supporting a diversity of different microorganisms, known as the "Plastisphere". This biotope could act as an important vector for the persistence and spread of pathogens, faecal indicator organisms (FIOs) and harmful algal bloom species (HABs) across beach and bathing environments. This review will focus on the existent knowledge and research gaps, and identify the possible consequences of plastic-associated microbes on human health, the spread of infectious diseases and bathing water quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. A Customized DNA Microarray for Microbial Source Tracking ...

    Science.gov (United States)

    It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance i

  4. Using ATP-driven bioluminescence assay to monitor microbial safety in a contemporary human cadaver laboratory.

    Science.gov (United States)

    Benninger, Brion; Maier, Thomas

    2015-03-01

    The objective of this study was to utilize a cost-effective method for assessing the levels of bacterial, yeast, and mold activity during a human dissection laboratory course. Nowadays, compliance with safety regulations is policed by institutions at higher standards than ever before. Fear of acquiring an unknown infection is one of the top concerns of professional healthcare students, and it provokes anti-laboratory anxiety. Human cadavers are not routinely tested for bacteria and viruses prior to embalming. Human anatomy dissecting rooms that house embalmed cadavers are normally cleaned after the dissected cadavers have been removed. There is no evidence that investigators have ever assessed bacterial and fungal activities using adenosine triphosphate (ATP)-driven bioluminescence assays. A literature search was conducted on texts, journals, and websites regarding bacterial, yeast, and mold activities in an active cadaver laboratory. Midway into a clinical anatomy course, ATP bioluminescence assays were used to swab various sites within the dissection room, including entrance and exiting door handles, water taps, cadaver tables, counter tops, imaging material, X-ray box switches, and the cadaver surfaces. The results demonstrated very low activities on cadaver tables, washing up areas, and exiting door handles. There was low activity on counter tops and X-ray boxes. There was medium activity on the entrance door handles. These findings suggest an inexpensive and accurate method for monitoring safety compliance and microbial activity. Students can feel confident and safe in the environment in which they work. © 2014 Wiley Periodicals, Inc.

  5. Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk.

    Science.gov (United States)

    Williams, Janet E; Price, William J; Shafii, Bahman; Yahvah, Katherine M; Bode, Lars; McGuire, Mark A; McGuire, Michelle K

    2017-08-01

    Human milk provides all essential nutrients necessary for early life and is rich in nonnutrients, maternally derived (host) cells, and bacteria, but almost nothing is known about the interplay among these components. Research aim: The primary objective of this research was to characterize relationships among macronutrients, maternal cells, and bacteria in milk. Milk samples were collected from 16 women and analyzed for protein, lipid, fatty acid, lactose, and human milk oligosaccharide concentrations. Concentrations of maternal cells were determined using microscopy, and somatic cell counts were enumerated. Microbial ecologies were characterized using culture-independent methods. Absolute and relative concentrations of maternal cells were mostly consistent within each woman as were relative abundances of bacterial genera, and there were many apparent relationships between these factors. For instance, relative abundance of Serratia was negatively associated with somatic cell counts ( r = -.47, p < .0001) and neutrophil concentration ( r = -.38, p < .0006). Concentrations of several oligosaccharides were correlated with maternally derived cell types as well as somatic cell counts; for example, lacto-N-tetraose and lacto-N-neotetraose were inversely correlated with somatic cell counts ( r = -.64, p = .0082; r = -.52, p = .0387, respectively), and relative abundance of Staphylococcus was positively associated with total oligosaccharide concentration ( r = .69, p = .0034). Complex relationships between milk nutrients and bacterial community profile, maternal cells, and milk oligosaccharides were also apparent. These data support the possibility that profiles of maternally derived cells, nutrient concentrations, and the microbiome of human milk might be interrelated.

  6. Inspection of fecal contamination on strawberries using fluorescence imaging

    Science.gov (United States)

    Chuang, Yung-Kun; Yang, Chun-Chieh; Kim, Moon S.; Delwiche, Stephen R.; Lo, Y. Martin; Chen, Suming; Chan, Diane E.

    2013-05-01

    Fecal contamination of produce is a food safety issue associated with pathogens such as Escherichia coli that can easily pollute agricultural products via animal and human fecal matters. Outbreaks of foodborne illnesses associated with consuming raw fruits and vegetables have occurred more frequently in recent years in the United States. Among fruits, strawberry is one high-potential vector of fecal contamination and foodborne illnesses since the fruit is often consumed raw and with minimal processing. In the present study, line-scan LED-induced fluorescence imaging techniques were applied for inspection of fecal material on strawberries, and the spectral characteristics and specific wavebands of strawberries were determined by detection algorithms. The results would improve the safety and quality of produce consumed by the public.

  7. Characterizing relationships among fecal indicator bacteria ...

    Science.gov (United States)

    Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

  8. The fecal microbiome of ALS patients.

    Science.gov (United States)

    Brenner, David; Hiergeist, Andreas; Adis, Carolin; Mayer, Benjamin; Gessner, André; Ludolph, Albert C; Weishaupt, Jochen H

    2018-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative motor neuron disease accompanied by both systemic and central nervous system-specific inflammation as well as deregulated energy metabolism. These potential pathogenetic factors have recently been found to mutually interact with the gut microbiota, raising the hypothesis of a link between microbiome alterations and ALS pathogenesis. The aim of our study was to assess whether ALS is associated with an altered composition of the fecal microbiota. We compared the fecal microbiota of 25 ALS patients with 32 age- and gender-matched healthy persons using 16S rRNA gene sequencing analysis. Confounding factors and secondary disease effects on the microbiome were minimized by selection of patients without dysphagia, gastrostomy, noninvasive ventilation, or reduced body mass index. Comparing the 2 carefully matched groups, the diversity and the abundance of the bacterial taxa on the different taxonomic levels as well as PICRUSt-predicted metagenomes were almost indistinguishable. Significant differences between ALS patients and healthy controls were only observed with regard to the overall number of microbial species (operational taxonomic units) and in the abundance of uncultured Ruminococcaceae. Conclusively, ALS patients do not exhibit a substantial alteration of the gut microbiota composition. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Microbial water quality of coastal recreational water in the Gaza Strip, Palestine

    Directory of Open Access Journals (Sweden)

    MAZEN T. ABUALTAYEF

    2014-05-01

    Full Text Available Abualtayef MT, Abd Rabou AN, Abu Foul AA, Ghabayen SM, Elsinwar HM. 2014. Microbial water quality of coastal recreational water in the Gaza Strip, Palestine. Nusantara Bioscience 6: 26-32. Wastewater disposal into the Mediterranean coast of the Gaza Strip has many negative effects, whether on the environment or on human health, thus microbiological analysis of seawater samples was carried out. The microbial analysis was confined on two types of fecal indicators (fecal coliform and fecal streptococci, in addition to a single type of bacteria (pseudomonas. This study was conducted between the beginning of July 2012 to the mid of October 2012 over an area extended from the proposed Khan Younis fishing port to Gaza fishing port, with a length of about 23 km. The study area was divided into five zones. The samples were collected in two rounds: the first round included 75 samples that collected along the study area during the summer season. The second round included 19 samples that collected in the autumn season to compare it with their counterparts that have been collected in the summer season. Laboratory analysis showed the presence of contamination in many of these samples. The results also showed that the pollution was concentrated in and surrounding the mouths of wastewater outfalls. Depending on the microbial analyses, which have been collected in the first round, the fecal coliform appeared in 61% of the samples, while fecal streptococci appeared in all samples and pseudomonas appeared in 33% of the samples. The pollutants were widespread along the study area, which are the result mainly from wastewater discharge into the sea. A risk analysis was done for season variations using the second moment method; in general, it was found that risk in both seasons was high especially in summer.

  10. TLR-dependent human mucosal epithelial cell responses to microbial pathogens.

    Directory of Open Access Journals (Sweden)

    Paola eMassari

    2014-08-01

    Full Text Available AbstractToll-Like Receptor (TLR signaling represents one of the best studied pathways to implement defense mechanisms against invading microbes in humans as well as in animals. TLRs respond to specific microbial ligands and to danger signals produced by the host during infection, and initiate downstream cascades that activate both innate and adaptive immunity. TLRs are expressed by professional immune cells and by the large majority of non-hematopoietic cells, including epithelial cells. In epithelial tissues, TLR functions are particularly important because these sites are constantly exposed to microorganisms, due to their location at the host interface with the environment. While at these sites, specific defense mechanisms and inflammatory responses are initiated via TLR signaling against pathogens, suppression or lack of TLR activation is also observed in response to the commensal microbiota. The mechanisms by which TLR signaling is regulated in mucosal epithelial cells include differential expression and levels of TLRs (and their signaling partners, their cellular localization and positioning within the tissue in a fashion that favors responses to pathogens while dampening responses to commensals and maintaining tissue homeostasis in physiologic conditions. In this review, the expression and activation of TLRs in mucosal epithelial cells of several sites of the human body are examined. Specifically, the oral cavity, the ear canal and eye, the airways, the gut and the reproductive tract are discussed, along with how site-specific host defense mechanisms are implemented via TLR signaling.

  11. Diversity of key players in the microbial ecosystems of the human body.

    Science.gov (United States)

    Jordán, Ferenc; Lauria, Mario; Scotti, Marco; Nguyen, Thanh-Phuong; Praveen, Paurush; Morine, Melissa; Priami, Corrado

    2015-10-30

    Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.

  12. Iron Isotope Fractionation in Microbial and Non-Biological Precipitates, and the Human Body

    Science.gov (United States)

    von Blanckenburg, F.; Boettcher, M. E.; Hofmann, B.; Walczyk, T.

    2001-12-01

    represent fossil remnants of microbial mats, have been found as encrustations in chalcedony. Delta57Fe is 3 permil heavier than the associated calcite (representing the Fe-rich fluids). Therefore, the fractionations found in microbial precipitates are not larger than those produced in the abiotic experiments. In contrast, major Fe isotope fractionations are produced by the human body: The major iron compartments in the human body, blood, liver, muscle tissues, and also hair, are all depleted by as much as 6 permil in the 57Fe isotope relative to 54Fe when compared to the average dietary intake. Since feces are similar to the average intake, we conclude that a significant Fe isotope fractionation occurs at the adsorptive stage in the intestine. In conclusion, with respect to the hypothesis that Fe isotope effects might serve as "biosignatures" it appears that microbial and abiotic reactions cause similar isotope effects which essentially depend on redox reactions and the speciation in the aqueous solution. On the other hand, higher organisms bear distinct Fe isotope signatures.

  13. Sample preparation optimization in fecal metabolic profiling.

    Science.gov (United States)

    Deda, Olga; Chatziioannou, Anastasia Chrysovalantou; Fasoula, Stella; Palachanis, Dimitris; Raikos, Νicolaos; Theodoridis, Georgios A; Gika, Helen G

    2017-03-15

    Metabolomic analysis of feces can provide useful insight on the metabolic status, the health/disease state of the human/animal and the symbiosis with the gut microbiome. As a result, recently there is increased interest on the application of holistic analysis of feces for biomarker discovery. For metabolomics applications, the sample preparation process used prior to the analysis of fecal samples is of high importance, as it greatly affects the obtained metabolic profile, especially since feces, as matrix are diversifying in their physicochemical characteristics and molecular content. However there is still little information in the literature and lack of a universal approach on sample treatment for fecal metabolic profiling. The scope of the present work was to study the conditions for sample preparation of rat feces with the ultimate goal of the acquisition of comprehensive metabolic profiles either untargeted by NMR spectroscopy and GC-MS or targeted by HILIC-MS/MS. A fecal sample pooled from male and female Wistar rats was extracted under various conditions by modifying the pH value, the nature of the organic solvent and the sample weight to solvent volume ratio. It was found that the 1/2 (w f /v s ) ratio provided the highest number of metabolites under neutral and basic conditions in both untargeted profiling techniques. Concerning LC-MS profiles, neutral acetonitrile and propanol provided higher signals and wide metabolite coverage, though extraction efficiency is metabolite dependent. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Novel bacterial ratio for predicting fecal age

    Energy Technology Data Exchange (ETDEWEB)

    Nieman, J.; Brion, G.M. [Univ. of Kentucky, Dept. of Civil Engineering, Lexington, Kentucky (United States)]. E-mail: gbrion@engr.uky.edu

    2002-06-15

    This study presents an extension of ongoing research into the utility of the ratio of bacterial colonies isolated on membrane filters during the total coliform test using m-Endo broth media for the prediction of fecal age. Analysis of the relative shifts in concentrations of indicator bacterial populations in Kentucky River water quality data collected from the inlet of a local water treatment plant showed a correlation between raw concentrations of atypical colonies (AC) and total coliform colonies (TC) formed on m-Endo membrane filter tests, and fecal age. Visual analysis of plant treatment records showed that low values of the AC/TC ratio were related to periods of high flow, when runoff added fresh fecal material to the river. A more detailed analysis of 2 years of Kentucky River water quality data showed the average AC/TC ratio during months with high river flow (rain) to be 3.4, rising to an average of 27.6 during months with low flow. The average AC/TC ratio during high flow months compared to that found in other studies for raw human sewage (3.9) and the ratio increased to values associated with animal impacted urban runoff (18.9) during low flow months. (author)

  15. Novel bacterial ratio for predicting fecal age

    International Nuclear Information System (INIS)

    Nieman, J.; Brion, G.M.

    2002-01-01

    This study presents an extension of ongoing research into the utility of the ratio of bacterial colonies isolated on membrane filters during the total coliform test using m-Endo broth media for the prediction of fecal age. Analysis of the relative shifts in concentrations of indicator bacterial populations in Kentucky River water quality data collected from the inlet of a local water treatment plant showed a correlation between raw concentrations of atypical colonies (AC) and total coliform colonies (TC) formed on m-Endo membrane filter tests, and fecal age. Visual analysis of plant treatment records showed that low values of the AC/TC ratio were related to periods of high flow, when runoff added fresh fecal material to the river. A more detailed analysis of 2 years of Kentucky River water quality data showed the average AC/TC ratio during months with high river flow (rain) to be 3.4, rising to an average of 27.6 during months with low flow. The average AC/TC ratio during high flow months compared to that found in other studies for raw human sewage (3.9) and the ratio increased to values associated with animal impacted urban runoff (18.9) during low flow months. (author)

  16. Bacterial Composition, Genotoxicity, and Cytotoxicity of Fecal Samples from Individuals Consuming Omnivorous or Vegetarian Diets

    Science.gov (United States)

    Federici, Ermanno; Prete, Roberta; Lazzi, Camilla; Pellegrini, Nicoletta; Moretti, Massimo; Corsetti, Aldo; Cenci, Giovanni

    2017-01-01

    This study analyzes the composition of viable fecal bacteria and gut toxicology biomarkers of 29 healthy volunteers, who followed omnivorous, lacto-ovo-vegetarian, or vegan diets. In particular, the research was focused on the prevalence of some representative viable bacteria from the four dominant phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) commonly present in human feces, in order to evaluate the relationship between microorganisms selected by the habitual dietary patterns and the potential risk due to fecal water (FW) genotoxicity and cytotoxicity, considered as biomarkers for cancer risk and protective food activity. The relative differences of viable bacteria among dietary groups were generally not statistically significant. However, compared to omnivores, lacto-ovo-vegetarians showed low levels of total anaerobes. Otherwise, vegans showed total anaerobes counts similar to those of omnivores, but with lower number of bifidobacteria and the highest levels of bacteria from the Bacteroides–Prevotella genera. FW genotoxicity of lacto-ovo-vegetarians resulted significantly lower either in relation to that of omnivores and vegans. Lacto-ovo-vegetarians also showed the lowest levels of cytotoxicity, while the highest were found for vegans. These results highlighted that lacto-ovo-vegetarian diet was particularly effective in a favorable modulation of microbial activity, thus contributing to a significant reduction of the genotoxic and cytotoxic risk in the gut. PMID:28293225

  17. Bacterial Composition, Genotoxicity, and Cytotoxicity of Fecal Samples from Individuals Consuming Omnivorous or Vegetarian Diets.

    Science.gov (United States)

    Federici, Ermanno; Prete, Roberta; Lazzi, Camilla; Pellegrini, Nicoletta; Moretti, Massimo; Corsetti, Aldo; Cenci, Giovanni

    2017-01-01

    This study analyzes the composition of viable fecal bacteria and gut toxicology biomarkers of 29 healthy volunteers, who followed omnivorous, lacto-ovo-vegetarian, or vegan diets. In particular, the research was focused on the prevalence of some representative viable bacteria from the four dominant phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) commonly present in human feces, in order to evaluate the relationship between microorganisms selected by the habitual dietary patterns and the potential risk due to fecal water (FW) genotoxicity and cytotoxicity, considered as biomarkers for cancer risk and protective food activity. The relative differences of viable bacteria among dietary groups were generally not statistically significant. However, compared to omnivores, lacto-ovo-vegetarians showed low levels of total anaerobes. Otherwise, vegans showed total anaerobes counts similar to those of omnivores, but with lower number of bifidobacteria and the highest levels of bacteria from the Bacteroides-Prevotella genera. FW genotoxicity of lacto-ovo-vegetarians resulted significantly lower either in relation to that of omnivores and vegans. Lacto-ovo-vegetarians also showed the lowest levels of cytotoxicity, while the highest were found for vegans. These results highlighted that lacto-ovo-vegetarian diet was particularly effective in a favorable modulation of microbial activity, thus contributing to a significant reduction of the genotoxic and cytotoxic risk in the gut.

  18. Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations.

    Science.gov (United States)

    Heaney, Christopher D; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R

    2015-04-01

    Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI]=1.03, 5.94) and 2.30 times (95% CI=0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI=1.21, 6.80) and 3.36 (95% CI=1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Comparison of Nested Polymerase Chain Reaction and Real-Time Polymerase Chain Reaction with Parasitological Methods for Detection of Strongyloides stercoralis in Human Fecal Samples

    Science.gov (United States)

    Sharifdini, Meysam; Mirhendi, Hossein; Ashrafi, Keyhan; Hosseini, Mostafa; Mohebali, Mehdi; Khodadadi, Hossein; Kia, Eshrat Beigom

    2015-01-01

    This study was performed to evaluate nested polymerase chain reaction (PCR) and real-time PCR methods for detection of Strongyloides stercoralis in fecal samples compared with parasitological methods. A total of 466 stool samples were examined by conventional parasitological methods (formalin ether concentration [FEC] and agar plate culture [APC]). DNA was extracted using an in-house method, and mitochondrial cytochrome c oxidase subunit 1 and 18S ribosomal genes were amplified by nested PCR and real-time PCR, respectively. Among 466 samples, 12.7% and 18.2% were found infected with S. stercoralis by FEC and APC, respectively. DNA of S. stercoralis was detected in 18.9% and 25.1% of samples by real-time PCR and nested PCR, respectively. Considering parasitological methods as the diagnostic gold standard, the sensitivity and specificity of nested PCR were 100% and 91.6%, respectively, and that of real-time PCR were 84.7% and 95.8%, respectively. However, considering sequence analyzes of the selected nested PCR products, the specificity of nested PCR is increased. In general, molecular methods were superior to parasitological methods. They were more sensitive and more reliable in detection of S. stercoralis in comparison with parasitological methods. Between the two molecular methods, the sensitivity of nested PCR was higher than real-time PCR. PMID:26350449

  20. Sewage reflects the microbiomes of human populations.

    Science.gov (United States)

    Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

    2015-02-24

    Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However

  1. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

    Directory of Open Access Journals (Sweden)

    Zachery T. Lewis

    2016-01-01

    Full Text Available Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides. No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status. However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

  2. Bacteriological (fecal and total coliform) quality of Pakistani coastal water

    International Nuclear Information System (INIS)

    Mashiatullah, A.; Qureshi, R.M.; Javed, T.; Khan, M.S.; Chaudhary, M.Z.; Khalid, F.

    2010-01-01

    The coliform bacteria group consists of several genera of bacteria belonging to the family enterobacteriaceae. These are harmless bacteria, mostly live in soil, water, and digestive system of animals. Fecal coliform bacteria, which belongs to this group, are present in large numbers in feces and intestinal tract of human beings and other warm-blooded animals which can enter into water bodies from human and animal waste. Swimming in water having high levels of Fecal coliform bacteria increases the chance of developing illness (fever, nausea or stomach cramps) from pathogens entering the body through mouth, nose, ears or cuts in the skin. The objective of the present study was to characterize the bathing quality of Pakistani coastal water with respect to coliform bacteria. Total and Fecal coliform bacteria were determined at seven different locations along Pakistan coast using membrane filtration (MF) technique. 100 ml of water was passed through 0.45 micron (mu) filter paper. These filter papers were put on pads, soaked in Lauryle sulphate broth in petri-dishes and incubated at 44 deg. C for Fecal and 37 deg. for Total coliform for 24 hours. Significantly high population of Fecal and Total coliform bacteria was recorded at Karachi harbour area and Indus delta region. Results indicate that a large amount of domestically originated waste is being discharged into these locations without any pre-treatment (e.g., screening, activated sludge, by using filtration beds etc.) resulting in a poor seawater quality making it unfit for bathing. (author)

  3. Effect of solar radiation and predacious microorganisms on survival of fecal and other bacteria.

    OpenAIRE

    McCambridge, J; McMeekin, T A

    1981-01-01

    The effect of solar radiation and predacious microorganisms on the survival of bacteria of fecal and plant origin was studied. The decline in the numbers of Escherichia coli cells in estuarine water samples was found to be significantly greater in the presence of both naturally occurring microbial predators and solar radiation than when each of these factors was acting independently. The effect of solar radiation on microbial predators was negligible, whereas the susceptibility of bacteria to...

  4. Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

    Directory of Open Access Journals (Sweden)

    Tianyi Zhang

    Full Text Available The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD. Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3-V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions.

  5. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions.

    Science.gov (United States)

    Schuerger, Andrew C; Lee, Pascal

    2015-06-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle.

  6. CDC Study Finds Fecal Contamination in Pools

    Science.gov (United States)

    ... Communication (404) 639-3286 CDC study finds fecal contamination in pools A study of public pools done ... The E. coli is a marker for fecal contamination. Finding a high percentage of E. coli-positive ...

  7. Degradation of copepod fecal pellets

    DEFF Research Database (Denmark)

    Poulsen, Louise K.; Iversen, Morten

    2008-01-01

    amount of fecal pellets. The total degradation rate of pellets by the natural plankton community of Oresund followed the phytoplankton biomass, with maximum degradation rate during the spring bloom (2.5 +/- 0.49 d(-1)) and minimum (0.52 +/- 0.14 d(-1)) during late winter. Total pellet removal rate ranged...

  8. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

    Science.gov (United States)

    Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

    2017-12-01

    The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and

  9. Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption.

    Science.gov (United States)

    Stoops, J; Crauwels, S; Waud, M; Claes, J; Lievens, B; Van Campenhout, L

    2016-02-01

    In Western countries, the popularity of edible insects as an alternative animal protein source is increasing. Nevertheless, there is a lack of profound insight into the microbial safety and shelf life of living insects sold for human consumption. The purpose of this study was to characterise the microflora of fresh edible mealworm larvae and grasshoppers in a quantitative and qualitative way. Therefore, culture-dependent analyses (the total viable aerobic count, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds, and bacterial endospores) and next-generation sequencing (454amplicon pyrosequencing) were performed. High microbial counts were obtained for both insect species. Different insect batches resulted in quite similar microbial numbers, except for bacterial endospores. However, the bacterial community composition differed between both insect species. The most abundant operational taxonomic unit in mealworm larvae was Propionibacterium. Also members of the genera Haemophilus, Staphylococcus and Clostridium were found. Grasshoppers were mainly dominated by Weissella, Lactococcus and Yersinia/Rahnella. Overall, a variety of potential spoilage bacteria and food pathogens were characterised. The results of this study suggest that a processing step with a microbiocidal effect is required to avoid or minimize risks involved with the consumption of edible insects. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Effects of microbial DNA on human DNA profiles generated using the PowerPlex® 16 HS system.

    Science.gov (United States)

    Dembinski, Gina M; Picard, Christine J

    2017-11-01

    Most crime scenes are not sterile and therefore may be contaminated with environmental DNA, especially if a decomposing body is found. Collecting biological evidence from this individual will yield DNA samples mixed with microbial DNA. This also becomes important if postmortem swabs are collected from sexually assaulted victims. Although genotyping kits undergo validation tests, including bacterial screens, they do not account for the diverse microbial load during decomposition. We investigated the effect of spiking human DNA samples with known concentrations of DNA from 17 microbe species associated with decomposition on DNA profiles produced using the Promega PowerPlex ® HS system. Two species, Bacillus subtilis and Mycobacterium smegmatis, produced an extraneous allele at the TPOX locus. When repeated with the PowerPlex ® Fusion kit, the extra allele no longer amplified with these two species. This experiment demonstrates that caution should be exhibited if microbial load is high and the PowerPlex ® 16HS system is used. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  11. Minimally processed vegetable salads: microbial quality evaluation.

    Science.gov (United States)

    Fröder, Hans; Martins, Cecília Geraldes; De Souza, Katia Leani Oliveira; Landgraf, Mariza; Franco, Bernadette D G M; Destro, Maria Teresa

    2007-05-01

    The increasing demand for fresh fruits and vegetables and for convenience foods is causing an expansion of the market share for minimally processed vegetables. Among the more common pathogenic microorganisms that can be transmitted to humans by these products are Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella. The aim of this study was to evaluate the microbial quality of a selection of minimally processed vegetables. A total of 181 samples of minimally processed leafy salads were collected from retailers in the city of Sao Paulo, Brazil. Counts of total coliforms, fecal coliforms, Enterobacteriaceae, psychrotrophic microorganisms, and Salmonella were conducted for 133 samples. L. monocytogenes was assessed in 181 samples using the BAX System and by plating the enrichment broth onto Palcam and Oxford agars. Suspected Listeria colonies were submitted to classical biochemical tests. Populations of psychrotrophic microorganisms >10(6) CFU/g were found in 51% of the 133 samples, and Enterobacteriaceae populations between 10(5) and 106 CFU/g were found in 42% of the samples. Fecal coliform concentrations higher than 10(2) CFU/g (Brazilian standard) were found in 97 (73%) of the samples, and Salmonella was detected in 4 (3%) of the samples. Two of the Salmonella-positive samples had minimally processed vegetables had poor microbiological quality, and these products could be a vehicle for pathogens such as Salmonella and L. monocytogenes.

  12. Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

    Science.gov (United States)

    LeBouder, Emmanuel; Rey-Nores, Julia E; Raby, Anne-Catherine; Affolter, Michael; Vidal, Karine; Thornton, Catherine A; Labéta, Mario O

    2006-03-15

    The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

  13. A human monocytic NF-κB fluorescent reporter cell line for detection of microbial contaminants in biological samples.

    Directory of Open Access Journals (Sweden)

    Claire Battin

    Full Text Available Sensing of pathogens by innate immune cells is essential for the initiation of appropriate immune responses. Toll-like receptors (TLRs, which are highly sensitive for various structurally and evolutionary conserved molecules derived from microbes have a prominent role in this process. TLR engagement results in the activation of the transcription factor NF-κB, which induces the expression of cytokines and other inflammatory mediators. The exquisite sensitivity of TLR signalling can be exploited for the detection of bacteria and microbial contaminants in tissue cultures and in protein preparations. Here we describe a cellular reporter system for the detection of TLR ligands in biological samples. The well-characterized human monocytic THP-1 cell line was chosen as host for an NF-ᴋB-inducible enhanced green fluorescent protein reporter gene. We studied the sensitivity of the resultant reporter cells for a variety of microbial components and observed a strong reactivity towards TLR1/2 and TLR2/6 ligands. Mycoplasma lipoproteins are potent TLR2/6 agonists and we demonstrate that our reporter cells can be used as reliable and robust detection system for mycoplasma contaminations in cell cultures. In addition, a TLR4-sensitive subline of our reporters was engineered, and probed with recombinant proteins expressed in different host systems. Bacterially expressed but not mammalian expressed proteins induced strong reporter activity. We also tested proteins expressed in an E. coli strain engineered to lack TLR4 agonists. Such preparations also induced reporter activation in THP-1 cells highlighting the importance of testing recombinant protein preparations for microbial contaminations beyond endotoxins. Our results demonstrate the usefulness of monocytic reporter cells for high-throughput screening for microbial contaminations in diverse biological samples, including tissue culture supernatants and recombinant protein preparations. Fluorescent reporter

  14. Effects of in vitro fermentation of barley β-glucan and sugar beet pectin using human fecal inocula on cytokine expression by dendritic cells

    NARCIS (Netherlands)

    Rosch, Christiane; Taverne, Nico; Venema, Koen; Gruppen, Harry; Wells, Jerry M.; Schols, Henk A.

    2017-01-01

    Scope: This study simulates the fermentation process of barley β-glucan and sugar beet pectin in the human colon and monitors the degradation products formed. Additionally, immune effects of the degradation products were investigated. Methods and results: Immunostimulatory activity of

  15. Multiple modes of water quality impairment by fecal contamination in a rapidly developing coastal area: southwest Brunswick County, North Carolina.

    Science.gov (United States)

    Cahoon, Lawrence B; Hales, Jason C; Carey, Erin S; Loucaides, Socratis; Rowland, Kevin R; Toothman, Byron R

    2016-02-01

    Fecal contamination of surface waters is a significant problem, particularly in rapidly developing coastal watersheds. Data from a water quality monitoring program in southwest Brunswick County, North Carolina, gathered in support of a regional wastewater and stormwater management program were used to examine likely modes and sources of fecal contamination. Sampling was conducted at 42 locations at 3-4-week intervals between 1996 and 2003, including streams, ponds, and estuarine waters in a variety of land use settings. Expected fecal sources included human wastewater systems (on-site and central), stormwater runoff, and direct deposition by animals. Fecal coliform levels were positively associated with rainfall measures, but frequent high fecal coliform concentrations at times of no rain indicated other modes of contamination as well. Fecal coliform levels were also positively associated with silicate levels, a groundwater source signal, indicating that flux of fecal-contaminated groundwater was a mode of contamination, potentially elevating FC levels in impacted waters independent of stormwater runoff. Fecal contamination by failing septic or sewer systems at many locations was significant and in addition to effects of stormwater runoff. Rainfall was also linked to fecal contamination by central sewage treatment system failures. These results highlight the importance of considering multiple modes of water pollution and different ways in which human activities cause water quality degradation. Management of water quality in coastal regions must therefore recognize diverse drivers of fecal contamination to surface waters.

  16. A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions.

    Science.gov (United States)

    Rochelle-Newall, Emma; Nguyen, Thi Mai Huong; Le, Thi Phuong Quynh; Sengtaheuanghoung, Oloth; Ribolzi, Olivier

    2015-01-01

    Given the high numbers of deaths and the debilitating nature of diseases caused by the use of unclean water it is imperative that we have an understanding of the factors that control the dispersion of water borne pathogens and their respective indicators. This is all the more important in developing countries where significant proportions of the population often have little or no access to clean drinking water supplies. Moreover, and notwithstanding the importance of these bacteria in terms of public health, at present little work exists on the persistence, transfer and proliferation of these pathogens and their respective indicator organisms, e.g., fecal indicator bacteria (FIB) such as Escherichia coli and fecal coliforms in humid tropical systems, such as are found in South East Asia or in the tropical regions of Africa. Both FIB and the waterborne pathogens they are supposed to indicate are particularly susceptible to shifts in water flow and quality and the predicted increases in rainfall and floods due to climate change will only exacerbate the problems of contamination. This will be furthermore compounded by the increasing urbanization and agricultural intensification that developing regions are experiencing. Therefore, recognizing and understanding the link between human activities, natural process and microbial functioning and their ultimate impacts on human health are prerequisites for reducing the risks to the exposed populations. Most of the existing work in tropical systems has been based on the application of temperate indicator organisms, models and mechanisms regardless of their applicability or appropriateness for tropical environments. Here, we present a short review on the factors that control FIB dynamics in temperate systems and discuss their applicability to tropical environments. We then highlight some of the knowledge gaps in order to stimulate future research in this field in the tropics.

  17. A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions

    Directory of Open Access Journals (Sweden)

    Emma Jane Rochelle-Newall

    2015-04-01

    Full Text Available Given the high numbers of deaths and the debilitating nature of diseases caused by the use of unclean water it is imperative that we have an understanding of the factors that control the dispersion of water borne pathogens and their respective indicators. This is all the more important in developing countries where significant proportions of the population often have little or no access to clean drinking water supplies. Moreover, and notwithstanding the importance of these bacteria in terms of public health, at present little work exists on the persistence, transfer and proliferation of these pathogens and their respective indicator organisms e.g. fecal indicator bacteria (FIB such as Escherichia coli and fecal coliforms in humid tropical systems, such as are found in South East Asia or in the tropical regions of Africa. Both FIB and the waterborne pathogens they are supposed to indicate are particularly susceptible to shifts in water flow and quality and the predicted increases in rainfall and floods due to climate change will only exacerbate the problems of contamination. This will be furthermore compounded by the increasing urbanization and agricultural intensification that developing regions are experiencing. Therefore, recognizing and understanding the link between human activities, natural process and microbial functioning and their ultimate impacts on human health are prerequisites for reducing the risks to the exposed populations. Most of the existing work in tropical systems has been based on the application of temperate indicator organisms, models and mechanisms regardless of their applicability or appropriateness for tropical environments. Here we present a short review on the factors that control FIB dynamics in temperate systems and discuss their applicability to tropical environments. We then highlight some of the knowledge gaps in order to stimulate future research in this field in the tropics.

  18. Strategy for nuclear-magnetic-resonance-based metabolomics of human feces

    DEFF Research Database (Denmark)

    Lamichhane, Santosh; Yde, Christian Clement; Schmedes, Mette Søndergaard

    2015-01-01

    Metabolomic analyses of fecal material are gaining increasing attention because the gut microbial ecology and activity have an impact on the human phenotype and regulate host metabolism. Sample preparation is a crucial step, and in this study we recommend a methodology for extraction and analysis......, chemical shift variability, and signal to noise ratio (SNR) of the 1H NMR spectra were evaluated. Based on our results, we suggest that fresh fecal extraction with a Wf:Vb ratio of 1:2 may be the optimum choice to determine the overall metabolite composition of feces. In fact, more than 60 metabolites have...

  19. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

    Science.gov (United States)

    Schuerger, Andrew C.; Lee, Pascal

    2015-01-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20C to -1C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. Key Words: Planetary protection-Contamination-Habitability-Haughton Crater-Mars. Astrobiology

  20. Comparative analysis of fecal microflora of healthy full-term Indian ...

    Indian Academy of Sciences (India)

    2012-10-18

    Oct 18, 2012 ... In this study fecal microflora of human infants born through vaginal delivery (VB) and through ... their study they have investigated the development of the gut .... from both libraries were deposited to NCBI GenBank with.

  1. Comparison of the Fecal Microbiota in Feral and Domestic Goats

    Directory of Open Access Journals (Sweden)

    María G. Domínguez-Bello

    2011-12-01

    Full Text Available Animals have co-evolved with mutualistic microbial communities, known as the microbiota, which are essential for organ development and function. We hypothesize that modern animal husbandry practices exert an impact on the intestinal microbiota. In this study, we compared the structure of the fecal microbiota between feral and domestic goats using the G2 PhyloChip and assessed the presence of five tetracycline resistance genes [tet(M, tet(S, tet(O, tet(Q and tet(W] by PCR. Feces were collected from 10 goats: 5 domestic from a farm in the main island of Puerto Rico and 5 feral from the remote dry island of Mona. There were 42 bacterial phyla from 153 families detected in the goats’ feces. A total of 84 PhyloChip-OTUs were different in the fecal microbiota of feral and domestic goat. Both feral and domestic goats carried antibiotic resistance genes tet(O and tet(W, but domestic goats additionally carried tet(Q. Diet, host genetics and antibiotic exposure are likely determinant factors in shaping the intestinal microbiota and may explain the differences observed between feral and domestic goats fecal microbiota.

  2. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  3. Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation

    DEFF Research Database (Denmark)

    Martinez Ruiz, José Luis; Liu, Lifang; Petranovic, Dina

    2012-01-01

    Since the approval of recombinant insulin from Escherichia coli for its clinical use in the early 1980s, the amount of recombinant pharmaceutical proteins obtained by microbial fermentations has significantly increased. The recent advances in genomics together with high throughput analysis...... of recombinant therapeutics using yeast Saccharomyces cerevisiae as a model platform, and discusses the future potential of this platform for production of blood proteins and substitutes....

  4. Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans

    OpenAIRE

    Sanapareddy, Nina; Legge, Ryan M; Jovov, Biljana; McCoy, Amber; Burcal, Lauren; Araujo-Perez, Felix; Randall, Thomas A; Galanko, Joseph; Benson, Andrew; Sandler, Robert S; Rawls, John F; Abdo, Zaid; Fodor, Anthony A; Keku, Temitope O

    2012-01-01

    Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1–V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria fr...

  5. Characterization of egg laying hen and broiler fecal microbiota in poultry farms in Croatia, Czech Republic, Hungary and Slovenia.

    Directory of Open Access Journals (Sweden)

    Petra Videnska

    Full Text Available Poultry meat is the most common protein source of animal origin for humans. However, intensive breeding of animals in confined spaces has led to poultry colonisation by microbiota with a zoonotic potential or encoding antibiotic resistances. In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. strA gene was present in 1 out of 10,000 bacteria. The prevalence of sul1, sul2 and tet(B in poultry microbiota was approx. 6 times lower than that of the strA gene. tet(A and cat were the least prevalent being present in around 3 out of 10,000,000 bacteria forming fecal microbiome. The core chicken fecal microbiota was formed by 26 different families. Rather unexpectedly, representatives of Desulfovibrionaceae and Campylobacteraceae, both capable of hydrogen utilisation in complex microbial communities, belonged among core microbiota families. Understanding the roles of individual population members in the total metabolism of the complex community may allow for interventions which might result in the replacement of Campylobacteraceae with Desulfovibrionaceae and a reduction of Campylobacter colonisation in broilers, carcasses, and consequently poultry meat products.

  6. Characterization of egg laying hen and broiler fecal microbiota in poultry farms in Croatia, Czech Republic, Hungary and Slovenia.

    Science.gov (United States)

    Videnska, Petra; Rahman, Md Masudur; Faldynova, Marcela; Babak, Vladimir; Matulova, Marta Elsheimer; Prukner-Radovcic, Estella; Krizek, Ivan; Smole-Mozina, Sonja; Kovac, Jasna; Szmolka, Ama; Nagy, Bela; Sedlar, Karel; Cejkova, Darina; Rychlik, Ivan

    2014-01-01

    Poultry meat is the most common protein source of animal origin for humans. However, intensive breeding of animals in confined spaces has led to poultry colonisation by microbiota with a zoonotic potential or encoding antibiotic resistances. In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. strA gene was present in 1 out of 10,000 bacteria. The prevalence of sul1, sul2 and tet(B) in poultry microbiota was approx. 6 times lower than that of the strA gene. tet(A) and cat were the least prevalent being present in around 3 out of 10,000,000 bacteria forming fecal microbiome. The core chicken fecal microbiota was formed by 26 different families. Rather unexpectedly, representatives of Desulfovibrionaceae and Campylobacteraceae, both capable of hydrogen utilisation in complex microbial communities, belonged among core microbiota families. Understanding the roles of individual population members in the total metabolism of the complex community may allow for interventions which might result in the replacement of Campylobacteraceae with Desulfovibrionaceae and a reduction of Campylobacter colonisation in broilers, carcasses, and consequently poultry meat products.

  7. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

    DEFF Research Database (Denmark)

    Zhang, Li; Bahl, Martin Iain; Roager, Henrik Munch

    2017-01-01

    Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human......, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain......, and insulin resistance. Spread of microbes between cages within isolators interacted with establishment of the transplanted microbiotas in mice, and contributed to the transmission of metabolic phenotypes. Our findings highlight the impact of donor variability and reveal that inter-individual spread...

  8. Prevalence of Campylobacter, Arcobacter, Helicobacter, and Sutterella spp. in human fecal samples as estimated by a reevaluation of isolation methods for Campylobacters

    DEFF Research Database (Denmark)

    Engberg, J.; On, Stephen L.W.; Harrington, C.S.

    2000-01-01

    for isolation of Campylobacter spp. Two charcoal-based selective media, modified charcoal cefoperazone deoxycholate agar (mCCDA) and cefoperazone-amphotericin-teicoplanin (CAT) agar, were compared with Skirrow's blood-based medium and with a filter method (filter) applied to a yeast-enriched blood agar. A total...... of 1,376 specimens were tested on all four media, and the percentages of thermophilic Campylobacter-positive specimens isolated on Skirrow's medium, filters, CAT agar, and mCCDA were 82, 83, 85, and 95%, respectively. When additional samples were professed with the three selective media, m...... butzleri, Arcobacter cryaerophilus, Helicobacter cinaedi, and Sutterella wadsworthensis. Most of these strains were isolated after 5 to 6 days of incubation by use of the filter technique. This paper pro,ides evidence for the existence of S. wadsworthensis in human feces from clinical cases...

  9. Metaproteomic analysis of human gut microbiota: where are we heading?

    Science.gov (United States)

    Lee, Pey Yee; Chin, Siok-Fong; Neoh, Hui-Min; Jamal, Rahman

    2017-06-12

    The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.

  10. The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water

    Science.gov (United States)

    Walker, Alan W.; Thompson, Corinne N.; Torres, Andres; Dongol, Sabina; Tran Vu Thieu, Nga; Pham Thanh, Duy; Tran Thi Ngoc, Dung; Voong Vinh, Phat; Singer, Andrew C.; Parkhill, Julian; Thwaites, Guy; Basnyat, Buddha; Ferguson, Neil; Baker, Stephen

    2016-01-01

    One of the UN sustainable development goals is to achieve universal access to safe and affordable drinking water by 2030. It is locations like Kathmandu, Nepal, a densely populated city in South Asia with endemic typhoid fever, where this goal is most pertinent. Aiming to understand the public health implications of water quality in Kathmandu we subjected weekly water samples from 10 sources for one year to a range of chemical and bacteriological analyses. We additionally aimed to detect the etiological agents of typhoid fever and longitudinally assess microbial diversity by 16S rRNA gene surveying. We found that the majority of water sources exhibited chemical and bacterial contamination exceeding WHO guidelines. Further analysis of the chemical and bacterial data indicated site-specific pollution, symptomatic of highly localized fecal contamination. Rainfall was found to be a key driver of this fecal contamination, correlating with nitrates and evidence of S. Typhi and S. Paratyphi A, for which DNA was detectable in 333 (77%) and 303 (70%) of 432 water samples, respectively. 16S rRNA gene surveying outlined a spectrum of fecal bacteria in the contaminated water, forming complex communities again displaying location-specific temporal signatures. Our data signify that the municipal water in Kathmandu is a predominant vehicle for the transmission of S. Typhi and S. Paratyphi A. This study represents the first extensive spatiotemporal investigation of water pollution in an endemic typhoid fever setting and implicates highly localized human waste as the major contributor to poor water quality in the Kathmandu Valley. PMID:26735696

  11. Shotgun metaproteomics of the human distal gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    VerBerkmoes, N.C.; Russell, A.L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarsson, J.; Lefsrud, M.G.; Apajalahti, J.; Tysk, C.; Hettich, R.L.; Jansson, Janet K.

    2008-10-15

    The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  12. Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

    Science.gov (United States)

    Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

    2018-02-06

    The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

  13. Recovery of the gut microbiome following fecal microbiota transplantation.

    Science.gov (United States)

    Seekatz, Anna M; Aas, Johannes; Gessert, Charles E; Rubin, Timothy A; Saman, Daniel M; Bakken, Johan S; Young, Vincent B

    2014-06-17

    Clostridium difficile infection is one of the most common health care-associated infections, and up to 40% of patients suffer from recurrence of disease following standard antibiotic therapy. Recently, fecal microbiota transplantation (FMT) has been successfully used to treat recurrent C. difficile infection. It is hypothesized that FMT aids in recovery of a microbiota capable of colonization resistance to C. difficile. However, it is not fully understood how this occurs. Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool. Increased relative abundance of Bacteroidetes and decreased abundance of Proteobacteria were observed following FMT. The fecal microbiota of recipients following transplantation was more diverse and more similar to the donor profile than the microbiota prior to transplantation. Additionally, we observed differences in the imputed metagenomic profile. In particular, amino acid transport systems were overrepresented in samples collected prior to transplantation. These results suggest that functional changes accompany microbial structural changes following this therapy. Further identification of the specific community members and functions that promote colonization resistance may aid in the development of improved treatment methods for C. difficile infection. Within the last decade, Clostridium difficile infection has surpassed other bacterial infections to become the leading cause of nosocomial infections. Antibiotic use, which disrupts the gut microbiota and its capability in providing colonization resistance against C. difficile, is a known risk factor in C. difficile infection. In particular, recurrent C. difficile remains difficult to treat with standard antibiotic therapy. Fecal microbiota transplantation (FMT) has provided a successful treatment method for

  14. Effects of DNA Extraction Procedures on Bacteroides Profiles in Fecal Samples From Various Animals Determined by Terminal Restriction Fragment Length Polymorphism Analysis

    Science.gov (United States)

    A major assumption in microbial source tracking is that some fecal bacteria are specific to a host animal, and thus provide unique microbial fingerprints that can be used to differentiate hosts. However, the DNA information obtained from a particular sample may be biased dependi...

  15. Changes in human fecal microbiota due to chemotherapy analyzed by TaqMan-PCR, 454 sequencing and PCR-DGGE fingerprinting.

    Directory of Open Access Journals (Sweden)

    Jutta Zwielehner

    Full Text Available BACKGROUND: We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037 following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. CONCLUSIONS/SIGNIFICANCE: Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C. difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.

  16. [Association between inflammatory markers and microbial translocation in patients with human immunodeficiency virus infection taking antiretroviral treatment].

    Science.gov (United States)

    Reus Bañuls, Sergio; Portilla Sogorb, Joaquín; Sanchez-Paya, José; Boix Martínez, Vicente; Giner Oncina, Livia; Frances, Rubén; Such, José; Merino Lucas, Esperanza; Gimeno Gascón, Adelina

    2014-01-21

    Inflammatory biomarkers are increased in patients with human immunodeficiency virus (HIV) infection. Antiretroviral treatment (ART) improves some parameters but do not normalize them. The aim of this study is to determine those factors (including microbial translocation) associated with higher inflammation in HIV treated patients. Transversal observational study. HIV patients receiving ART with an HIV viral load (VL)<400 copies/mL. Selection of patients: consecutively between November 2011 and January 2012. Main variable: plasma levels of interleukin 6 (IL-6) and tumour necrosis factor α (TNF-α). Main explanatory variable: microbial translocation markers (16S ribosomal DNA and sCD14). Patients with IL-6 or TNF-α levels above percentile 75 (group 1) were compared with the rest of patients (group 2). Odds ratio (OR) were determined. Eighty-one patients were included (73% male, median age 45 years, 48% stage C). Twenty-six percent had chronic hepatitis C. Median CD4 cell was 493/mm(3) and 30% had detectable HIV VL. 16S ribosomal DNA was detected in 21% of patients. Factors associated with the higher levels of inflammatory markers were 16S ribosomal DNA (OR 77, P<.0001), sCD14 levels (P<.0001) and history of cardiovascular disease (OR 15, P<.01). In multivariate analysis, associations remained for 16S ribosomal DNA (OR 62, P<.0001) and previous cardiovascular disease (OR 25, P<.01). In patients with HIV infection receiving treatment, the higher levels of inflammatory markers are associated with microbial translocation and past cardiovascular events. Copyright © 2013 Elsevier España, S.L. All rights reserved.

  17. Surveillance of Enteric Viruses and Microbial Indicators in the Eastern Oysters (Crassostrea virginica) and Harvest Waters along Louisiana Gulf Coast.

    Science.gov (United States)

    Montazeri, Naim; Maite, Morgan; Liu, Da; Cormier, Jiemin; Landry, Matthew; Shackleford, John; Lampila, Lucina E; Achberger, Eric C; Janes, Marlene E

    2015-05-01

    Noroviruses are the most common causative agent of viral gastroenteritis in humans, and are responsible for major foodborne illnesses in the United States. Filter-feeding molluscan shellfish exposed to sewage-contaminated waters bioaccumulate viruses, and if consumed raw, transmit the viruses to humans and cause illness. We investigated the occurrence of norovirus GI and GII and microbial indicators of fecal contamination in the eastern oysters (Crassostrea virginica) and water from commercial harvesting areas along the Louisiana Gulf Coast (January to November of 2013). Microbial indicators (aerobic plate count, enterococci, fecal coliforms, Escherichia coli, male-specific coliphages, and somatic coliphages) were detected at the densities lower than public health concerns. Only one oyster sample was positive for norovirus GII at 3.5 ± 0.2 log10 genomic equivalent copies/g digestive tissues. A stool specimen obtained from an infected individual associated with a norovirus outbreak and the suspected oysters (Cameron Parish, La., area 30, January 2013) were also analyzed. The norovirus strain in the stool belonged to GII.4 Sydney; however, the oysters were negative and could not be linked. In general, no temporal trend was observed in the microbial indicators. Low correlation among bacterial indicators was observed in oysters. Strongest correlations among microbial indicators were observed between enterococci and fecal coliforms (r = 0.63) and between enterococci and E. coli (r = 0.64) in water (P oysters (r oysters and harvest water (r ≤ 0.36, P > 0.05). Our results emphasize the need for regular monitoring of pathogenic viruses in commercial oyster harvesting areas to reduce the risks of viral gastroenteritis incidences. © 2015 Institute of Food Technologists®

  18. Storm loads of culturable and molecular fecal indicators in an inland urban stream.

    Science.gov (United States)

    Liao, Hehuan; Krometis, Leigh-Anne H; Cully Hession, W; Benitez, Romina; Sawyer, Richard; Schaberg, Erin; von Wagoner, Emily; Badgley, Brian D

    2015-10-15

    Elevated concentrations of fecal indicator bacteria in receiving waters during wet-weather flows are a considerable public health concern that is likely to be exacerbated by future climate change and urbanization. Knowledge of factors driving the fate and transport of fecal indicator bacteria in stormwater is limited, and even less is known about molecular fecal indicators, which may eventually supplant traditional culturable indicators. In this study, concentrations and loading rates of both culturable and molecular fecal indicators were quantified throughout six storm events in an instrumented inland urban stream. While both concentrations and loading rates of each fecal indicator increased rapidly during the rising limb of the storm hydrographs, it is the loading rates rather than instantaneous concentrations that provide a better estimate of transport through the stream during the entire storm. Concentrations of general fecal indicators (both culturable and molecular) correlated most highly with each other during storm events but not with the human-associated HF183 Bacteroides marker. Event loads of general fecal indicators most strongly correlated with total runoff volume, maximum discharge, and maximum turbidity, while event loads of HF183 most strongly correlated with the time to peak flow in a hydrograph. These observations suggest that collection of multiple samples during a storm event is critical for accurate predictions of fecal indicator loading rates and total loads during wet-weather flows, which are required for effective watershed management. In addition, existing predictive models based on general fecal indicators may not be sufficient to predict source-specific genetic markers of fecal contamination. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Cytotoxic effect of microbial biosurfactants against human embryonic kidney cancerous cell: HEK-293 and their possible role in apoptosis.

    Science.gov (United States)

    Pradhan, Arun Kumar; Pradhan, Nilotpala; Mohapatra, Purusottam; Kundu, Chanakya Nath; Panda, Prasanna Kumar; Mishra, Barada Kanta

    2014-11-01

    Two different microbial biosurfactants S9BS and CHBS were isolated from Lysinibacillus fusiformis S9 and Bacillus tequilensis CH. Cytotoxicity effect of these biosurfactants on human embryonic kidney cancerous cell (HEK-293) were studied with the help of 3-(4,5-dimethylthiazol-2yl-)-2, 5-diphenyl tetrazolium bromide (MTT) assay and morphological changes were observed under inverted microscope. The biosurfactants exhibited positive cytotoxic effect on HEK-293 cell line. It was found that LC50 of S9BS and CHBS were 75 and 100 μg ml(-1), respectively. Further cell cycle and apoptosis analysis of biosurfactant-treated HEK-293 cell line were done by FACS. In this study, cytotoxic effect of glycolipid biosurfactant against HEK-293 cell lines is reported for the first time. Mechanism towards increased membrane permeability of biosurfactant-treated cancer cell may be the incorporation of its lipid moiety into the plasma membrane leading to formation of pores and membrane disruption. Hence, these microbial biosurfactants can prove to be significant biomolecule for cancer treatment.

  20. Effective photodynamic therapy against microbial populations in human deep tissue abscess aspirates.

    Science.gov (United States)

    Haidaris, Constantine G; Foster, Thomas H; Waldman, David L; Mathes, Edward J; McNamara, Joanne; Curran, Timothy

    2013-10-01

    The primary therapy for deep tissue abscesses is drainage accompanied by systemic antimicrobial treatment. However, the long antibiotic course required increases the probability of acquired resistance, and the high incidence of polymicrobial infections in abscesses complicates treatment choices. Photodynamic therapy (PDT) is effective against multiple classes of organisms, including those displaying drug resistance, and may serve as a useful adjunct to the standard of care by reduction of abscess microbial burden following drainage. Aspirates were obtained from 32 patients who underwent image-guided percutaneous drainage of the abscess cavity. The majority of the specimens (24/32) were abdominal, with the remainder from liver and lung. Conventional microbiological techniques and nucleotide sequence analysis of rRNA gene fragments were used to characterize microbial populations from abscess aspirates. We evaluated the sensitivity of microorganisms to methylene blue-sensitized PDT in vitro both within the context of an abscess aspirate and as individual isolates. Most isolates were bacterial, with the fungus Candida tropicalis also isolated from two specimens. We examined the sensitivity of these microorganisms to methylene blue-PDT. Complete elimination of culturable microorganisms was achieved in three different aspirates, and significant killing (P abscess treatment. © 2013 Wiley Periodicals, Inc.

  1. Characterization of fecal microbiota across seven Chinese ethnic groups by quantitative polymerase chain reaction.

    Directory of Open Access Journals (Sweden)

    Lai-yu Kwok

    Full Text Available The human gut microbiota consists of complex microbial communities, which possibly play crucial roles in physiological functioning and health maintenance. China has evolved into a multicultural society consisting of the major ethnic group, Han, and 55 official ethnic minority groups. Nowadays, these minority groups inhabit in different Chinese provinces and some of them still keep their unique culture and lifestyle. Currently, only limited data are available on the gut microbiota of these Chinese ethnic groups. In this study, 10 major fecal bacterial groups of 314 healthy individuals from 7 Chinese ethnic origins were enumerated by quantitative polymerase chain reaction. Our data confirmed that the selected bacterial groups were common to all 7 surveyed ethnicities, but the amount of the individual bacterial groups varied to different degree. By principal component and canonical variate analyses of the 314 individuals or the 91 Han subjects, no distinct group clustering pattern was observed. Nevertheless, weak differences were noted between the Han and Zhuang from other ethnic minority groups, and between the Heilongjiang Hans from those of the other provinces. Thus, our results suggest that the ethnic origin may contribute to shaping the human gut microbiota.

  2. Estimates of Nitrogen, Phosphorus, Biochemical Oxygen Demand, and Fecal Coliforms Entering the Environment Due to Inadequate Sanitation Treatment Technologies in 108 Low and Middle Income Countries.

    Science.gov (United States)

    Fuhrmeister, Erica R; Schwab, Kellogg J; Julian, Timothy R

    2015-10-06

    Understanding the excretion and treatment of human waste (feces and urine) in low and middle income countries (LMICs) is necessary to design appropriate waste management strategies. However, excretion and treatment are often difficult to quantify due to decentralization of excreta management. We address this gap by developing a mechanistic, stochastic model to characterize phosphorus, nitrogen, biochemical oxygen demand (BOD), and fecal coliform pollution from human excreta for 108 LMICs. The model estimates excretion and treatment given three scenarios: (1) use of existing sanitation systems, (2) use of World Health Organization-defined "improved sanitation", and (3) use of best available technologies. Our model estimates that more than 10(9) kg/yr each of phosphorus, nitrogen and BOD are produced. Of this, 22(19-27)%, 11(7-15)%, 17(10-23)%, and 35 (23-47)% (mean and 95% range) BOD, nitrogen, phosphorus, and fecal coliforms, respectively, are removed by existing sanitation systems. Our model estimates that upgrading to "improved sanitation" increases mean removal slightly to between 17 and 53%. Under the best available technology scenario, only approximately 60-80% of pollutants are treated. To reduce impact of nutrient and microbial pollution on human and environmental health, improvements in both access to adequate sanitation and sanitation treatment efficiency are needed.

  3. Resveratrol ameliorates the chemical and microbial induction of inflammation and insulin resistance in human placenta, adipose tissue and skeletal muscle.

    Science.gov (United States)

    Tran, Ha T; Liong, Stella; Lim, Ratana; Barker, Gillian; Lappas, Martha

    2017-01-01

    Gestational diabetes mellitus (GDM), which complicates up to 20% of all pregnancies, is associated with low-grade maternal inflammation and peripheral insulin resistance. Sterile inflammation and infection are key mediators of this inflammation and peripheral insulin resistance. Resveratrol, a stilbene-type phytophenol, has been implicated to exert beneficial properties including potent anti-inflammatory and antidiabetic effects in non-pregnant humans and experimental animal models of GDM. However, studies showing the effects of resveratrol on inflammation and insulin resistance associated with GDM in human tissues have been limited. In this study, human placenta, adipose (omental and subcutaneous) tissue and skeletal muscle were stimulated with pro-inflammatory cytokines TNF-α and IL-1β, the bacterial product lipopolysaccharide (LPS) and the synthetic viral dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) to induce a GDM-like model. Treatment with resveratrol significantly reduced the expression and secretion of pro-inflammatory cytokines IL-6, IL-1α, IL-1β and pro-inflammatory chemokines IL-8 and MCP-1 in human placenta and omental and subcutaneous adipose tissue. Resveratrol also significantly restored the defects in the insulin signalling pathway and glucose uptake induced by TNF-α, LPS and poly(I:C). Collectively, these findings suggest that resveratrol reduces inflammation and insulin resistance induced by chemical and microbial products. Resveratrol may be a useful preventative therapeutic for pregnancies complicated by inflammation and insulin resistance, like GDM.

  4. Variability in the characterization of total coliforms, fecal coliforms, and escherichia coli in recreational water supplies of North Mississippi, USA

    Science.gov (United States)

    The fecal coliform, Escherichia coli, is a historical organism for the detection of fecal pollution in water supplies. The presence of E. coli indicates a potential contamination of the water supply by other more hazardous human pathogens. In order to accurately determine the presence and degree o...

  5. Recent developments in microbial oils production: a possible alternative to vegetable oils for biodiesel without competition with human food?

    Directory of Open Access Journals (Sweden)

    Gwendoline Christophe

    2012-02-01

    Full Text Available Since centuries vegetable oils are consumed as human food but it also finds applications in biodiesel production which is attracting more attention. But due to being in competition with food it could not be sustainable and leads the need to search for alternative. Nowdays microbes-derived oils (single cell oils seem to be alternatives for biodiesel production due to their similar composition to that of vegetable oils. However, the cold flow properties of the biodiesel produced from microbial oils are unacceptable and have to be modified by an efficient transesterification. Glycerol which is by product of transesterification can be valorised into some more useful products so that it can also be utilised along with biodiesel to simplify the downstream processing. The review paper discusses about various potent microorganisms for biodiesel production, enzymes involved in the lipid accumulation, lipid quantification methods, catalysts used in transesterification (including enzymatic catalyst and valorisation of glycerol.

  6. Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans.

    Science.gov (United States)

    Sanapareddy, Nina; Legge, Ryan M; Jovov, Biljana; McCoy, Amber; Burcal, Lauren; Araujo-Perez, Felix; Randall, Thomas A; Galanko, Joseph; Benson, Andrew; Sandler, Robert S; Rawls, John F; Abdo, Zaid; Fodor, Anthony A; Keku, Temitope O

    2012-10-01

    Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1-V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.

  7. Quantification of microbial risks to human health caused by waterborne viruses and bacteria in an urban slum.

    Science.gov (United States)

    Katukiza, A Y; Ronteltap, M; van der Steen, P; Foppen, J W A; Lens, P N L

    2014-02-01

    To determine the magnitude of microbial risks from waterborne viruses and bacteria in Bwaise III in Kampala (Uganda), a typical slum in Sub-Saharan Africa. A quantitative microbial risk assessment (QMRA) was carried out to determine the magnitude of microbial risks from waterborne pathogens through various exposure pathways in Bwaise III in Kampala (Uganda). This was based on the concentration of Escherichia coli O157:H7, Salmonella spp., rotavirus (RV) and human adenoviruses F and G (HAdV) in spring water, tap water, surface water, grey water and contaminated soil samples. The total disease burden was 680 disability-adjusted life years (DALYs) per 1000 persons per year. The highest disease burden contribution was caused by exposure to surface water open drainage channels (39%) followed by exposure to grey water in tertiary drains (24%), storage containers (22%), unprotected springs (8%), contaminated soil (7%) and tap water (0.02%). The highest percentage of the mean estimated infections was caused by E. coli O157:H7 (41%) followed by HAdV (32%), RV (20%) and Salmonella spp. (7%). In addition, the highest infection risk was 1 caused by HAdV in surface water at the slum outlet, while the lowest infection risk was 2.71 × 10(-6) caused by E. coli O157:H7 in tap water. The results show that the slum environment is polluted, and the disease burden from each of the exposure routes in Bwaise III slum, with the exception of tap water, was much higher than the WHO reference level of tolerable risk of 1 × 10(-6) DALYs per person per year. The findings of this study provide guidance to governments, local authorities and nongovernment organizations in making decisions on measures to reduce infection risk and the disease burden by 10(2) to 10(5) depending on the source of exposure to achieve the desired health impacts. The infection risk may be reduced by sustainable management of human excreta and grey water, coupled with risk communication during hygiene awareness

  8. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

    Directory of Open Access Journals (Sweden)

    Ellen Li

    Full Text Available We tested the hypothesis that Crohn's disease (CD-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA gene and 454 sequencing of 16S rRNA gene hypervariable regions (V1-V3 and V3-V5, were conducted on macroscopically disease-unaffected ileal biopsies collected from 52 ileal CD, 58 ulcerative colitis and 60 control patients without inflammatory bowel diseases (IBD undergoing initial surgical resection. These subjects also were genotyped for the three major NOD2 risk alleles (Leu1007fs, R708W, G908R and the ATG16L1 risk allele (T300A. The samples were linked to clinical metadata, including body mass index, smoking status and Clostridia difficile infection. The sequences were classified into seven phyla/subphyla categories using the Naïve Bayesian Classifier of the Ribosome Database Project. Centered log ratio transformation of six predominant categories was included as the dependent variable in the permutation based MANCOVA for the overall composition with stepwise variable selection. Polymerase chain reaction (PCR assays were conducted to measure the relative frequencies of the Clostridium coccoides - Eubacterium rectales group and the Faecalibacterium prausnitzii spp. Empiric logit transformations of the relative frequencies of these two microbial groups were included in permutation-based ANCOVA. Regardless of sequencing method, IBD phenotype, Clostridia difficile and NOD2 genotype were selected as associated (FDR ≤ 0.05 with shifts in overall microbial composition. IBD phenotype and NOD2 genotype were also selected as associated with shifts in the relative frequency of the C. coccoides--E. rectales group. IBD phenotype, smoking and IBD medications were selected as associated with shifts in the relative frequency of F. prausnitzii spp. These

  9. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

    Science.gov (United States)

    Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; Sodergren, Erica; Frank, Daniel N

    2012-01-01

    We tested the hypothesis that Crohn's disease (CD)-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA) gene and 454 sequencing of 16S rRNA gene hypervariable regions (V1-V3 and V3-V5), were conducted on macroscopically disease-unaffected ileal biopsies collected from 52 ileal CD, 58 ulcerative colitis and 60 control patients without inflammatory bowel diseases (IBD) undergoing initial surgical resection. These subjects also were genotyped for the three major NOD2 risk alleles (Leu1007fs, R708W, G908R) and the ATG16L1 risk allele (T300A). The samples were linked to clinical metadata, including body mass index, smoking status and Clostridia difficile infection. The sequences were classified into seven phyla/subphyla categories using the Naïve Bayesian Classifier of the Ribosome Database Project. Centered log ratio transformation of six predominant categories was included as the dependent variable in the permutation based MANCOVA for the overall composition with stepwise variable selection. Polymerase chain reaction (PCR) assays were conducted to measure the relative frequencies of the Clostridium coccoides - Eubacterium rectales group and the Faecalibacterium prausnitzii spp. Empiric logit transformations of the relative frequencies of these two microbial groups were included in permutation-based ANCOVA. Regardless of sequencing method, IBD phenotype, Clostridia difficile and NOD2 genotype were selected as associated (FDR ≤ 0.05) with shifts in overall microbial composition. IBD phenotype and NOD2 genotype were also selected as associated with shifts in the relative frequency of the C. coccoides--E. rectales group. IBD phenotype, smoking and IBD medications were selected as associated with shifts in the relative frequency of F. prausnitzii spp. These results indicate

  10. Measurement of fecal glucocorticoids in parrotfishes to assess stress

    Science.gov (United States)

    Turner, J.W.; Nemeth, R.; Rogers, C.

    2003-01-01

    Coral reefs are in decline worldwide from a combination of natural and human forces. The environmental compromises faced by coral reef habitats and their associated fishes are potentially stressful, and in this study we examined the potential for assessing stress levels in coral reef fish. We determined the feasibility of using fecal casts from parrotfishes for remote assessment of stress-related hormones (cortisol and corticosterone), and the response of these hormones to the stress of restraint and hypoxia. Measurement of these hormones in fecal extracts by high performance liquid chromatography (HPLC) was validated using mass spectrometry, chemical derivitization, and radioactive tracer methods. In aquarium-adapted parrotfish, baseline levels of cortisol and corticosterone averaged 3.4??1.1 and 14.8??2.8ng/g feces, respectively, across 32 days. During 13 days of periodic stress these hormones, respectively, average 10.8-fold and 3.2-fold greater than baseline, with a return to near baseline during a 23-day follow-up. Testosterone was also measured as a reference hormone which is not part of the stress-response axis. Levels of this hormone were similar across the study. These fecal hormones were also measured in a field study of parrotfish in 10 fringing coral reef areas around the Caribbean Island of St. John, US Virgin Islands. Extracts of remotely collected fecal casts of three parrotfish species revealed no difference in respective average hormone levels among these species. Also, there was no difference in respective hormone levels between aquarium and field environments. However, levels of both cortisol and corticosterone, but not testosterone, were elevated in two of the 10 reef sites surveyed. This study demonstrates that parrotfish fecals can be collected in aquarium and field conditions and that steroid hormones in these fecals can be extracted and reliably measured. The study also demonstrates that cortisol and corticosterone in parrotfish fecals can

  11. Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State

    Science.gov (United States)

    Lin, Hong; An, Yanpeng; Hao, Fuhua; Wang, Yulan; Tang, Huiru

    2016-02-01

    Obesity resulting from interactions of genetic and environmental factors becomes a serious public health problem worldwide with alterations of the metabolic phenotypes in multiple biological matrices involving multiple metabolic pathways. To understand the contributions of gut microbiota to obesity development, we analyzed dynamic alterations in fecal metabonomic phenotype using NMR and fecal microorganism composition in rats using pyrosequencing technology during the high-fat diet (HFD) feeding for 81 days (pre-obesity state). Integrated analysis of these two phenotypic datasets was further conducted to establish correlations between the altered rat fecal metabonome and gut microbiome. We found that one-week HFD feeding already caused significant changes in rat fecal metabonome and such changes sustained throughout 81-days feeding with the host and gut microbiota co-metabolites clearly featured. We also found that HFD caused outstanding decreases in most fecal metabolites implying enhancement of gut absorptions. We further established comprehensive correlations between the HFD-induced changes in fecal metabonome and fecal microbial composition indicating contributions of gut microbiota in pathogenesis and progression of the HFD-induced obesity. These findings provided essential information about the functions of gut microbiota in pathogenesis of metabolic disorders which could be potentially important for developing obesity prevention and treatment therapies.

  12. Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

    Science.gov (United States)

    Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

  13. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

    NARCIS (Netherlands)

    Coolen, MJL; Post, E; Davis, CC; Forney, LJ

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the

  14. Fecal zonulin is elevated in Crohn's disease and in cigarette smokers.

    Science.gov (United States)

    Malíčková, Karin; Francová, Irena; Lukáš, Milan; Kolář, Martin; Králíková, Eva; Bortlík, Martin; Ďuricová, Dana; Štěpánková, Lenka; Zvolská, Kamila; Pánková, Alexandra; Zima, Tomáš

    2017-12-01

    Human zonulin is a protein that increases permeability in the epithelial layer of the small intestine by reversibly modulating the intercellular tight junctions. There is not sufficient information available about zonulin's participation in inflammatory bowel diseases (IBD). The aim of this study was therefore to investigate fecal and serum zonulin in IBD patients and its relation to the disease localization, behavior and smoking status. Forty IBD patients and forty healthy persons were examined for fecal and serum zonulin concentrations by competitive ELISA (DRG International Inc). Values were correlated to IBD type, localization and behavior, and smoking. Serum and fecal zonulin were significantly higher in patients with Crohn's disease compared to ulcerative colitis (p = 0.038 for fecal zonulin, and p = 0.041 for serum zonulin concentrations). No association of serum or fecal zonulin was found with respect to IBD localization and behavior. The only difference was found with respect to smoking. Both the IBD cohort and healthy smokers showed significantly higher fecal zonulin levels (median 203 ng/mL) compared to non-smokers (median 35.8 ng/mL), p zonulin levels are elevated in patients with active Crohn's disease but not with ulcerative colitis. High fecal zonulin levels in smokers irrespective of IBD point to the significant and undesirable up-regulation of gut permeability in cigarette smokers.

  15. Urban microbial ecology of a freshwater estuary of Lake Michigan.

    Science.gov (United States)

    Fisher, Jenny C; Newton, Ryan J; Dila, Deborah K; McLellan, Sandra L

    Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas , and Pseudomonas , which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential

  16. Urban microbial ecology of a freshwater estuary of Lake Michigan

    Directory of Open Access Journals (Sweden)

    Jenny C. Fisher

    2015-07-01

    Full Text Available Abstract Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an “urban microbial signature,” and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is

  17. Urban microbial ecology of a freshwater estuary of Lake Michigan

    Science.gov (United States)

    Fisher, Jenny C.; Newton, Ryan J.; Dila, Deborah K.

    2015-01-01

    Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an “urban microbial signature,” and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with

  18. Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

    Science.gov (United States)

    Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about...

  19. Clinical anatomy of fecal incontinence in women.

    Science.gov (United States)

    Kadam-Halani, Priyanka K; Arya, Lily A; Andy, Uduak U

    2017-10-01

    Fecal incontinence is a devastating condition that has a severe impact on quality of life. This condition disproportionately affects women and its incidence is increasing with the aging United States population. Fecal continence is maintained by coordination of a functioning anal sphincter complex, intact sensation of the anorectum, rectal compliance, and the ability to consciously control defecation. Particularly important are the puborectalis sling of the levator ani muscle complex and intact innervation of the central and peripheral nervous systems. An understanding of the intricate anatomy required to maintain continence and regulate defecation will help clinicians to provide appropriate medical and surgical management and diminish the negative impact of fecal incontinence. In this article, we describe the anatomic and neural basis of fecal continence and normal defecation as well as changes that occur with fecal incontinence in women. Clin. Anat. 30:901-911, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model

    NARCIS (Netherlands)

    Martin, F.P.J.; Wang, Y.; Sprenger, N.; Yap, K.S.; Rezzi, S.; Ramadan, Z.; Peré-Trepat, E.; Rochat, F.; Cherbut, C.; Bladeren, van P.J.; Fay, L.B.; Kochhar, S.; LindOn, J.C.; Holmes, E.; Nicholson, J.K.

    2008-01-01

    The transgenomic metabolic effects of exposure to either Lactobacillus paracasei or Lactobacillus rhamnosus probiotics have been measured and mapped in humanized extended genome mice (germ-free mice colonized with human baby flora). Statistical analysis of the compartmental fluctuations in diverse

  1. Fecal Contamination on Produce from Wholesale and Retail Food Markets in Dhaka, Bangladesh.

    Science.gov (United States)

    Harris, Angela R; Islam, Mohammad Aminul; Unicomb, Leanne; Boehm, Alexandria B; Luby, Stephen; Davis, Jennifer; Pickering, Amy J

    2018-01-01

    Fresh produce items can become contaminated with enteric pathogens along the supply chain at the preharvest (e.g., irrigation water, soil, fertilizer) or postharvest (e.g., vendor handling or consumer handling) stages. This study assesses the concentrations of fecal indicator bacteria Escherichia coli , enterococci (ENT), and Bacteriodales on surfaces of carrots, eggplants, red amaranth leaves, and tomatoes obtained from both a wholesale market (recently harvested) and neighborhood retail markets in Dhaka, Bangladesh. We detected E. coli in 100% of carrot and red amaranth rinses, 92% of eggplant rinses, and 46% of tomato rinses. Using a molecular microbial source tracking assay, we found that 32% of produce samples were positive for ruminant fecal contamination. Fecal indicator bacteria were more likely to be detected on produce collected in retail markets compared with that in the wholesale market; retail market produce were 1.25 times more likely to have E. coli detected ( P = 0.03) and 1.24 times more likely to have ENT detected ( P = 0.03) as compared with wholesale market produce. Bacteriodales was detected in higher concentrations in retail market produce samples compared with wholesale market produce samples (0.40 log 10 gene copies per 100 cm 2 higher, P = 0.03). Our results suggest that ruminant and general fecal contamination of produce in markets in Dhaka is common, and suggest that unsanitary conditions in markets are an important source of produce fecal contamination postharvest.

  2. Quantitative Real-Time PCR Fecal Source Identification in the ...

    Science.gov (United States)

    Rivers in the Tillamook Basin play a vital role in supporting a thriving dairy and cheese-making industry, as well as providing a safe water resource for local human and wildlife populations. Historical concentrations of fecal bacteria in these waters are at times too high to allow for safe use leading to economic loss, endangerment of local wildlife, and poor conditions for recreational use. In this study, we employ host-associated qPCR methods for human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution combined with high-resolution geographic information system (GIS) land use data and general indicator bacteria measurements to elucidatewater quality spatial and temporal trends. Water samples (n=584) were collected over a 1-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries (Tillamook Basin, OR). A total of 16.6% of samples (n=97) yielded E. coli levels considered impaired based on Oregon Department of Environmental Quality bacteria criteria (406 MPN/100mL). Hostassociated genetic indicators were detected at frequencies of 39.2% (HF183/BacR287), 16.3% (HumM2), 74.6% (Rum2Bac), 13.0% (CowM2), 26.7% (CowM3), 19.8% (DG3), 3.2% (DG37), and 53.4% (GFD) across all water samples (n=584). Seasonal trends in avian, cattle, and human fecal pollution sources were evident over the study area. On a sample site basis, quantitative fecal source identification and

  3. Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

    Directory of Open Access Journals (Sweden)

    Brett E. Etchebarne

    2017-12-01

    Full Text Available Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70–120 min genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx. The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1 real-time thermocycler fluorescent detection of LAMP amplification and (2 visual discrimination of color change in the presence of Eriochrome Black T (EBT dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp was 97.3%, with a positive predictive value (PPV of 53.7% and a negative predictive value (NPV of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a

  4. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach.

    Science.gov (United States)

    Durso, Lisa M; Harhay, Gregory P; Bono, James L; Smith, Timothy P L

    2011-02-01

    The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats. Published by Elsevier B.V.

  5. Fecal Microbiome and Food Allergy in Pediatric Atopic Dermatitis: A Cross-Sectional Pilot Study.

    Science.gov (United States)

    Fieten, Karin B; Totté, Joan E E; Levin, Evgeni; Reyman, Marta; Meijer, Yolanda; Knulst, André; Schuren, Frank; Pasmans, Suzanne G M A

    2018-01-01

    Exposure to microbes may be important in the development of atopic disease. Atopic diseases have been associated with specific characteristics of the intestinal microbiome. The link between intestinal microbiota and food allergy has rarely been studied, and the gold standard for diagnosing food allergy (double-blind placebo-controlled food challenge [DBPCFC]) has seldom been used. We aimed to distinguish fecal microbial signatures for food allergy in children with atopic dermatitis (AD). Pediatric patients with AD, with and without food allergy, were included in this cross-sectional observational pilot study. AD was diagnosed according to the UK Working Party criteria. Food allergy was defined as a positive DBPCFC or a convincing clinical history, in combination with sensitization to the relevant food allergen. Fecal samples were analyzed using 16S rRNA microbial analysis. Microbial signature species, discriminating between the presence and absence food allergy, were selected by elastic net regression. Eighty-two children with AD (39 girls) with a median age of 2.5 years, and 20 of whom were diagnosed with food allergy, provided fecal samples. Food allergy to peanut and cow's milk was the most common. Six bacterial species from the fecal microbiome were identified, that, when combined, distinguished between children with and without food allergy: Bifidobacterium breve, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Escherichia coli, Faecalibacterium prausnitzii, and Akkermansia muciniphila (AUC 0.83, sensitivity 0.77, specificity 0.80). In this pilot study, we identified a microbial signature in children with AD that discriminates between the absence and presence of food allergy. Future studies are needed to confirm our findings. © 2018 The Author(s) Published by S. Karger AG, Basel.

  6. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

    Science.gov (United States)

    Amir, Amnon; Metcalf, Jessica L.; Amato, Katherine R.; Xu, Zhenjiang Zech; Humphrey, Greg

    2016-01-01

    ABSTRACT Immediate freezing at −20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods—95% ethanol, FTA cards, and the OMNIgene Gut kit—can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze

  7. Towards diagnostic metagenomics of Campylobacter in fecal samples

    DEFF Research Database (Denmark)

    Andersen, Sandra Christine; Kiil, Kristoffer; Harder, Christoffer Bugge

    2017-01-01

    The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, and often culture-based laboratory procedures for epidemiological source-tracing. Some...... of the challenges in diagnostic metagenomics are, that it requires a great next-generation sequencing depth and unautomated data analysis. DNA from human fecal samples spiked with 7.75 × 101-7.75 × 107 colony forming unit (CFU)/ml Campylobacter jejuni and chicken fecal samples spiked with 1 × 102-1 × 106 CFU...... Campylobacter in all the clinical samples. Sensitivity in diagnostic metagenomics is improving and has reached a clinically relevant level. There are still challenges to overcome before real-time diagnostic metagenomics can replace quantitative polymerase chain reaction (qPCR) or culture-based surveillance...

  8. The influence of Staphylococcus aureus on gut microbial ecology in an in vitro continuous culture human colonic model system.

    Science.gov (United States)

    Sannasiddappa, Thippeswamy H; Costabile, Adele; Gibson, Glenn R; Clarke, Simon R

    2011-01-01

    An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furthermore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens.

  9. An occurrence of sepsis during inpatient fecal disimpaction.

    Science.gov (United States)

    Darrow, Cory J; Devito, Justin F

    2014-01-01

    Functional constipation is a common pediatric problem that is often treated through well-established algorithms. Fecal disimpaction is the initial therapeutic step, and severe cases require hospitalization for intensive therapies. We describe a significant unexpected complication of this common clinical situation. An 8-year-old boy with suspected chronic functional constipation was hospitalized for disimpaction by continuous nasogastric administration of polyethylene glycol electrolyte (PEG-E) solution. On the sixth day of disimpaction, the patient abruptly developed fever, tachycardia, and tachypnea. Evaluation included blood culture, which grew Escherichia coli, and treatment with a course of appropriate antibiotics was provided. The safety of PEG-E solutions has been shown in studies of children with constipation, which made this patient's illness surprising. Several potential etiologies of his infection were considered, including bacterial translocation (BT). BT is defined as the passage of live microbes and microbial products from the gastrointestinal tract to extraintestinal sites, such as the bloodstream. It has been shown to occur in a variety of clinical conditions but is of unclear clinical significance. In this case, physical damage to the intestinal mucosa was thought to contribute to the potential occurrence of BT, and prolonged disimpaction was considered as a risk factor. E coli sepsis in a child undergoing inpatient nasogastric fecal disimpaction with PEG-E represents a clinical problem never before reported in the literature and should increase clinicians' indices of suspicion for uncommon complications of common procedures.

  10. Challenges of metabolomics in human gut microbiota research.

    Science.gov (United States)

    Smirnov, Kirill S; Maier, Tanja V; Walker, Alesia; Heinzmann, Silke S; Forcisi, Sara; Martinez, Inés; Walter, Jens; Schmitt-Kopplin, Philippe

    2016-08-01

    The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine. Copyright © 2016 Elsevier GmbH. All rights reserved.

  11. Step-up fecal microbiota transplantation (FMT) strategy

    Science.gov (United States)

    Cui, Bota; Li, Pan; Xu, Lijuan; Peng, Zhaoyuan; Xiang, Jie; He, Zhi; Zhang, Ting; Ji, Guozhong; Nie, Yongzhan; Wu, Kaichun; Fan, Daiming; Zhang, Faming

    2016-01-01

    ABSTRACT Gut dysbiosis is a characteristic of inflammatory bowel disease (IBD) and is believed to play a role in the pathogenesis of IBD. Fecal microbiota transplantation (FMT) is an effective strategy to restore intestinal microbial diversity and has been reported to have a potential therapeutic value in IBD. Our recent study reported a holistic integrative therapy called “step-up FMT strategy,” which was beneficial in treating steroid-dependent IBD patients. This strategy consists of scheduled FMTs combined with steroids, anti-TNF-α antibody treatment or enteral nutrition. Herein, we will elaborate the strategy thoroughly, introducing the concept, potential indication, methodology, and safety of “step-up FMT strategy” in detail. PMID:26939622

  12. A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface.

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Li

    Full Text Available Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.

  13. The impact of long-term dietary pattern of fecal donor on in vitro fecal fermentation properties of inulin.

    Science.gov (United States)

    Yang, Junyi; Rose, Devin J

    2016-04-01

    Although the composition of the gut microbiota is of interest, the functionality, or metabolic activity, of the gut microbiota is of equal importance: the gut microbiota can produce either harmful metabolites associated with human disease or beneficial metabolites that protect against disease. The purposes of this study were to determine the associations between dietary intake variables and fecal short and branched chain fatty acid (S/BCFA) concentrations; to determine the associations between dietary intake variables and inulin degradation, short and branched chain fatty acid (S/BCFA) production, and ammonia production during in vitro fecal fermentation of a highly fermentable substrate (inulin); and finally to compare results from the fermentation of inulin with those obtained in a previous report using a poorly fermentable substrate (whole wheat; Yang and Rose, Nutr. Res., 2014, 34, 749-759). Stool samples from eighteen individuals that had completed one-year dietary records were used in an in vitro fecal fermentation system with long-chain inulin as substrate. Few dietary intake variables were correlated with fecal S/BCFA concentrations; however, intakes of several plant-based foods, especially whole grain, dry beans, and certain vegetables that provided dietary fiber, plant protein, and B vitamins, were associated with acetate, propionate, butyrate, and total SCFA production during inulin fermentation. In contrast, intake of dairy and processed meats that provided cholesterol and little fiber, were associated with ammonia and BCFA production. Comparing results between inulin and whole wheat fermentations, significant correlations were only found for butyrate and BCFA, suggesting that regardless of the type of carbohydrate provided to the microbiota, long-term diet may have a pronounced effect on the propensity of the gut microbiota toward either beneficial metabolism (butyrate production) or detrimental metabolism (BCFA production). These results may help in

  14. Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators

    Science.gov (United States)

    Haack, S.K.; Duris, J.W.; Fogarty, L.R.; Kolpin, D.W.; Focazio, M.J.; Furlong, E.T.; Meyer, M.T.

    2009-01-01

    The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with animal sources of STEC) were detected in eight. Only the EC eaeA gene was positively correlated with FIB concentrations. Human-source fecal pollution was indicated by the esp gene and the human pharmaceutical carbamazepine in one of the nine samples that met all FIB recreational water quality standards. Escherichia coli rfbO157 and stx2c genes, which are typically associated with cattle sources and are of potential human health significance, were detected in one sample in the absence of tested chemicals. Chemical and gene-based indicators of fecal contamination may be present even when FIB standards are met, and some may, unlike FIB, indicate potential sources. Application of multiple water quality indicators with variable environmental persistence and fate may yield greater confidence in fecal pollution assessment and may inform remediation decisions. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

  15. Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha

    Directory of Open Access Journals (Sweden)

    Ana L. Freire

    2016-04-01

    Full Text Available Indigenous beers (chicha are part of the indigenous culture in Ecuador. The fermentation process of these beers probably relies on microorganisms from fermented substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava using bacterial culture and 16S ribosomal RNA (rRNA gene-based tag-encoded FLX amplicon pyrosequencing (bTEFAP. Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota were among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.

  16. Use of N stable isotope and microbial analyses to define wastewater influence in Mobile Bay, AL

    Energy Technology Data Exchange (ETDEWEB)

    Daskin, Joshua H. [MB 0193 Brandeis University, Waltham, MA 02454 (United States); Calci, Kevin R.; Burkhardt, William [1 Iberville Road, US Food and Drug Administration Gulf Coast Seafood Laboratory, Dauphin Island, AL 36528 (United States); Carmichael, Ruth H. [101 Bienville Boulevard, Dauphin Island Sea Lab, Dauphin Island, AL 36528 (United States); University of South Alabama, Mobile, AL, 36688 (United States)], E-mail: rcarmichael@disl.org

    2008-05-15

    We assessed short-term ecological and potential human health effects of wastewater treatment plant (WTP) effluent by measuring {delta}{sup 15}N per mille and microbial concentrations in oysters and suspended particulate matter (SPM). We also tested male-specific bacteriophage (MSB) as an alternative to fecal coliforms, to assess potential influence of wastewater contamination on shellfish. WTP effluent did not affect oyster growth or survival, but SPM and oysters acquired wastewater-specific {delta}{sup 15}N per mille . {delta}{sup 15}N values were depleted near the WTP, typical of low-level processed wastewater. Fecal coliform and MSB concentrations were higher in samples taken closest to the WTP, and MSB values were significantly correlated with {delta}{sup 15}N per mille in oyster tissues. Overall, oysters demonstrated relatively rapid integration and accumulation of wastewater-specific {delta}{sup 15}N per mille and indicator microorganisms compared to water samples. These data suggest oysters were superior sentinels compared to water, and MSB was a more reliable indicator of wastewater influence on shellfish than fecal coliforms.

  17. Use of N stable isotope and microbial analyses to define wastewater influence in Mobile Bay, AL

    International Nuclear Information System (INIS)

    Daskin, Joshua H.; Calci, Kevin R.; Burkhardt, William; Carmichael, Ruth H.

    2008-01-01

    We assessed short-term ecological and potential human health effects of wastewater treatment plant (WTP) effluent by measuring δ 15 N per mille and microbial concentrations in oysters and suspended particulate matter (SPM). We also tested male-specific bacteriophage (MSB) as an alternative to fecal coliforms, to assess potential influence of wastewater contamination on shellfish. WTP effluent did not affect oyster growth or survival, but SPM and oysters acquired wastewater-specific δ 15 N per mille . δ 15 N values were depleted near the WTP, typical of low-level processed wastewater. Fecal coliform and MSB concentrations were higher in samples taken closest to the WTP, and MSB values were significantly correlated with δ 15 N per mille in oyster tissues. Overall, oysters demonstrated relatively rapid integration and accumulation of wastewater-specific δ 15 N per mille and indicator microorganisms compared to water samples. These data suggest oysters were superior sentinels compared to water, and MSB was a more reliable indicator of wastewater influence on shellfish than fecal coliforms

  18. Use of N stable isotope and microbial analyses to define wastewater influence in Mobile Bay, AL.

    Science.gov (United States)

    Daskin, Joshua H; Calci, Kevin R; Burkhardt, William; Carmichael, Ruth H

    2008-05-01

    We assessed short-term ecological and potential human health effects of wastewater treatment plant (WTP) effluent by measuring delta 15N per thousand and microbial concentrations in oysters and suspended particulate matter (SPM). We also tested male-specific bacteriophage (MSB) as an alternative to fecal coliforms, to assess potential influence of wastewater contamination on shellfish. WTP effluent did not affect oyster growth or survival, but SPM and oysters acquired wastewater-specific delta 15N per thousand. delta 15N values were depleted near the WTP, typical of low-level processed wastewater. Fecal coliform and MSB concentrations were higher in samples taken closest to the WTP, and MSB values were significantly correlated with delta 15N per thousand in oyster tissues. Overall, oysters demonstrated relatively rapid integration and accumulation of wastewater-specific delta 15N per thousand and indicator microorganisms compared to water samples. These data suggest oysters were superior sentinels compared to water, and MSB was a more reliable indicator of wastewater influence on shellfish than fecal coliforms.

  19. Comparison of methods and animal models commonly used for investigation of fecal microbiota: Effects of time, host and gender

    DEFF Research Database (Denmark)

    Bernbom, Nete; Nørrung, Birgit; Saadbye, Peter

    2006-01-01

    and specific pathogen free (SPF). or human flora associated (HFA). A higher variation (p animals. Analysis of DGGE and T-RFLP profiles of fecal microbiota from SPF and HFA rats revealed that variation over time was less significant than...

  20. Dynamics and associations of microbial community types across the human body.

    Science.gov (United States)

    Ding, Tao; Schloss, Patrick D

    2014-05-15

    A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point. Using additional data collected over the course of 12-18 months, we used Dirichlet multinomial mixture models to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.

  1. Establishment of fecal bioassay facility at Kalpakkam

    International Nuclear Information System (INIS)

    Krishnan, H.; Yuvaraj, Ramani; Mohanty, B.N.; Sivasubramanian, K.; Venkatraman, B.

    2016-01-01

    In the event of an unusual occurrence, occupational radiation workers employed in fuel reprocessing/fuel fabrication facilities have potential risk of acquiring internal contamination, in spite of implementation of efficient engineering and administrative control measures. Quantification of internally deposited radionuclides is achieved either by (i) direct methods and/or (ii) indirect methods. In general, urinalysis is preferred for moderately absorbing (Type M-compounds of Americium) compounds, while analysis of fecal samples are preferred for slow absorption (Type S - Oxides of Plutonium) compounds. The predicted clearance of Type S and Type M compounds deposited in respiratory tract via fecal is about three to five orders higher than urinary excretion. In view of this, a facility for ashing fecal samples was established and standardization of radioanalytical procedure for quantification of Pu/Am using synthetic fecal (SF) samples was carried out

  2. Therapeutic potential of fecal microbiota transplantation

    NARCIS (Netherlands)

    Smits, Loek P.; Bouter, Kristien E. C.; de Vos, Willem M.; Borody, Thomas J.; Nieuwdorp, Max

    2013-01-01

    There has been growing interest in the use of fecal microbiota for the treatment of patients with chronic gastrointestinal infections and inflammatory bowel diseases. Lately, there has also been interest in its therapeutic potential for cardiometabolic, autoimmune, and other extraintestinal

  3. Highly Efficient Fecal Waste Incinerator, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Volume reduction is a critical element of Solid Waste Management for manned spacecraft and planetary habitations. To this end, the proposed fecal waste incinerator...

  4. Fecal microbiota transplantation: facts and controversies

    NARCIS (Netherlands)

    van Nood, Els; Speelman, Peter; Nieuwdorp, Max; Keller, Josbert

    2014-01-01

    To review the current evidence on fecal microbiota transplantations (FMTs) for recurrent Clostridium difficile infections (CDIs), metabolic syndrome and inflammatory bowel disease. Recently, a randomized trial confirmed the efficacy of this treatment strategy in patients with recurrent CDI. For

  5. Fecal Microbiota Transplantation: Clinical and experimental studies

    NARCIS (Netherlands)

    van Nood, E.

    2015-01-01

    In this thesis, several aspects of donor feces infusion, also called Fecal Microbiota Transplantation (FMT), are investigated. Historically, FMTs are given mainly for antibiotic associated diarrhea, caused by the anaerobic bacteria Clostridium difficile. Clostridium difficile infections (CDI) are

  6. Fecal Coliform Removal by River Networks

    Science.gov (United States)

    Huang, T.; Wollheim, W. M.; Stewart, R. J.

    2015-12-01

    Bacterial pathogens are a major cause of water quality impairment in the United States. Freshwater ecosystems provide the ecosystem service of reducing pathogen levels by diluting and removing pathogens as water flows from source areas through the river network. However, the integration of field-scale monitoring data and watershed-scale hydrologic models to estimate pathogen loads and removal in varied aquatic ecosystems is still limited. In this study we applied a biogeochemical river network model (the Framework for Aquatic Modeling in the Earth System or FrAMES) and utilized available field data the Oyster R. watershed, a small (51.7 km2) draining coastal New Hampshire (NH, USA), to quantify pathogen removal at the river network scale, using fecal coliform as an indicator. The Oyster R. Watershed is comprised of various land use types, and has had its water quality monitored for fecal coliform, dissolved oxygen, and turbidity since 2001. Water samples were also collected during storm events to account for storm responses. FrAMES was updated to incorporate the dominant processes controlling fecal coliform concentrations in aquatic ecosystems: spatially distributed terrestrial loading, in-stream removal, dilution, and downstream transport. We applied an empirical loading function to estimate the terrestrial loading of fecal coliform across flow conditions. Data was collected from various land use types across a range of hydrologic conditions. The loading relationship includes total daily precipitation, antecedent 24-hour rainfall, air temperature, and catchment impervious surface percentage. Attenuation is due to bacterial "die-off" and dilution processes. Results show that fecal coliform input loads varied among different land use types. At low flow, fecal coliform concentrations were similar among watersheds. However, at high flow the concentrations were significantly higher in urbanized watersheds than forested watersheds. The mainstem had lower fecal coliform

  7. Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves.

    Directory of Open Access Journals (Sweden)

    Richard Van Vleck Pereira

    Full Text Available Although antimicrobial drugs are central to combat disease in modern medicine, the use of these drugs can have undesired consequences for human and animal health. One consequence is the post-therapy excretion of pharmacological agents, such as the elimination of drug residues at very low concentrations in the milk of lactating mammals. Limited information is currently available on the impact from the exposure of the gut microbiota to drug residues using in vivo natural models. The objective of our study was to address this knowledge gap and evaluate the effect on the fecal microbiota composition from feeding preweaned dairy calves raw milk with residual concentrations of ampicillin, ceftiofur, penicillin, and oxytetracycline from birth to weaning. At birth, thirty calves were randomly assigned to a controlled feeding trial where: 15 calves were fed raw milk with no drug residues (NR, and 15 calves were fed raw milk with drug residues (DR by adding ceftiofur, penicillin, ampicillin, and oxytetracycline at final concentrations in the milk of 0.1, 0.005, 0.01, and 0.3 μg/ml, respectively. Fecal samples were rectally collected from each calf once a week starting at birth, prior to the first feeding in the trial (pre-treatment, until 6 weeks of age. Sequencing of the microbial 16S rRNA genes was conducted using the Illumina MiSeq, which provides a high resolution of the microbiota down to the genus level. Discriminant analysis showed that, except for pre-treatment samples, calves fed milk with drug residues and calves fed milk without drug residues easily discriminated at the genus level on their weekly microbial profile. However, analysis comparing the abundance of taxon between NR and DR showed significant differences only at the genus levels, and not at the phylum, class, order or family levels. These results suggest that although drug residues can result in clear discriminate gut microbial communities, they do not result in disruption of

  8. Ribonuclease 7, an antimicrobial peptide up-regulated during infection, contributes to microbial defense of the human urinary tract

    Science.gov (United States)

    Spencer, John David; Schwaderer, Andrew L.; Wang, Huanyu; Bartz, Julianne; Kline, Jennifer; Eichler, Tad; DeSouza, Kristin R.; Sims-Lucas, Sunder; Baker, Peter; Hains, David S.

    2012-01-01

    The mechanisms that maintain sterility in the urinary tract are incompletely understood; however, recent studies stress the importance of antimicrobial peptides in protecting the urinary tract from infection. Ribonuclease 7 (RNase 7), a potent antimicrobial peptide contributing to urinary tract sterility, is expressed by intercalated cells in the renal collecting tubules and is present in the urine at levels sufficient to kill bacteria at baseline. Here, we characterize the expression and function of RNase 7 in the human urinary tract during infection. Both quantitative real-time PCR and ELISA assays demonstrated increases in RNASE7 expression in the kidney along with kidney and urinary RNase 7 peptide concentrations with infection. While immunostaining localized RNase 7 production to the intercalated cells of the collecting tubule during sterility, its expression during pyelonephritis was found to increase throughout the nephron but not in glomeruli or the interstitium. Recombinant RNase 7 exhibited antimicrobial activity against uropathogens at low micromolar concentrations by disrupting the microbial membrane as determined by atomic force microscopy. Thus, RNase 7 expression is increased in the urinary tract with infection, and has antibacterial activity against uropathogens at micromolar concentrations. PMID:23302724

  9. Fecal indicator bacteria at Havana Bay

    International Nuclear Information System (INIS)

    Lopez Perez, Lisse; Gomez D'Angelo, Yamiris; Beltran Gonzalez, Jesus; Alvarez Valiente, Reinaldo

    2013-01-01

    Aims: Fecal indicator bacteria concentrations were evaluated in Havana Bay. Methods: Concentrations of traditional fecal indicator bacteria were calculated between April 2010 and February 2011, by MPN methods. Concentrations of thermo tolerant coliform (CTT), Escherichia coli, fecal streptococci (EF), intestinal enterococci (ENT) in seawater, and Clostridium perfringens in sediment surface, were determined. Results: CTT and E. coli levels were far above Cuban water quality standard for indirect contact with water, showing the negative influence of sewage and rivers on the bay. The EF and ENT were measured during sewage spills at the discharge site and they were suitable indicators of fecal contamination, but these indicators didn't show the same behavior in other selected sites. This result comes from its well-known inactivation by solar light in tropical zones and the presumable presence of humid acids in the waters of the bay. Conclusion: Fecal indicator bacteria and its statistical relationships reflect recent and chronic fecal contamination at the bay and near shores.

  10. Survival of fecal coliforms in dry-composting toilets.

    Science.gov (United States)

    Redlinger, T; Graham, J; Corella-Barud, V; Avitia, R

    2001-09-01

    The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integral de Reciclamiento de Desechos Orgánicos [SIRDOs]) that were installed on the U.S.-Mexico border in Ciudad Juárez, Chihuahua, Mexico. The purpose of this study was to determine fecal coliform reduction over time and the most probable method of this reduction. Biosolid waste samples were collected and analyzed at approximately 3 and 6 months and were classified based on U.S. Environmental Protection Agency standards. Results showed that class A compost (high grade) was present in only 35.8% of SIRDOs after 6 months. The primary mechanism for fecal coliform reduction was found to be desiccation rather than biodegradation. There was a significant correlation (P = 0.008) between classification rating and percent moisture categories of the biosolid samples: drier samples had a greater proportion of class A samples. Solar exposure was critical for maximal class A biosolid end products (P = 0.001). This study only addressed fecal coliforms as an indicator organism, and further research is necessary to determine the safety of composting toilets with respect to other pathogenic microorganisms, some of which are more resistant to desiccation.

  11. Production of human milk oligosaccharides by enzymatic and whole-cell microbial biotransformations.

    Science.gov (United States)

    Sprenger, Georg A; Baumgärtner, Florian; Albermann, Christoph

    2017-09-20

    Human milk oligosaccharides (HMO) are almost unique constituents of breast milk and are not found in appreciable amounts in cow milk. Due to several positive aspects of HMO for the development, health, and wellbeing of infants, production of HMO would be desirable. As a result, scientists from different disciplines have developed methods for the preparation of single HMO compounds. Here, we review approaches to HMO preparation by (chemo-)enzymatic syntheses or by whole-cell biotransformation with recombinant bacterial cells. With lactose as acceptor (in vitro or in vivo), fucosyltransferases can be used for the production of 2'-fucosyllactose, 3-fucosyllactose, or more complex fucosylated core structures. Sialylated HMO can be produced by sialyltransferases and trans-sialidases. Core structures as lacto-N-tetraose can be obtained by glycosyltransferases from chemical donor compounds or by multi-enzyme cascades; recent publications also show production of lacto-N-tetraose by recombinant Escherichia coli bacteria and approaches to obtain fucosylated core structures. In view of an industrial production of HMOs, the whole cell biotransformation is at this stage the most promising option to provide human milk oligosaccharides as food additive. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. The Gut Microbial Metabolite Trimethylamine-N-Oxide Is Present in Human Cerebrospinal Fluid

    Directory of Open Access Journals (Sweden)

    Daniele Del Rio

    2017-09-01

    Full Text Available Trimethylamine-N-oxide (TMAO is a small organic molecule, derived from the intestinal and hepatic metabolism of dietary choline and carnitine. Although the involvement of TMAO in the framework of many chronic diseases has been recently described, no evidence on its putative role in the central nervous system has been provided. The aim of this study was to evaluate whether TMAO is present at detectable levels in human cerebrospinal fluid (CSF. CSF was collected for diagnostic purposes from 58 subjects by lumbar puncture and TMAO was quantified by using liquid chromatography coupled with multiple-reaction monitoring mass spectrometry. The molecule was detected in all samples, at concentrations ranging between 0.11 and 6.43 µmol/L. Further analysis on CSF revealed that a total of 22 subjects were affected by Alzheimer’s disease (AD, 16 were affected by non-AD related dementia, and 20 were affected by other neurological disorders. However, the stratification of TMAO levels according to the neurological diagnoses revealed no differences among the three groups. In conclusion, we provide the first evidence that TMAO can be assessed in human CSF, but the actual impact of this dietary metabolite in the patho-physiolgy of the central nervous system requires further study.

  13. Detection of fecal contamination on beef meat surfaces using handheld fluorescence imaging device (HFID)

    Science.gov (United States)

    Current meat inspection in slaughter plants, for food safety and quality attributes including potential fecal contamination, is conducted through by visual examination human inspectors. A handheld fluorescence-based imaging device (HFID) was developed to be an assistive tool for human inspectors by ...

  14. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

    Science.gov (United States)

    Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

    2015-01-01

    The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

  15. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

    Directory of Open Access Journals (Sweden)

    Brett eWagner Mackenzie

    2015-02-01

    Full Text Available The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation, with a smaller proportion of variation associated with DNA extraction method (technical variation and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

  16. Fecal zonulin is elevated in Crohn’s disease and in cigarette smokers

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    Karin Malíčková

    2017-12-01

    Full Text Available Objectives: Human zonulin is a protein that increases permeability in the epithelial layer of the small intestine by reversibly modulating the intercellular tight junctions. There is not sufficient information available about zonulin's participation in inflammatory bowel diseases (IBD. The aim of this study was therefore to investigate fecal and serum zonulin in IBD patients and its relation to the disease localization, behavior and smoking status. Design and methods: Forty IBD patients and forty healthy persons were examined for fecal and serum zonulin concentrations by competitive ELISA (DRG International Inc. Values were correlated to IBD type, localization and behavior, and smoking. Results: Serum and fecal zonulin were significantly higher in patients with Crohn’s disease compared to ulcerative colitis (p = 0.038 for fecal zonulin, and p = 0.041 for serum zonulin concentrations. No association of serum or fecal zonulin was found with respect to IBD localization and behavior. The only difference was found with respect to smoking. Both the IBD cohort and healthy smokers showed significantly higher fecal zonulin levels (median 203 ng/mL compared to non-smokers (median 35.8 ng/mL, p < 0.001. Conclusions: Fecal and serum zonulin levels are elevated in patients with active Crohn’s disease but not with ulcerative colitis. High fecal zonulin levels in smokers irrespective of IBD point to the significant and undesirable up-regulation of gut permeability in cigarette smokers. Keywords: Zonulin, Inflammatory bowel disease, Crohn's disease, Ulcerative colitis, Smoking

  17. Interaction of Human Enteric Viruses with Microbial Compounds: Implication for Virus Persistence and Disinfection Treatments.

    Science.gov (United States)

    Waldman, Prunelle; Meseguer, Alba; Lucas, Françoise; Moulin, Laurent; Wurtzer, Sébastien

    2017-12-05

    Although the interaction between phages and bacteria has already been well described, it only recently emerged that human viruses also interact with bacteria in the mammalian gut. We studied whether this interaction could occur in tap water and thus confer enteric viruses protection against temperature and the classical disinfection treatments used in drinking water production. We demonstrated that the addition of lipopolysaccharide or peptidoglycan of bacterial origin to enterovirus provides thermal protection through stabilization of the viral capsid. This interaction plays a role when viruses are exposed to disinfection that targets the capsid, but less so when the virus genome is directly targeted. The interaction seems to be serotype-specific, suggesting that the capsid protein sequence could be important. The protection is linked to a direct association between viral particles and bacterial compounds as observed by microscopy. These results show that bacterial compounds present in the environment can affect virus inactivation.

  18. Comparison of recreational health risks associated with surfing and swimming in dry weather and post-storm conditions at Southern California beaches using quantitative microbial risk assessment (QMRA).

    Science.gov (United States)

    Tseng, Linda Y; Jiang, Sunny C

    2012-05-01

    Southern California is an increasingly urbanized hotspot for surfing, thus it is of great interest to assess the human illness risks associated with this popular ocean recreational water sport from exposure to fecal bacteria contaminated coastal waters. Quantitative microbial risk assessments were applied to eight popular Southern California beaches using readily available enterococcus and fecal coliform data and dose-response models to compare health risks associated with surfing during dry weather and storm conditions. The results showed that the level of gastrointestinal illness risks from surfing post-storm events was elevated, with the probability of exceeding the US EPA health risk guideline up to 28% of the time. The surfing risk was also elevated in comparison with swimming at the same beach due to ingestion of greater volume of water. The study suggests that refinement of dose-response model, improving monitoring practice and better surfer behavior surveillance will improve the risk estimation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water.

    Science.gov (United States)

    Fernandez-Cassi, X; Timoneda, N; Gonzales-Gustavson, E; Abril, J F; Bofill-Mas, S; Girones, R

    2017-09-18

    Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants

  20. Duckweed (Lemna minor) as a Model Plant System for the Study of Human Microbial Pathogenesis

    Science.gov (United States)

    Zhang, Yong; Hu, Yangbo; Yang, Baoyu; Ma, Fang; Lu, Pei; Li, Lamei; Wan, Chengsong; Rayner, Simon; Chen, Shiyun

    2010-01-01

    Background Plant infection models provide certain advantages over animal models in the study of pathogenesis. However, current plant models face some limitations, e.g., plant and pathogen cannot co-culture in a contained environment. Development of such a plant model is needed to better illustrate host-pathogen interactions. Methodology/Principal Findings We describe a novel model plant system for the study of human pathogenic bacterial infection on a large scale. This system was initiated by co-cultivation of axenic duckweed (Lemna minor) plants with pathogenic bacteria in 24-well polystyrene cell culture plate. Pathogenesis of bacteria to duckweed was demonstrated with Pseudomonas aeruginosa and Staphylococcus aureus as two model pathogens. P. aeruginosa PAO1 caused severe detriment to duckweed as judged from inhibition to frond multiplication and chlorophyll formation. Using a GFP-marked PAO1 strain, we demonstrated that bacteria colonized on both fronds and roots and formed biofilms. Virulence of PAO1 to duckweed was attenuated in its quorum sensing (QS) mutants and in recombinant strains overexpressing the QS quenching enzymes. RN4220, a virulent strain of S. aureus, caused severe toxicity to duckweed while an avirulent strain showed little effect. Using this system for antimicrobial chemical selection, green tea polyphenols exhibited inhibitory activity against S. aureus virulence. This system was further confirmed to be effective as a pathogenesis model using a number of pathogenic bacterial species. Conclusions/Significance Our results demonstrate that duckweed can be used as a fast, inexpensive and reproducible model plant system for the study of host-pathogen interactions, could serve as an alternative choice for the study of some virulence factors, and could also potentially be used in large-scale screening for the discovery of antimicrobial chemicals. PMID:21049039

  1. Duckweed (Lemna minor as a model plant system for the study of human microbial pathogenesis.

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    Full Text Available BACKGROUND: Plant infection models provide certain advantages over animal models in the study of pathogenesis. However, current plant models face some limitations, e.g., plant and pathogen cannot co-culture in a contained environment. Development of such a plant model is needed to better illustrate host-pathogen interactions. METHODOLOGY/PRINCIPAL FINDINGS: We describe a novel model plant system for the study of human pathogenic bacterial infection on a large scale. This system was initiated by co-cultivation of axenic duckweed (Lemna minor plants with pathogenic bacteria in 24-well polystyrene cell culture plate. Pathogenesis of bacteria to duckweed was demonstrated with Pseudomonas aeruginosa and Staphylococcus aureus as two model pathogens. P. aeruginosa PAO1 caused severe detriment to duckweed as judged from inhibition to frond multiplication and chlorophyll formation. Using a GFP-marked PAO1 strain, we demonstrated that bacteria colonized on both fronds and roots and formed biofilms. Virulence of PAO1 to duckweed was attenuated in its quorum sensing (QS mutants and in recombinant strains overexpressing the QS quenching enzymes. RN4220, a virulent strain of S. aureus, caused severe toxicity to duckweed while an avirulent strain showed little effect. Using this system for antimicrobial chemical selection, green tea polyphenols exhibited inhibitory activity against S. aureus virulence. This system was further confirmed to be effective as a pathogenesis model using a number of pathogenic bacterial species. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that duckweed can be used as a fast, inexpensive and reproducible model plant system for the study of host-pathogen interactions, could serve as an alternative choice for the study of some virulence factors, and could also potentially be used in large-scale screening for the discovery of antimicrobial chemicals.

  2. Microbial Culturomics Broadens Human Vaginal Flora Diversity: Genome Sequence and Description of Prevotella lascolaii sp. nov. Isolated from a Patient with Bacterial Vaginosis.

    Science.gov (United States)

    Diop, Khoudia; Diop, Awa; Levasseur, Anthony; Mediannikov, Oleg; Robert, Catherine; Armstrong, Nicholas; Couderc, Carine; Bretelle, Florence; Raoult, Didier; Fournier, Pierre-Edouard; Fenollar, Florence

    2018-03-01

    Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%). Based on an analysis of the full-length 16S rRNA gene sequences, phylogenetic analysis showed that the strain khD1 T exhibited 90% sequence similarity with Prevotella loescheii, the phylogenetically closest validated Prevotella species. With 3,763,057 bp length, the genome of strain khD1 T contained (mol%) 48.7 G + C and 3248 predicted genes, including 3194 protein-coding and 54 RNA genes. Given the phenotypical and biochemical characteristic results as well as genome sequencing, strain khD1 T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella lascolaii sp. nov. is proposed. The type strain is khD1 T ( = CSUR P0109, = DSM 101754). These results show that microbial culturomics greatly improves the characterization of the human microbiome repertoire by isolating potential putative new species. Further studies will certainly clarify the microbial mechanisms of pathogenesis of these new microbes and their role in health and disease. Microbial culturomics is an important new addition to the diagnostic medicine toolbox and warrants attention in future medical, global health, and integrative biology postgraduate teaching curricula.

  3. Occurrence of fecal indicator bacteria in surface waters and the subsurface aquifer in Key Largo, Florida.

    Science.gov (United States)

    Paul, J H; Rose, J B; Jiang, S; Kellogg, C; Shinn, E A

    1995-01-01

    Sewage waste disposal facilities in the Florida Keys include septic tanks and individual package plants in place of municipal collection facilities in most locations. In Key Largo, both facilities discharge into the extremely porous Key Largo limestone. To determine whether there was potential contamination of the subsurface aquifer and nearby coastal surface waters by such waste disposal practices, we examined the presence of microbial indicators commonly found in sewage (fecal coliforms, Clostridium perfringens, and enterococci) and aquatic microbial parameters (viral direct counts, bacterial direct counts, chlorophyll a, and marine vibriophage) in injection well effluent, monitoring wells that followed a transect from onshore to offshore, and surface waters above these wells in two separate locations in Key Largo in August 1993 and March 1994. Effluent and waters from onshore shallow monitoring wells (1.8- to 3.7-m depth) contained two or all three of the fecal indicators in all three samples taken, whereas deeper wells (10.7- to 12.2-m depth) at these same sites contained few or none. The presence of fecal indicators was found in two of five nearshore wells (i.e., those that were or = 2.1 to 5.7 miles [aquifer, parts of the nearshore aquifer, and certain surface waters has occurred.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7793943

  4. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray.

    Science.gov (United States)

    Colombo, Ana Paula V; Boches, Susan K; Cotton, Sean L; Goodson, J Max; Kent, Ralph; Haffajee, Anne D; Socransky, Sigmund S; Hasturk, Hatice; Van Dyke, Thomas E; Dewhirst, Floyd; Paster, Bruce J

    2009-09-01

    This study compared the subgingival microbiota of subjects with refractory periodontitis (RP) to those in subjects with treatable periodontitis (GRs = good responders) or periodontal health (PH) using the Human Oral Microbe Identification Microarray (HOMIM). At baseline, subgingival plaque samples were taken from 47 subjects with periodontitis and 20 individuals with PH and analyzed for the presence of 300 species by HOMIM. The subjects with periodontitis were classified as having RP (n = 17) based on mean attachment loss (AL) and/or more than three sites with AL >or=2.5 mm after scaling and root planing, surgery, and systemically administered amoxicillin and metronidazole or as GRs (n = 30) based on mean attachment gain and no sites with AL >or=2.5 mm after treatment. Significant differences in taxa among the groups were sought using the Kruskal-Wallis and chi(2) tests. More species were detected in patients with disease (GR or RP) than in those without disease (PH). Subjects with RP were distinguished from GRs or those with PH by a significantly higher frequency of putative periodontal pathogens, such as Parvimonas micra (previously Peptostreptococcus micros or Micromonas micros), Campylobacter gracilis, Eubacterium nodatum, Selenomonas noxia, Tannerella forsythia (previously T. forsythensis), Porphyromonas gingivalis, Prevotella spp., Treponema spp., and Eikenella corrodens, as well as unusual species (Pseudoramibacter alactolyticus, TM7 spp. oral taxon [OT] 346/356, Bacteroidetes sp. OT 272/274, Solobacterium moorei, Desulfobulbus sp. OT 041, Brevundimonas diminuta, Sphaerocytophaga sp. OT 337, Shuttleworthia satelles, Filifactor alocis, Dialister invisus/pneumosintes, Granulicatella adiacens, Mogibacterium timidum, Veillonella atypica, Mycoplasma salivarium, Synergistes sp. cluster II, and Acidaminococcaceae [G-1] sp. OT 132/150/155/148/135) (P spp. cluster I, Capnocytophaga sputigena, Cardiobacterium hominis, Haemophilus parainfluenzae, Lautropia mirabilis

  5. Isotopic nitrogen in fecal fiber as an indicator of winter diet in caribou and muskoxen

    Science.gov (United States)

    Gustine, David D.; Barboza, Perry S.; Addison, Jennifer; Shively, Rachel; Oliver, Lola

    2014-01-01

    RATIONALE: The ratios of stable nitrogen isotopes (δ15N values) in excreta have been used to examine aspects of trophic and nutritional ecology across taxa. Nitrogen fractions in feces of herbivores include endogenous (e.g., sloughed intestinal cells, unresorbed digestive secretions, and microbial debris) and dietary sources. For animals such as large herbivores, that have diets and feces with high concentrations of indigestible fiber, endogenous 15N may constrain the use of fecal δ15N values to estimate dietary δ15N values and reconstruct diets. METHODS: We compared two techniques (detergent and detergent-free) to isolate fractions of plant fibers in the forages of caribou (Rangifer tarandus) and muskoxen (Ovibos moschatus); estimated the discrimination factors between the δ15N values of fecal fiber residues and of the diets of captive animals; and used the more effective isotopic tracer of dietary δ15N values to examine the relationships between the δ15N values of fecal residues and diet composition in several populations of wild caribou and muskoxen throughout North America in winter. RESULTS: The detergent-based approach contaminated the fractions of plant fibers in forages and feces with 14N, whereas the detergent-free method was a good proxy to estimate δ15N values of plant fibers (r2= 0.92) and provided a better estimate of the fecal-fiber to diet discrimination factor for both species (caribou = 3.6‰; muskoxen = 2.8‰). In wild populations, the δ15N values of fecal fibers reflected diet composition in muskoxen (adjusted R2= 0.43) but not caribou (adjusted R2= 0.06). CONCLUSIONS: Contamination from detergent residues prohibited the use of detergent extraction in isolating forage 15N from endogenous 15N in the feces of herbivores. Although δ15N values in fecal fibers can be used to track dietary δ15N values in wild herbivores, discrimination between fecal extracts and diet may vary with the contribution of endogenous nitrogen (N), and

  6. Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

    Science.gov (United States)

    Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

    2015-03-15

    Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Effect of probiotics in poultry diet on microbial hazards of poultry meat

    Directory of Open Access Journals (Sweden)

    A Javadi

    2009-05-01

    Full Text Available Probiotics are products from microbial cells that have useful influence on health and tranquility of humans. According to numerous studies, many valuable properties such as anti-mutagenic, anti-carcinogenic, boosting body immunity and resistance against enteric pathogens have been attributed to probiotics. Therefore the aim of this study is to specify the effect of probiotics use in the diet of broilers on microbial hazards of poultry meat. For this purpose, two groups of treatment and control each containing 40 broiler chicks were chosen and edible probiotic were given to the treatment group throughout the whole 55 days of the rearing period under the same conditions and following slaughter 100 grams of skin and breast meat samples were collected from each carcass and transferred to food hygiene laboratory of the veterinary faculty under sterile conditions. Total microbial count,    Staphylococcus aureous, fecal Streptococci, Clostridium perferingens, Coliforms counts and detection of Salmonella and E.coli were performedon the samples according to standard approaches of Iran. The results were analyzed using independent t-Test and Chi-square test. Comparison of the means of total microbial count, coliform, enteric streptococci and meat staphylococcus counts in the control and treatment group using independent t-Test showed a significant reduction (p

  8. Molecular detection of Campylobacter spp. and fecal indicator bacteria during the northern migration of Sandhill Cranes (Grus canadensis) at the Central Platte River

    Science.gov (United States)

    The annual Sandhill crane (Grus canadensis) migration through Nebraska is thought to be a major source of fecal pollution to the Platte River, but of unknown human health risk. To better understand potential risks, the presence of Campylobacter species and fecal bacteria were exa...

  9. Modeling Fate and Transport of Fecal Coliform Bacteria Using SWAT 2005 (Case Study: Jajrood River Watershed, Iran)

    Science.gov (United States)

    Maghrebi, M.; Tajrishy, M.

    2010-12-01

    Jajrood River watershed is one of the main drinking water resources of the capital city of Tehran, Iran. In addition it has been available as many recreational usages especially in the warm months. As a result of being located near one of the crowded cities of the world, a variety of microbial pollutions is commonly perceived in the Jajrood River. Among them, there are strong concerns about fecal coliform bacteria concentration. This article aimed to model fate and transport of fecal coliform bacteria in Jajrood River watershed using Soil and Water Assessment Tool (SWAT) model version 2005. Potential pollutant sources in the study area were detected and quantified for modeling purposes. In spite of being lack of knowledge about bacteria die-off rate in small river bodies, as well as in other watershed-based forms, fecal coliform bacteria die-off rates were estimated using both laboratory and field data investigations with some simplifications. The SWAT model was calibrated over an extended time period (1997-2002) for this watershed. The river flow calibrated using SUFI-2 software and resulted in a very good outputs (R2=0.82, E=0.81). Furthermore SWAT model was validated over January 2003 to September 2005 in the study area and has resulted in good outputs (R2=0.61, E=0.57). This research illustrates SWAT 2005 capability to model fecal coliform bacteria in a populated watershed, and deals with most of watershed microbial pollution sources that are usually observed in developing countries. Fecal coliform concentration simulation results were mostly in the same order in comparison with real data. However, Differences were judged to be related to lack of input data. In this article different aspects of SWAT capabilities for modeling of fecal coliform bacteria concentration will be reviewed and it will present new insights in bacteria modeling procedures especially for mountainous, high populated and small sized watersheds.

  10. Anthropogenic Pollution Impact on Microbial Contamination of Lake ...

    African Journals Online (AJOL)

    Indicator bacteria were enumerated by membrane filtration while pathogenic bacteria were recovered by broth enrichment of water samples. Microbial load did not differ significantly with season and locations but fecal coliform (FC) had positive significant correlation (r = 0.36*; P < 0.05) with season. Mean total coliform (TC) ...

  11. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.

    Directory of Open Access Journals (Sweden)

    Teresia Hallström

    Full Text Available Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13 bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352-374. This specific interaction leaves the terminal complement complex (TCC regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response.

  12. Microbial quality of water in rural communities of Trinidad

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    Pedro Welch

    2000-09-01

    Full Text Available A cross-sectional study was conducted in four rural communities of northeastern Trinidad to determine the microbial quality of water supply to households and that quality's relationship to source and storage device. Of the 167 household water samples tested, total coliforms were detected in 132 of the samples (79.0%, fecal coliforms in 102 (61.1%, and E. coli in 111 (66.5%. There were significant differences among the towns in the proportion of the samples contaminated with coliforms (P < 0.001 and E. coli (P < 0.001. Of 253 strains of E. coli studied, 4 (1.6% were mucoid, 9 (3.6% were hemolytic, and 37 (14.6% were nonsorbitol fermenters. Of 69 isolates of E. coli tested, 10 (14.5% were verocytotoxigenic. Twenty-eight (14.0% of 200 E. coli isolates tested belonged to enteropathogenic serogroups. Standpipe, the most common water source, was utilized by 57 (34.1% of the 167 households. Treated water (pipeborne in homes, standpipes, or truckborne was supplied to 119 households (71.3%, while 48 households (28.7% used water from untreated sources (rain, river/stream, or well as their primary water supply. The type of household storage device was associated with coli-form contamination. Water stored in drums, barrels, or buckets was more likely to harbor fecal coliforms (74.2% of samples than was water stored in tanks (53.3% of samples, even after controlling for water source (P = 0.04. Compared with water from other sources, water piped into homes was significantly less likely to be contaminated with total coliforms (56.9% versus 88.8%, P < 0.001 and fecal coliforms (41.2% versus 69.8%, P < 0.01, even when the type of storage device was taken into account. However, fecal contamination was not associated with whether the water came from a treated or untreated source. We concluded that the drinking water in rural communities in Trinidad was grossly unfit for human consumption, due both to contamination of various water sources and during household

  13. Microbial quality of water in rural communities of Trinidad

    Directory of Open Access Journals (Sweden)

    Welch Pedro

    2000-01-01

    Full Text Available A cross-sectional study was conducted in four rural communities of northeastern Trinidad to determine the microbial quality of water supply to households and that quality's relationship to source and storage device. Of the 167 household water samples tested, total coliforms were detected in 132 of the samples (79.0%, fecal coliforms in 102 (61.1%, and E. coli in 111 (66.5%. There were significant differences among the towns in the proportion of the samples contaminated with coliforms (P < 0.001 and E. coli (P < 0.001. Of 253 strains of E. coli studied, 4 (1.6% were mucoid, 9 (3.6% were hemolytic, and 37 (14.6% were nonsorbitol fermenters. Of 69 isolates of E. coli tested, 10 (14.5% were verocytotoxigenic. Twenty-eight (14.0% of 200 E. coli isolates tested belonged to enteropathogenic serogroups. Standpipe, the most common water source, was utilized by 57 (34.1% of the 167 households. Treated water (pipeborne in homes, standpipes, or truckborne was supplied to 119 households (71.3%, while 48 households (28.7% used water from untreated sources (rain, river/stream, or well as their primary water supply. The type of household storage device was associated with coli-form contamination. Water stored in drums, barrels, or buckets was more likely to harbor fecal coliforms (74.2% of samples than was water stored in tanks (53.3% of samples, even after controlling for water source (P = 0.04. Compared with water from other sources, water piped into homes was significantly less likely to be contaminated with total coliforms (56.9% versus 88.8%, P < 0.001 and fecal coliforms (41.2% versus 69.8%, P < 0.01, even when the type of storage device was taken into account. However, fecal contamination was not associated with whether the water came from a treated or untreated source. We concluded that the drinking water in rural communities in Trinidad was grossly unfit for human consumption, due both to contamination of various water sources and during household

  14. Microbial dynamics during industrial rearing, processing, and storage of the tropical house cricket (Gryllodes sigillatus) for human consumption.

    Science.gov (United States)

    Vandeweyer, Dries; Wynants, Enya; Crauwels, Sam; Verreth, Christel; Viaene, Nikolaas; Claes, Johan; Lievens, Bart; Van Campenhout, Leen

    2018-04-06

    In this study, the microbiota during industrial rearing, processing, and storage of the edible tropical house cricket, Gryllodes sigillatus , was investigated. To this end, samples were analyzed of the cricket feed, before feeding as well as taken from the cages, and the crickets during rearing, after harvest, and after processing into frozen, oven-dried, and smoked and subsequently oven-dried end products. Although the feed contained lower microbial numbers than the crickets, both were dominated by the same species-level operational taxonomic units as determined by Illumina Miseq sequencing. They corresponded, among others, to members of Porphyromonadaceae, Fusobacterium , Parabacteroides and Erwinia The harvested crickets contained high microbial numbers, but none of the investigated food pathogens Salmonella spp., Listeria monocytogenes , Bacillus cereus , and coagulase-positive staphylococci. However, some possible mycotoxin-producing fungi were isolated from the crickets. A post-harvest heat treatment, shortly boiling the crickets, reduced microbial numbers, but an endospore load of 2.4 log cfu/g remained. After processing, an increase in microbial counts was observed for dried and smoked plus dried crickets. Additionally, in the smoked plus dried crickets, a high abundance of a Bacillus sp. was observed. Considering the possible occurrence of food-pathogenic species from this genus, it is advised to apply a heat treatment which is sufficient to eliminate spores. Nevertheless, the microbial numbers remained constant over a six-month storage period, frozen (frozen end product) or at ambient temperature (oven-dried and smoked plus dried end products). Importance. The need for sustainable protein sources has led to the emergence of a new food sector, producing and processing edible insects into foods. However, insight into the microbial quality of this new food and into the microbial dynamics during rearing, processing and storage of edible insects is still

  15. Fermentation of animal components in strict carnivores: a comparative study with cheetah fecal inoculum.

    Science.gov (United States)

    Depauw, S; Bosch, G; Hesta, M; Whitehouse-Tedd, K; Hendriks, W H; Kaandorp, J; Janssens, G P J

    2012-08-01

    The natural diet of felids contains highly digestible animal tissues but also fractions resistant to small intestinal digestion, which enter the large intestine where they may be fermented by the resident microbial population. Little information exists on the microbial degradability of animal tissues in the large intestine of felids consuming a natural diet. This study aimed to rank animal substrates in their microbial degradability by means of an in vitro study using captive cheetahs fed a strict carnivorous diet as fecal donors. Fresh cheetah fecal samples were collected, pooled, and incubated with various raw animal substrates (chicken cartilage, collagen, glucosamine-chondroitin, glucosamine, rabbit bone, rabbit hair, and rabbit skin; 4 replicates per substrate) for cumulative gas production measurement in a batch culture technique. Negative (cellulose) and positive (casein and fructo-oligosaccharides; FOS) controls were incorporated in the study. Additionally, after 72 h of incubation, short-chain fatty acids (SCFA), including branched-chain fatty acids (BCFA), and ammonia concentrations were determined for each substrate. Glucosamine and glucosamine-chondroitin yielded the greatest organic matter cumulative gas volume (OMCV) among animal substrates (P carnivore, and indicates that animal tissues have potentially similar functions as soluble or insoluble plant fibers in vitro. Further research is warranted to assess the impact of fermentation of each type of animal tissue on gastro-intestinal function and health in the cheetah and other felid species.

  16. Spatio-temporal distribution of fecal indicators in three rivers of the Haihe River Basin, China.

    Science.gov (United States)

    Wang, Yawei; Chen, Yanan; Zheng, Xiang; Gui, Chengmin; Wei, Yuansong

    2017-04-01

    Because of their significant impact on public health, waterborne pathogens, especially bacteria and viruses, are frequently monitored in surface water to assess microbial quality of water bodies. However, more than one billion people worldwide currently lack access to safe drinking water, and a diversity of waterborne outbreaks caused by pathogens is reported in nations at all levels of economic development. Spatio-temporal distribution of conventional pollutants and five pathogenic microorganisms were discussed for the Haihe River Basin. Land use and socio-economic assessments were coupled with comprehensive water quality monitoring. Physical, chemical, and biological parameters were measured at 20 different sites in the watershed for 1 year, including pH, temperature, conductivity, dissolved oxygen, turbidity, chemical oxygen demand, ammonia-N, total and fecal coliforms, E. coli, and Enterococcus. The results highlighted the high spatio-temporal variability in pathogen distribution at watershed scale: high concentration of somatic coliphages and fecal indicator bacteria in March and December and their very low concentration in June and September. All pathogens were positively correlated to urban/rural residential/industrial land and negatively correlated to other four land use types. Microbial pollution was greatly correlated with population density, urbanization rate, and percentage of the tertiary industry in the gross domestic product. In the future, river microbial risk control strategy should focus more on the effective management of secondary effluent of wastewater treatment plant and land around rivers.

  17. Human neutrophil clearance of bacterial pathogens triggers anti-microbial γδ T cell responses in early infection.

    Directory of Open Access Journals (Sweden)

    Martin S Davey

    2011-05-01

    Full Text Available Human blood Vγ9/Vδ2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vγ9/Vδ2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8. In turn, Vγ9/Vδ2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN-γ and tumor necrosis factor (TNF-α. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP, requires cell-cell contact of Vγ9/Vδ2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1, and results in a TNF-α dependent proliferation of Vγ9/Vδ2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting γδ T cell responses in vitro. Patients with acute peritoneal-dialysis (PD-associated bacterial peritonitis--characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity--show a selective activation of local Vγ9/Vδ2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The γδ T cell-driven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of γδ T cells and TNF-α and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive γδ T cells in

  18. Effect of Probiotic Bacteria on Microbial Host Defense, Growth, and Immune Function in Human Immunodeficiency Virus Type-1 Infection

    Directory of Open Access Journals (Sweden)

    Stig Bengmark

    2011-12-01

    Full Text Available The hypothesis that probiotic administration protects the gut surface and could delay progression of Human Immunodeficiency Virus type1 (HIV-1 infection to the Acquired Immunodeficiency Syndrome (AIDS was proposed in 1995. Over the last five years, new studies have clarified the significance of HIV-1 infection of the gut associated lymphoid tissue (GALT for subsequent alterations in the microflora and breakdown of the gut mucosal barrier leading to pathogenesis and development of AIDS. Current studies show that loss of gut CD4+ Th17 cells, which differentiate in response to normal microflora, occurs early in HIV-1 disease. Microbial translocation and suppression of the T regulatory (Treg cell response is associated with chronic immune activation and inflammation. Combinations of probiotic bacteria which upregulate Treg activation have shown promise in suppressing pro inflammatory immune response in models of autoimmunity including inflammatory bowel disease and provide a rationale for use of probiotics in HIV-1/AIDS. Disturbance of the microbiota early in HIV-1 infection leads to greater dominance of potential pathogens, reducing levels of bifidobacteria and lactobacillus species and increasing mucosal inflammation. The interaction of chronic or recurrent infections, and immune activation contributes to nutritional deficiencies that have lasting consequences especially in the HIV-1 infected child. While effective anti-retroviral therapy (ART has enhanced survival, wasting is still an independent predictor of survival and a major presenting symptom. Congenital exposure to HIV-1 is a risk factor for growth delay in both infected and non-infected infants. Nutritional intervention after 6 months of age appears to be largely ineffective. A meta analysis of randomized, controlled clinical trials of infant formulae supplemented with Bifidobacterium lactis showed that weight gain was significantly greater in infants who received B. lactis compared to

  19. Human Neutrophil Clearance of Bacterial Pathogens Triggers Anti-Microbial γδ T Cell Responses in Early Infection

    Science.gov (United States)

    Roberts, Gareth W.; Heuston, Sinéad; Brown, Amanda C.; Chess, James A.; Toleman, Mark A.; Gahan, Cormac G. M.; Hill, Colin; Parish, Tanya; Williams, John D.; Davies, Simon J.; Johnson, David W.; Topley, Nicholas; Moser, Bernhard; Eberl, Matthias

    2011-01-01

    Human blood Vγ9/Vδ2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vγ9/Vδ2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vγ9/Vδ2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-γ and tumor necrosis factor (TNF)-α. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vγ9/Vδ2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-α dependent proliferation of Vγ9/Vδ2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting γδ T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vγ9/Vδ2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The γδ T cell-driven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of γδ T cells and TNF-α and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive γδ T cells in early

  20. Lack of direct effects of agrochemicals on zoonotic pathogens and fecal indicator bacteria.

    Science.gov (United States)

    Staley, Zachery R; Senkbeil, Jacob K; Rohr, Jason R; Harwood, Valerie J

    2012-11-01

    Agrochemicals, fecal indicator bacteria (FIB), and pathogens frequently contaminate water simultaneously. No significant direct effects of fertilizer, atrazine, malathion, and chlorothalonil on the survival of Escherichia coli, Enterococcus faecalis, Salmonella enterica, human polyomaviruses, and adenovirus were detected, supporting the assertion that previously observed effects of agrochemicals on FIB were indirect.

  1. An evaluation of the therapeutic potential of fecal microbiota transplantation to treat infectious and metabolic diseases

    NARCIS (Netherlands)

    Groen, Albert K.; Nieuwdorp, Max

    2017-01-01

    Fecal microbiota transplantation (FMT) has had a long history in medicine for treating a number of human diseases. As early as during the 4(th) century BC, FMT was used in China to treat patients with food poisoning and diarrhea. Over time, the method became obsolete, particularly after the

  2. Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults.

    Science.gov (United States)

    Karl, J Philip; Meydani, Mohsen; Barnett, Junaidah B; Vanegas, Sally M; Barger, Kathryn; Fu, Xueyan; Goldin, Barry; Kane, Anne; Rasmussen, Helen; Vangay, Pajau; Knights, Dan; Jonnalagadda, Satya S; Saltzman, Edward; Roberts, Susan B; Meydani, Simin N; Booth, Sarah L

    2017-10-01

    Background: Emerging evidence suggests novel roles for bacterially derived vitamin K forms known as menaquinones in health and disease, which may be attributable in part to anti-inflammatory effects. However, the relevance of menaquinones produced by gut bacteria to vitamin K requirements and inflammation is undetermined. Objective: This study aimed to quantify fecal menaquinone concentrations and identify associations between fecal menaquinone concentrations and serum vitamin K concentrations, gut microbiota composition, and inflammation. Design: Fecal and serum menaquinone concentrations, fecal microbiota composition, and plasma and fecal cytokine concentrations were measured in 80 men and postmenopausal women (48 men, 32 women, age 40-65 y) enrolled in a randomized, parallel-arm, provided-food trial. After consuming a run-in diet for 2 wk, participants were randomly assigned to consume a whole grain-rich (WG) or a refined grain-based (RG) diet for 6 wk. Outcomes were measured at weeks 2 and 8. Results: The median total daily excretion of menaquinones in feces was 850 nmol/d but was highly variable (range: 64-5358 nmol/d). The total median (IQR) fecal concentrations of menaquinones decreased in the WG diet compared with the RG diet [-6.8 nmol/g (13.0 nmol/g) dry weight for WG compared with 1.8 nmol/g (12.3 nmol/g) dry weight for RG; P < 0.01)]. However, interindividual variability in fecal menaquinone concentrations partitioned individuals into 2 distinct groups based on interindividual differences in concentrations of different menaquinone forms rather than the diet group or the time point. The relative abundances of several gut bacteria taxa, Bacteroides and Prevotella in particular, differed between these groups, and 42% of identified genera were associated with ≥1 menaquinone form. Menaquinones were not detected in serum, and neither fecal concentrations of individual menaquinones nor the menaquinone group was associated with any marker of inflammation

  3. Functional fecal retention with encopresis in childhood.

    Science.gov (United States)

    Loening-Baucke, Vera

    2004-01-01

    The most common cause of encopresis in children is functional fecal retention (FFR). An international working team suggested that FFR be defined by the following criteria: a history of >12 weeks of passage of encopresis; to compare these patients to those identified as having FFR by historical symptoms or physical examination; to determine whether 1-year treatment outcome varied depending on which definition for FFR was used; and to suggest improvements to the ROME II criteria, if necessary. Data were reviewed from the history and physical examination of 213 children with encopresis. One-year outcomes identified were failure, successful treatment, or full recovery. Only 88 (41%) of the patients with encopresis fit the ROME II criteria for FFR, whereas 181 (85%) had symptoms of FFR by history or physical examination. Thirty-two (15%) patients did not fit criteria for FFR, but only 6 (3%) appeared to have nonretentive fecal soiling. Rates of successful treatment (50%) and recovery (39%) were not significantly different in the two groups. The ROME II criteria for FFR are too restrictive and do not identify many children with encopresis who have symptoms of FFR. The author suggests that the ROME II criteria for FFR could be improved by including the following additional items: a history of BMs that obstruct the toilet, a history of chronic abdominal pain relieved by enemas or laxatives, and the presence of an abdominal fecal mass or rectal fecal mass.

  4. [Biofeedback effectiveness in patients with fecal incontinence].

    Science.gov (United States)

    Guerra-Mora, José Raúl; Buenrostro-Acebes, José María; Erciga-Vergara, Nancy; Zubieta-O'Farrill, Gregorio; Castillo-Calcáneo, Juan de Dios; Mosqueda, Maria Elena; Monroy-Argumedo, Montserrat; González-Alvarado, Carlos; Villanueva-Saenz, Eduardo

    2015-01-01

    Fecal incontinence is defined as an involuntary bowel movement through the anal canal in inadequate time and place. There are different types of therapies for the management of fecal incontinence, being biofeedback therapy one of the most effective techniques. The aim of this study was to evaluate the necessary number of sessions of biofeedback electromyographyc therapy to achieve the maximum sphincteric complex contraction. Descriptive, retrospective and longitudinal study. 65 patients with fecal incontinence were included. Weekly electromyographyc biofeedback therapies were applied, with a maximum of 6, in which the sphincteric complex contraction was measured. A two ways Friedman analysis was made to determine the significant differences between the sessions. A total of 65 patients were evaluated for fecal incontinence. The values for pelvic floor contraction were significantly higher in the third session, and did not show any significant difference in posterior sessions. The maximum contraction of the sphicnteric complex was achieved in the third weekly biofeedback session, without any significant differences in the posterior sessions.

  5. Prevalence of fecal shedding of Salmonella organisms among captive green iguanas and potential public health implications.

    Science.gov (United States)

    Burnham, B R; Atchley, D H; DeFusco, R P; Ferris, K E; Zicarelli, J C; Lee, J H; Angulo, F J

    1998-07-01

    To determine prevalence of fecal shedding of Salmonella organisms among captive green iguanas (Iguana iguana). Cohort study. 12 captive green iguanas. Iguanas were isolated in an environmental chamber, and fecal samples were collected weekly for 10 consecutive weeks. Samples were incubated aerobically in tetrathionate broth for 18 to 24 hours. Aliquots were then transferred to Hektoen and Salmonella-Shigella agar plates and incubated for an additional 18 to 24 hours. Isolated colonies were subcultured on nutrient agar slants, and Salmonella isolates were serogrouped and serotyped. All 12 iguanas were found to be shedding Salmonella organisms at least once during the study, and multiple serotypes were isolated from 7 of the 12. Salmonella organisms were isolated from 88 of 106 (83%) fecal samples; 21 samples contained multiple Salmonella serotypes. Overall, 11 Salmonella serotypes were identified. In 74 of 100 instances, when a particular Salmonella serotype was isolated from an individual iguana, the same serotype was also isolated from a subsequent fecal sample from that iguana. Results suggested that most iguanas have a stable mixture of Salmonella serotypes in their intestinal tracts and intermittently or continuously shed Salmonella organisms in their feces. Veterinarians should advise their clients on precautions for reducing the risk of acquiring these organisms from their pets. Public health officials trying to determine whether an iguana is the source of a specific Salmonella serotype that caused infection in human patients should submit at least 3 fecal samples collected from the iguana 1 week apart for bacterial culture.

  6. Case report: Stercoral sigmoid colonic perforation with fecal peritonitis

    International Nuclear Information System (INIS)

    Sharma, Monika; Agrawal, Anjali

    2010-01-01

    Chronic constipation can lead to fecal impaction. It can also rarely lead to catastrophic complications like perforation, colonic obstruction, and fecal peritonitis. We report a rare case of stercoral sigmoid colonic perforation with fecal peritonitis and pneumoperitoneum, which was diagnosed on preoperative CT scan

  7. Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome.

    Science.gov (United States)

    Mizuno, Shinta; Masaoka, Tatsuhiro; Naganuma, Makoto; Kishimoto, Taishiro; Kitazawa, Momoko; Kurokawa, Shunya; Nakashima, Moeko; Takeshita, Kozue; Suda, Wataru; Mimura, Masaru; Hattori, Masahira; Kanai, Takanori

    2017-01-01

    Dysbiosis is associated with various systemic disorders including irritable bowel syndrome (IBS). Fecal microbiota transplantation (FMT) might restore intestinal microbial balance. The study aimed to determine the safety and efficacy of FMT in IBS patients, as well as also positive predictors for FMT. This was a single-arm, open-label study. Eligible patients were diagnosed based on Rome III Diagnostic Criteria. Fecal materials were administered to the patient via colonoscopy. The primary end point was a change in the Bristol stool form scale at 4 weeks after FMT. Recovery to types 3-4 was considered a clinical response. The secondary end point was a change in intestinal microbiota and psychological status using the Hamilton Rating Scale. Ten patients were enrolled. Six patients achieved a clinical response. The diversity of patients 4 weeks after FMT increased significantly compared with patients before FMT, and that of responding patients was significantly higher than non-responder patients. The abundance of Bifidobacterium in effective donors was significantly higher than in ineffective donors and patients. Psychological status of all patients was significantly improved after FMT. FMT for patients with IBS is safe, and relatively effective. Bifidobacterium-rich fecal donor may be a positive predictor for successful FMT. Key Summary: (1) Dysbiosis is associated with various gastrointestinal disorders including IBS. (2) FMT has potential to restore intestinal microbial balance. (3) We showed that FMT improved stool form and psychological status of IBS patients. (4) Bifidobacterium-rich donor efficiently induced symbiosis in IBS patients. © 2017 The Author(s) Published by S. Karger AG, Basel.

  8. Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies

    Science.gov (United States)

    Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992–2013). Sites were chosen from 718 public drinking-water systems with a range of hydrogeological conditions. Focus was on testing the value of indicato...

  9. The Fecal Microbiota in the Domestic Cat (Felis catus Is Influenced by Interactions Between Age and Diet; A Five Year Longitudinal Study

    Directory of Open Access Journals (Sweden)

    Emma N. Bermingham

    2018-06-01

    Full Text Available In humans, aging is associated with changes in the gastrointestinal microbiota; these changes may contribute to the age-related increase in incidence of many chronic diseases, including Type 2 diabetes. The life expectancies of cats are increasing, and they are also exhibiting the same types of diseases. While there are some studies investigating the impacts of diets on gastrointestinal microbiota in young cats, the impacts of aging in older cats has not been explored. We followed a cohort of related kittens, maintained on two commercial diets (kibbled and canned from weaning (8 weeks to 5 years of age (260 weeks. We hypothesized that the long-term feeding of specific diet formats would (a lead to microbial composition changes due to aging, (b impact body composition, and (c affect insulin sensitivity in the aging cat. We observed that both diet and age affected fecal microbial composition, and while age correlated with changes in body composition, diet had no effect on body composition. Similarly insulin sensitivity was not affected by age nor diet. 16S rRNA sequencing found unclassified Peptostreptococcaceae were prominent across all ages averaging 21.3% of gene sequence reads and were higher in cats fed canned diets (average of 25.7% of gene sequence reads, vs. 17.0% for kibble-fed cats. Age-related effects on body composition and insulin sensitivity may become apparent as the cats grow older; this study will continue to assess these parameters.

  10. Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX.

    Science.gov (United States)

    Van den Abbeele, Pieter; Grootaert, Charlotte; Marzorati, Massimo; Possemiers, Sam; Verstraete, Willy; Gérard, Philippe; Rabot, Sylvie; Bruneau, Aurélia; El Aidy, Sahar; Derrien, Muriel; Zoetendal, Erwin; Kleerebezem, Michiel; Smidt, Hauke; Van de Wiele, Tom

    2010-08-01

    Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.

  11. Identification of hotspots and trends of fecal surface water pollution in developing countries

    Science.gov (United States)

    Reder, Klara; Flörke, Martina; Alcamo, Joseph

    2015-04-01

    Water is the essential resource ensuring human life on earth, which can only prosper when water is available and accessible. But of importance is not only the quantity of accessible water but also its quality, which in case of pollution may pose a risk to human health. The pollutants which pose a risk to human health are manifold, covering several groups such as pathogens, nutrients, human pharmaceuticals, heavy metals, and others. With regards to human health, pathogen contamination is of major interest as 4% of all death and 5.7% of disability or ill health in the world can be attributed to poor water supply, sanitation and personal and domestic hygiene. In developing countries, 2.6 billion people lacked access to improved sanitation in 2011. The lack of sanitation poses a risk to surface water pollution which is a threat to human health. A typical indicator for pathogen pollution is fecal coliform bacteria. The objective our study is to assess fecal pollution in the developing regions Africa, Asia and Latin America using the large-scale water quality model WorldQual. Model runs were carried-out to calculate in-stream concentrations and the respective loadings reaching rivers for the time period 1990 to 2010. We identified hotspots of fecal coliform loadings and in-stream concentrations which were further analyzed and ranked in terms of fecal surface water pollution. Main findings are that loadings mainly originate from the domestic sector, thus loadings are high in highly populated areas. In general, domestic loadings can be attributed to the two subsectors domestic sewered and domestic non sewered. The spatial distribution of both sectors varies across catchments. Hotspot pattern of in-stream concentrations are similar to the loadings pattern although they are different in seasonality. As the dilution varies with climate its dilution capacity is high during seasons with high precipitation, which in turn decreases the in-stream concentrations. The fecal

  12. Microbial biogeography of public restroom surfaces.

    Directory of Open Access Journals (Sweden)

    Gilberto E Flores

    Full Text Available We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high

  13. Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

    Science.gov (United States)

    Hyer, Kenneth; Moyer, Douglas

    2003-01-01

    (maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

  14. 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.

  15. Water quality and sources of fecal coliform bacteria in the Meduxnekeag River, Houlton, Maine

    Science.gov (United States)

    Culbertson, Charles W.; Huntington, Thomas G.; Stoeckel, Donald M.; Caldwell, James M.; O'Donnell, Cara

    2014-01-01

    In response to bacterial contamination in the Meduxnekeag River and the desire to manage the watershed to reduce contaminant sources, the Houlton Band of Maliseet Indians (HBMI) and the U.S. Geological Survey began a cooperative effort to establish a baseline of water-quality data that can be used in future studies and to indicate potential sources of nutrient and bacterial contamination. This study was conducted during the summer of 2005 in the Meduxnekeag River Basin near Houlton, Maine. Continuously recorded specific conductance can be a good indicator for water quality. Specific conductance increased downstream from the town of Houlton, between runoff events, and decreased sharply following major runoff events. Collections of discrete samples during the summer of 2005 indicated seasonal positive concentration-discharge relations for total phosphorus and total nitrogen; these results indicate that storm runoff may mobilize and transport these nutrients from the terrestrial environment to the river. Data collected by the HBMI on fecal coliform bacteria indicated that bacterial contamination enters the Meduxnekeag River from multiple paths including tributaries and surface drains (ditches) in developed areas in Houlton, Maine. The Houlton wastewater treatment discharge was not an important source of bacterial contamination. Bacteroidales-based tests for general fecal contamination (Bac32 marker) were predominantly positive in samples that had excessive fecal contamination as indicated by Enterococci density greater than 104 colony-forming units per 100 millilters. Of the 22 samples tested for Bacteroidales-based markers of human-associated fecal contamination (HF134 and HF183), 8 were positive. Of the 22 samples tested for Bacteroidales-based markers of ruminant-associated fecal contamination (CF128 and CF193), 7 were positive. Human fecal contamination was detected consistently at two sites (surface drains in urban areas in the town of Houlton) and occasionally

  16. Weight gain after fecal microbiota transplantation.

    Science.gov (United States)

    Alang, Neha; Kelly, Colleen R

    2015-01-01

    Fecal microbiota transplantation (FMT) is a promising treatment for recurrent Clostridium difficile infection. We report a case of a woman successfully treated with FMT who developed new-onset obesity after receiving stool from a healthy but overweight donor. This case may stimulate further studies on the mechanisms of the nutritional-neural-microbiota axis and reports of outcomes in patients who have used nonideal donors for FMT.

  17. THE POWER OF POOP: FECAL MICROBIOTA TRANSPLANTATION FOR CLOSTRIDIUM DIFFICILE INFECTION

    OpenAIRE

    EDMOND, MICHAEL B.

    2016-01-01

    The human gut is colonized with 200 to 1,000 bacterial species. Administration of antibiotics reduces the diversity of the intestinal microbiota, reduces colonization resistance, and can lead to infection with Clostridium difficile. These infections have become more prevalent and increasingly patients are experiencing multiple recurrences that are incurable with standard treatment. Although fecal microbiota transplantation (FMT) has been used for centuries in human and veterinary medicine, on...

  18. Fecal Molecular Markers for Colorectal Cancer Screening

    Directory of Open Access Journals (Sweden)

    Rani Kanthan

    2012-01-01

    Full Text Available Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.

  19. Connections between the human gut microbiome and gestational diabetes mellitus.

    Science.gov (United States)

    Kuang, Ya-Shu; Lu, Jin-Hua; Li, Sheng-Hui; Li, Jun-Hua; Yuan, Ming-Yang; He, Jian-Rong; Chen, Nian-Nian; Xiao, Wan-Qing; Shen, Song-Ying; Qiu, Lan; Wu, Ying-Fang; Hu, Cui-Yue; Wu, Yan-Yan; Li, Wei-Dong; Chen, Qiao-Zhu; Deng, Hong-Wen; Papasian, Christopher J; Xia, Hui-Min; Qiu, Xiu

    2017-08-01

    The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21-29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts. Parabacteroides distasonis, Klebsiella variicola, etc., were enriched in GDM patients, whereas Methanobrevibacter smithii, Alistipes spp., Bifidobacterium spp., and Eubacterium spp. were enriched in controls. The ratios of the gross abundances of GDM-enriched MLGs to control-enriched MLGs were positively correlated with blood glucose levels. A random forest model shows that fecal MLGs have excellent discriminatory power to predict GDM status. Our study discovered novel relationships between the gut microbiome and GDM status and suggests that changes in microbial composition may potentially be used to identify individuals at risk for GDM. © The Author 2017. Published by Oxford University Press.

  20. Hydrogeological controls of variable microbial water quality in a complex subtropical karst system in Northern Vietnam

    Science.gov (United States)

    Ender, Anna; Goeppert, Nadine; Goldscheider, Nico

    2018-05-01

    Karst aquifers are particularly vulnerable to bacterial contamination. Especially in developing countries, poor microbial water quality poses a threat to human health. In order to develop effective groundwater protection strategies, a profound understanding of the hydrogeological setting is crucial. The goal of this study was to elucidate the relationships between high spatio-temporal variability in microbial contamination and the hydrogeological conditions. Based on extensive field studies, including mapping, tracer tests and hydrochemical analyses, a conceptual hydrogeological model was developed for a remote and geologically complex karst area in Northern Vietnam called Dong Van. Four different physicochemical water types were identified; the most important ones correspond to the karstified Bac Son and the fractured Na Quan aquifer. Alongside comprehensive investigation of the local hydrogeology, water quality was evaluated by analysis for three types of fecal indicator bacteria (FIB): Escherichia coli, enterococci and thermotolerant coliforms. The major findings are: (1) Springs from the Bac Son formation displayed the highest microbial contamination, while (2) springs that are involved in a polje series with connections to sinking streams were distinctly more contaminated than springs with a catchment area characterized by a more diffuse infiltration. (3) FIB concentrations are dependent on the season, with higher values under wet season conditions. Furthermore, (4) the type of spring capture also affects the water quality. Nevertheless, all studied springs were faecally impacted, along with several shallow wells within the confined karst aquifer. Based on these findings, effective protection strategies can be developed to improve groundwater quality.

  1. A case study characterizing animal fecal sources in surface water using a mitochondrial DNA marker.

    Science.gov (United States)

    Bucci, John P; Shattuck, Michelle D; Aytur, Semra A; Carey, Richard; McDowell, William H

    2017-08-01

    Water quality impairment by fecal waste in coastal watersheds is a public health issue. The present study provided evidence for the use of a mitochondrial (mtDNA) marker to detect animal fecal sources in surface water. The accurate identification of fecal pollution is based on the notion that fecal microorganisms preferentially inhabit a host animal's gut environment. In contrast, mtDNA host-specific markers are inherent to eukaryotic host cells, which offers the advantage by detecting DNA from the host rather than its fecal bacteria. The present study focused on sampling water presumably from non-point sources (NPS), which can increase bacterial and nitrogen concentrations to receiving water bodies. Stream sampling sites located within the Piscataqua River Watershed (PRW), New Hampshire, USA, were sampled from a range of sites that experienced nitrogen inputs such as sewer and septic systems and suburban runoff. Three mitochondrial (mtDNA) gene marker assays (human, bovine, and canine) were tested from surface water. Nineteen sites were sampled during an 18-month period. Analyses of the combined single and multiplex assay results showed that the proportion of occurrence was highest for bovine (15.6%; n = 77) compared to canine (5.6%; n = 70) and human (5.7%; n = 107) mtDNA gene markers. For the human mtDNA marker, there was a statistically significant relationship between presence vs. absence and land use (Fisher's test p = 0.0031). This result was evident particularly for rural suburban septic, which showed the highest proportion of presence (19.2%) compared to the urban sewered (3.3%), suburban sewered (0%), and agricultural (0%) as well as forested septic (0%) sites. Although further testing across varied land use is needed, our study provides evidence for using the mtDNA marker in large watersheds.

  2. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    2012-01-01

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  3. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  4. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  5. Modeling the Transport and Fate of Fecal Pollution and Nutrients of Miyun Reservoir

    Science.gov (United States)

    Liu, L.; Fu, X.; Wang, G.

    2009-12-01

    Miyun Reservoir, a mountain valley reservoir, is located 100 km northeast of Beijing City. Besides the functions of flood control, irrigation and fishery for Beijing area, Miyun Reservoir is the main drinking water storage for Beijing city. The water quality is therefore of great importance. Recently, the concentration of fecal pollution and nutrients in the reservoir are constantly rising to arrest the attention of Beijing municipality. Fecal pollution from sewage is a significant public health concern due to the known presence of human viruses and parasites in these discharges. To investigate the transport and fate of the fecal pollution and nutrients at Miyun reservoir and the health risks associated with drinking and fishery, the reservoir and two tributaries, Chaohe river and Baihe river discharging into it are being examined for bacterial, nutrients and other routine pollution. To understand the relative importance of different processes influencing pollution transport and inactivation, a finite-element model of surf-zone hydrodynamics (coupled with models for temperature, fecal pollution, nutrients and other routine contaminants) is used. The developed models are being verified by the observed water quality data including water temperature, conductivities and dissolved oxygen from the reservoir and its tributaries. Different factors impacting the inactivation of fecal pollution and the transport of nutrients such as water temperature, sedimentation, sunlight insolation are evaluated for Miyun reservoir by a sensitivity analysis analogized from the previous research of Lake Michigan (figure 1, indicating that solar insolation dominates the inactivation of E. Coli, an indicator of fecal pollution, Liu et al. 2006). The calibrated modeling system can be used to temporally and spatially simulate and predict the variation of the concentration of fecal pollution and nutrients of Miyun reservoir. Therefore this research can provide a forecasting tool for the

  6. Fecal bacteria in the rivers of the Seine drainage network (France): sources, fate and modelling.

    Science.gov (United States)

    Servais, Pierre; Garcia-Armisen, Tamara; George, Isabelle; Billen, Gilles

    2007-04-01

    The Seine river watershed (France) is a deeply anthropogenically impacted area, due to the high population density, intense industrial activities and intensive agriculture. The water quality and ecological functioning of the different rivers of the Seine drainage network have been extensively studied during the last fifteen years within the framework of a large French multidisciplinary scientific program (PIREN Seine program). This paper presents a synthesis of the main data gained in the scope of this program concerning the microbiological water contamination of the rivers of the Seine drainage network. The more common indicator of fecal contamination (fecal coliforms) was mainly used; some complementary works used E. coli and intestinal enterococci as alternative fecal indicators. Point sources (outfall of wastewater treatment plants) and non point sources (surface runoff and soil leaching) of fecal pollution to the rivers of the watershed were quantified. Results showed that, at the scale of a large urbanised watershed as the Seine basin, the input of fecal micro-organisms by non-point sources is much lower than the inputs by point sources. However, the local impact of diffuse non-human sources (especially surface runoff of pastured fields) can be of major importance on the microbiological quality of small headwater rivers. Fecal contamination of the main rivers of the Seine watershed (Seine, Marne, Oise rivers) was studied showing high level of microbiological pollution when compared to European guidelines for bathing waters. The strong negative impact of treated wastewater effluents outfall on the microbiological quality of receiving rivers was observed in different areas of the watershed. Once released in rivers, culturable fecal bacteria disappeared relatively rapidly due to mortality (protozoan grazing, lysis) or loss of culturability induced by stress conditions (sunlight effect, nutrient concentration, temperature). Mortality rates of E. coli were studied

  7. Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome.

    Science.gov (United States)

    McCall, Laura-Isobel; Tripathi, Anupriya; Vargas, Fernando; Knight, Rob; Dorrestein, Pieter C; Siqueira-Neto, Jair L

    2018-03-01

    Trypanosoma cruzi parasites are the causative agents of Chagas disease. These parasites infect cardiac and gastrointestinal tissues, leading to local inflammation and tissue damage. Digestive Chagas disease is associated with perturbations in food absorption, intestinal traffic and defecation. However, the impact of T. cruzi infection on the gut microbiota and metabolome have yet to be characterized. In this study, we applied mass spectrometry-based metabolomics and 16S rRNA sequencing to profile infection-associated alterations in fecal bacterial composition and fecal metabolome through the acute-stage and into the chronic stage of infection, in a murine model of Chagas disease. We observed joint microbial and chemical perturbations associated with T. cruzi infection. These included alterations in conjugated linoleic acid (CLA) derivatives and in specific members of families Ruminococcaceae and Lachnospiraceae, as well as alterations in secondary bile acids and members of order Clostridiales. These results highlight the importance of multi-'omics' and poly-microbial studies in understanding parasitic diseases in general, and Chagas disease in particular.

  8. Fecal short-chain fatty acids at different time points after ceftriaxone administration in rats

    Directory of Open Access Journals (Sweden)

    Yu. V. Holota

    2017-02-01

    Full Text Available Short-chain fatty acids (SCFAs are major products of the microbial fermentation of dietary fiber in the colon. Recent studies suggest that these products of microbial metabolism in the gut act as signaling molecules, influence host energy homeostasis and play major immunological roles. In the present study, defined the long-term effects of ceftriaxone administration on the fecal SCFAs concentration in Wistar rats. Ceftriaxone (300 mg/kg, i.m. was administered daily for 14 days. Rats were euthanized in 1, 15 and 56 days after ceftriaxone withdrawal. Caecal weight and fecal concentration of SCFAs by gas chromatography were measured. Ceftriaxone administration induced time-dependent rats’ caecal enlargement through accumulation of undigestable substances. In 1 day after ceftriaxone withdrawal, the concentrations of acetic, propionic, butyric acids and total SCFAs were decreased 2.9-, 13.8-, 8.5-, 4.8-fold (P < 0.05, respectively. Concentration of valeric, isovaleric and caproic acids was below the detectable level. That was accompanied by decreased 4.3-fold anaerobic index and increased the relative amount of acetic acid (P < 0.05. In 56 days, concentration of SCFAs was still below control value but higher than in 1 day (except propionic acid. Anaerobic index was lower 1.3-fold (P < 0.05 vs. control. Conclusion: antibiotic therapy induced long-term disturbance in colonic microbiota metabolic activity.

  9. Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

    Science.gov (United States)

    de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

    2017-01-01

    The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial

  10. Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project.

    Science.gov (United States)

    Hua, Xing; Goedert, James J; Pu, Angela; Yu, Guoqin; Shi, Jianxin

    2016-01-01

    Alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. This study sought to clarify the relationship of dysbiosis with allergies in adults. Publicly available American Gut Project questionnaire and fecal 16S rRNA sequence data were analyzed. Fecal microbiota richness (number of observed species) and composition (UniFrac) were used to compare adults with versus without allergy to foods (peanuts, tree nuts, shellfish, other) and non-foods (drug, bee sting, dander, asthma, seasonal, eczema). Logistic and Poisson regression models adjusted for potential confounders. Odds ratios and 95% confidence intervals (CI) were calculated for lowest vs highest richness tertile. Taxonomy associations considered 122 non-redundant taxa (of 2379 total taxa) with ≥ 0.1% mean abundance. Self-reported allergy prevalence among the 1879 participants (mean age, 45.5 years; 46.9% male) was 81.5%, ranging from 2.5% for peanuts to 40.5% for seasonal. Fecal microbiota richness was markedly lower with total allergies (P = 10(-9)) and five particular allergies (P ≤ 10(-4)). Richness odds ratios were 1.7 (CI 1.3-2.2) with seasonal, 1.8 (CI 1.3-2.5) with drug, and 7.8 (CI 2.3-26.5) with peanut allergy. These allergic participants also had markedly altered microbial community composition (unweighted UniFrac, P = 10(-4) to 10(-7)). Total food and non-food allergies were significantly associated with 7 and 9 altered taxa, respectively. The dysbiosis was most marked with nut and seasonal allergies, driven by higher Bacteroidales and reduced Clostridiales taxa. American adults with allergies, especially to nuts and seasonal pollen, have low diversity, reduced Clostridiales, and increased Bacteroidales in their gut microbiota. This dysbiosis might be targeted to improve treatment or prevention of allergy.

  11. Dysbiosis of gut microbiota and microbial metabolites in Parkinson's Disease.

    Science.gov (United States)

    Sun, Meng-Fei; Shen, Yan-Qin

    2018-04-26

    Gut microbial dysbiosis and alteration of microbial metabolites in Parkinson's disease (PD) have been increasingly reported. Dysbiosis in the composition and abundance of gut microbiota can affect both the enteric nervous system and the central nervous system (CNS), indicating the existence of a microbiota-gut-brain axis and thereby causing CNS diseases. Disturbance of the microbiota-gut-brain axis has been linked to specific microbial products that are related to gut inflammation and neuroinflammation. Future directions should therefore focus on the exploration of specific gut microbes or microbial metabolites that contribute to the development of PD. Microbiota-targeted interventions, such as antibiotics, probiotics and fecal microbiota transplantation, have been shown to favorably affect host health. In this review, recent findings regarding alterations and the role of gut microbiota and microbial metabolites in PD are summarized, and potential molecular mechanisms and microbiota-targeted interventions in PD are discussed. Copyright © 2018. Published by Elsevier B.V.

  12. Assessment of statistical methods used in library-based approaches to microbial source tracking.

    Science.gov (United States)

    Ritter, Kerry J; Carruthers, Ethan; Carson, C Andrew; Ellender, R D; Harwood, Valerie J; Kingsley, Kyle; Nakatsu, Cindy; Sadowsky, Michael; Shear, Brian; West, Brian; Whitlock, John E; Wiggins, Bruce A; Wilbur, Jayson D

    2003-12-01

    Several commonly used statistical methods for fingerprint identification in microbial source tracking (MST) were examined to assess the effectiveness of pattern-matching algorithms to correctly identify sources. Although numerous statistical methods have been employed for source identification, no widespread consensus exists as to which is most appropriate. A large-scale comparison of several MST methods, using identical fecal sources, presented a unique opportunity to assess the utility of several popular statistical methods. These included discriminant analysis, nearest neighbour analysis, maximum similarity and average similarity, along with several measures of distance or similarity. Threshold criteria for excluding uncertain or poorly matched isolates from final analysis were also examined for their ability to reduce false positives and increase prediction success. Six independent libraries used in the study were constructed from indicator bacteria isolated from fecal materials of humans, seagulls, cows and dogs. Three of these libraries were constructed using the rep-PCR technique and three relied on antibiotic resistance analysis (ARA). Five of the libraries were constructed using Escherichia coli and one using Enterococcus spp. (ARA). Overall, the outcome of this study suggests a high degree of variability across statistical methods. Despite large differences in correct classification rates among the statistical methods, no single statistical approach emerged as superior. Thresholds failed to consistently increase rates of correct classification and improvement was often associated with substantial effective sample size reduction. Recommendations are provided to aid in selecting appropriate analyses for these types of data.

  13. Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis.

    Science.gov (United States)

    Velmurugan, Ganesan; Ramprasath, Tharmarajan; Swaminathan, Krishnan; Mithieux, Gilles; Rajendhran, Jeyaprakash; Dhivakar, Mani; Parthasarathy, Ayothi; Babu, D D Venkatesh; Thumburaj, Leishman John; Freddy, Allen J; Dinakaran, Vasudevan; Puhari, Shanavas Syed Mohamed; Rekha, Balakrishnan; Christy, Yacob Jenifer; Anusha, Sivakumar; Divya, Ganesan; Suganya, Kannan; Meganathan, Boominathan; Kalyanaraman, Narayanan; Vasudevan, Varadaraj; Kamaraj, Raju; Karthik, Maruthan; Jeyakumar, Balakrishnan; Abhishek, Albert; Paul, Eldho; Pushpanathan, Muthuirulan; Rajmohan, Rajamani Koushick; Velayutham, Kumaravel; Lyon, Alexander R; Ramasamy, Subbiah

    2017-01-24

    Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. The diabetogenic nature of organophosphates was recently reported but the underlying molecular mechanism is unclear. We aimed to understand the role of gut microbiota in organophosphate-induced hyperglycemia and to unravel the molecular mechanism behind this process. Here we demonstrate a high prevalence of diabetes among people directly exposed to organophosphates in rural India (n = 3080). Correlation and linear regression analysis reveal a strong association between plasma organophosphate residues and HbA1c but no association with acetylcholine esterase was noticed. Chronic treatment of mice with organophosphate for 180 days confirms the induction of glucose intolerance with no significant change in acetylcholine esterase. Further fecal transplantation and culture transplantation experiments confirm the involvement of gut microbiota in organophosphate-induced glucose intolerance. Intestinal metatranscriptomic and host metabolomic analyses reveal that gut microbial organophosphate degradation produces short chain fatty acids like acetic acid, which induces gluconeogenesis and thereby accounts for glucose intolerance. Plasma organophosphate residues are positively correlated with fecal esterase activity and acetate level of human diabetes. Collectively, our results implicate gluconeogenesis as the key mechanism behind organophosphate-induced hyperglycemia, mediated by the organophosphate-degrading potential of gut microbiota. This study reveals the gut microbiome-mediated diabetogenic nature of organophosphates and hence that the usage of these insecticides should be reconsidered.

  14. A Molecular MST Approach to Investigate Fecal Indicator Bacteria in Bioaerosols, Bathing Water, Seaweed Wrack, and Sand at Recreational Beaches

    Science.gov (United States)

    Thoren, K. M.; Sinigalliano, C. D.

    2016-02-01

    Despite numerous cases of beach bacteria affecting millions of people worldwide, the persistence of the bacteria populations in coastal areas is still not well understood. The purpose of this study was to test the levels of persistence of Fecal Indicating Bacteria (FIB) of enterococci, Escherichia coli, and Human-source Bacteroidales, within the intertidal "swash zone" and the deeper waist zone in which people commonly bathe and play. In addition, the study sought to determine if these bacterial contaminants may also be found in aerosols at the beach. Measuring solar insolation in relation to bacterial persistence in seaweed wrack was used to determine if sunlight plays a role in modifying concentrations of FIB at the beach. Light intensity measured by a solar photometer and air quality measured by aerosol plate counts and qPCR Microbial Source Tracking (MST) was compared to varying locations where the beach samples were collected. Results from water samples demonstrate that bacteria measured using plate counts and qPCR were indeed higher within the swash zone than in the waist zone. This is in contrast with the way that the EPA currently measures and determines the public safety of beach waters. They commonly measure the waist zone, but disregard the swash zone. Results from beach bio-aerosol samples showed a wide variety of fungi and bacteria in the beach air, and qPCR MST analysis of these bio-aerosols showed the presence of FIBs such as enterococci on several of the aerosol collection plates. This emphasizes the need to collect samples from the entire beach instead of just measuring at an isolated area, and that exposure to microbial contaminants may include bathing water, beach sand, seaweed wrack, and bio-aerosols. Thus, the data reveals a potential way to identify harmful levels of bacteria and dangerous levels of poor air quality at recreational beaches. These results expound the need for broader assessment of potential beach contamination, not only the

  15. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.

    Directory of Open Access Journals (Sweden)

    Frederiek-Maarten Kerckhof

    Full Text Available The use of mixed microbial communities (microbiomes for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA. Microbiomes were selected based upon relevance towards applications: (1 a methanotrophic co-culture (MOB, with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2 an oxygen limited autotrophic nitrification/denitrification (OLAND biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3 fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB and anaerobic AOB (AnAOB, anammox in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO and DMSO plus trehalose and tryptic soy broth (DMSO+TT] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.

  16. Animal Feces Contribute to Domestic Fecal Contamination: Evidence from E. coli Measured in Water, Hands, Food, Flies, and Soil in Bangladesh.

    Science.gov (United States)

    Ercumen, Ayse; Pickering, Amy J; Kwong, Laura H; Arnold, Benjamin F; Parvez, Sarker Masud; Alam, Mahfuja; Sen, Debashis; Islam, Sharmin; Kullmann, Craig; Chase, Claire; Ahmed, Rokeya; Unicomb, Leanne; Luby, Stephen P; Colford, John M

    2017-08-01

    Fecal-oral pathogens are transmitted through complex, environmentally mediated pathways. Sanitation interventions that isolate human feces from the environment may reduce transmission but have shown limited impact on environmental contamination. We conducted a study in rural Bangladesh to (1) quantify domestic fecal contamination in settings with high on-site sanitation coverage; (2) determine how domestic animals affect fecal contamination; and (3) assess how each environmental pathway affects others. We collected water, hand rinse, food, soil, and fly samples from 608 households. We analyzed samples with IDEXX Quantitray for the most probable number (MPN) of E. coli. We detected E. coli in source water (25%), stored water (77%), child hands (43%), food (58%), flies (50%), ponds (97%), and soil (95%). Soil had >120 000 mean MPN E. coli per gram. In compounds with vs without animals, E. coli was higher by 0.54 log 10 in soil, 0.40 log 10 in stored water and 0.61 log 10 in food (p food increased with increasing E. coli in soil, ponds, source water and hands. We provide empirical evidence of fecal transmission in the domestic environment despite on-site sanitation. Animal feces contribute to fecal contamination, and fecal indicator bacteria do not strictly indicate human fecal contamination when animals are present.

  17. Plutonium fecal and urinary excretion functions: Derivation from a systematic whole-body retention function

    International Nuclear Information System (INIS)

    Sun, C.; Lee, D.

    1999-01-01

    Liver-bile secretion directly influences the content of plutonium in feces. To assess the reliability of plutonium metabolic models and to improve the accuracy of interpreting plutonium fecal data, the authors developed a compartmental model that simulates the metabolism of plutonium in humans. With this model, they can describe the transport of plutonium contaminants in the systemic organs and tissues of the body, including fecal and urine excretions, without using elaborate kinetic information. The parameter values of the models, which describe the translocation rates and recycling of plutonium in the body, can be derived from a multi-term exponential systemic function for whole-body retention. The analytical derivations and algorithms for solving translocation parameter values are established for the model and illustrated by applying them to the biokinetics and bioassay of plutonium. This study describes how to (1) design a physiological model for incorporating liver biliary secretion and for obtaining a fecal-excretion function, (2) develop an analytical solution for identifying the translocation-parameter values incorporating the recycling of plutonium in the body, and (3) derive a set of urinary and fecal excretion-functions from a published systemic whole-body retention function, generally acknowledged to be accurate, as a real and practical example

  18. Fecal incontinence after single-stage Soave's pull-through ...

    African Journals Online (AJOL)

    Journal Home > Vol 8, No 1 (2012) > ... Demographic, clinical data, preoperative investigations, operative records, postoperative ... Keywords: fecal continence, Hirschsprung's disease, Soave's operation, transanal endorectal pull-through ...

  19. Multipathway Quantitative Assessment of Exposure to Fecal Contamination for Young Children in Low-Income Urban Environments in Accra, Ghana: The SaniPath Analytical Approach.

    Science.gov (United States)

    Wang, Yuke; Moe, Christine L; Null, Clair; Raj, Suraja J; Baker, Kelly K; Robb, Katharine A; Yakubu, Habib; Ampofo, Joseph A; Wellington, Nii; Freeman, Matthew C; Armah, George; Reese, Heather E; Peprah, Dorothy; Teunis, Peter F M

    2017-10-01

    Lack of adequate sanitation results in fecal contamination of the environment and poses a risk of disease transmission via multiple exposure pathways. To better understand how eight different sources contribute to overall exposure to fecal contamination, we quantified exposure through multiple pathways for children under 5 years old in four high-density, low-income, urban neighborhoods in Accra, Ghana. We collected more than 500 hours of structured observation of behaviors of 156 children, 800 household surveys, and 1,855 environmental samples. Data were analyzed using Bayesian models, estimating the environmental and behavioral factors associated with exposure to fecal contamination. These estimates were applied in exposure models simulating sequences of behaviors and transfers of fecal indicators. This approach allows us to identify the contribution of any sources of fecal contamination in the environment to child exposure and use dynamic fecal microbe transfer networks to track fecal indicators from the environment to oral ingestion. The contributions of different sources to exposure were categorized into four types (high/low by dose and frequency), as a basis for ranking pathways by the potential to reduce exposure. Although we observed variation in estimated exposure (10 8 -10 16 CFU/day for Escherichia coli ) between different age groups and neighborhoods, the greatest contribution was consistently from food (contributing > 99.9% to total exposure). Hands played a pivotal role in fecal microbe transfer, linking environmental sources to oral ingestion. The fecal microbe transfer network constructed here provides a systematic approach to study the complex interaction between contaminated environment and human behavior on exposure to fecal contamination.

  20. Short-term effect of antibiotics on human gut microbiota.

    Directory of Open Access Journals (Sweden)

    Suchita Panda

    Full Text Available From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002. At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016. Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04. The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.

  1. Mortality of fecal bacteria in seawater

    International Nuclear Information System (INIS)

    Garcia-Lara, J.; Menon, P.; Servais, P.; Billen, G.

    1991-01-01

    The authors propose a method for determining the mortality rate for allochthonous bacteria released in aquatic environments without interference due to the loss of culturability in specific culture media. This method consists of following the disappearance of radioactivity from the trichloracetic acid-insoluble fraction in water samples to which [ 3 H]thymidine-prelabeled allochthonous bacteria have been added. In coastal seawater, they found that the actual rate of disappearance of fecal bacteria was 1 order of magnitude lower than the rate of loss of culturability on specific media. Minor adaptation of the procedure may facilitate assessment of the effect of protozoan grazing and bacteriophage lysis on the overall bacterial mortality rate

  2. Determination of human pathogen profiles in food by quality assured microbial assays. Proceedings of a final Research Coordination Meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-01-15

    This publication includes the results of a Coordinated Research Project (CRP). Major food microbial contaminants were identified in some of the main foods exported in the international food market. Thousands of samples in a wide variety of foods were selected to be studied during different points of the food chain: meat (chicken, beef and pork), seafood (shellfish such as shrimp, prawns, scampi, squid, and lobsters, and different types of fish such as salmon, cuttle fish, rohu, fin herring, catfish, milkfish, and tilapia), spices (pepper, paprika), frozen vegetables (asparagus, peas and corn) and other products (coconut and dairy products). The analysis included pathogenic bacteria such as Salmonella spp. (several serotypes), Escherichia coli, E. coli 0157:H7, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, Vibrio choleare, Vibrio parahaemolitycus and Yersinia enterolítica. This publication includes data that may be used to conduct better risk assessments on food by importing as well as exporting countries.

  3. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.

    Directory of Open Access Journals (Sweden)

    Shi Ying

    Full Text Available Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.

  4. [Immunomodulators of microbial origin enhance cytotoxicity of human mononuclear leukocytes and reduce metastatic progression of Lewis lung carcinoma in mice].

    Science.gov (United States)

    Akhmatova, N K; Semenova, I B; Donenko, F V; Kiselevskiĭ, M V; Kurbatova, E A; Egorova, N B

    2006-01-01

    Effect of immunomodulators for microbial origin on innate immunity and antitumor system was continued to study. Immunomodificator Immunovac VP-4, purified staphylococcal toxoid and glucosaminyl muramyl dipeptide (GMDP) equally enhanced cytotoxicity of mononuclear leukocytes of peripheral blood of healthy donors. Index of cytotoxicity was 2.78, 2.77 and 2.70 respectively. Reduced metastatic progression of Lewis lung carcinoma in mice was observed after Immunovac VP-4 and GMDP administration. Effectiveness was seen when preparations administered according to schedules including their administration before implantation of the tumor. If preparations were administered number of metastases reduced in 4.4-5.6 times and size of metastases reduced in 7-10 times. Interplay between antitumor activity of studied immunomodulators and cytotoxic activity of NK-cells, which are base effectors of antitumor immune response, are discussed.

  5. Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies

    Science.gov (United States)

    Fout, G. Shay; Borchardt, Mark A.; Kieke, Burney A.; Karim, Mohammad R.

    2017-06-01

    Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992-2013) of 718 public drinking-water systems located in a range of hydrogeological settings. Focus was on testing the value of indicator organisms for identifying virus-contaminated wells. One or more indicators and viruses were present in 37 and 15% of 2,273 samples and 44 and 27% of 746 wells, respectively. Escherichia coli ( E. coli) and somatic coliphage are 7-9 times more likely to be associated with culturable virus-positive samples when the indicator is present versus when it is absent, while F-specific and somatic coliphages are 8-9 times more likely to be associated with culturable virus-positive wells. However, single indicators are only marginally associated with viruses detected by molecular methods, and all microbial indicators have low sensitivity and positive predictive values for virus occurrence, whether by culturable or molecular assays, i.e., indicators are often absent when viruses are present and the indicators have a high false-positive rate. Wells were divided into three susceptibility subsets based on presence of (1) total coliform bacteria or (2) multiple indicators, or (3) location of wells in karst, fractured bedrock, or gravel/cobble settings. Better associations of some indicators with viruses were observed for (1) and (3). Findings indicate the best indicators are E. coli or somatic coliphage, although both indicators may underestimate virus occurrence. Repeat sampling for indicators improves evaluation of the potential for viral contamination in a well.

  6. Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles.

    Science.gov (United States)

    Gotoh, Aina; Nara, Misaki; Sugiyama, Yuta; Sakanaka, Mikiyasu; Yachi, Hiroyuki; Kitakata, Aya; Nakagawa, Akira; Minami, Hiromichi; Okuda, Shujiro; Katoh, Toshihiko; Katayama, Takane; Kurihara, Shin

    2017-10-01

    Recently, a "human gut microbial gene catalogue," which ranks the dominance of microbe genus/species in human fecal samples, was published. Most of the bacteria ranked in the catalog are currently publicly available; however, the growth media recommended by the distributors vary among species, hampering physiological comparisons among the bacteria. To address this problem, we evaluated Gifu anaerobic medium (GAM) as a standard medium. Forty-four publicly available species of the top 56 species listed in the "human gut microbial gene catalogue" were cultured in GAM, and out of these, 32 (72%) were successfully cultured. Short-chain fatty acids from the bacterial culture supernatants were then quantified, and bacterial metabolic pathways were predicted based on in silico genomic sequence analysis. Our system provides a useful platform for assessing growth properties and analyzing metabolites of dominant human gut bacteria grown in GAM and supplemented with compounds of interest.

  7. Evaluation of Microbial Contamination and Chemical Qualities of Cream-filled Pastries in Confectioneries of Chaharmahal Va Bakhtiari Province (Southwestern Iran).

    Science.gov (United States)

    Sharifzadeh, Ali; Hajsharifi-Shahreza, Mohammad; Ghasemi-Dehkordi, Payam

    2016-12-01

    High consumption of bakery products such as cream-filled pastries may cause serious health risks and food poisoning to humans. Therefore, investigation of the microbial and chemical qualities of bakery products containing cream is necessary. The purpose of the present study was to investigate the chemical qualities and microbial contaminations of cream-filled pastries collected from confectioneries located in six cities in Chaharmahal Va Bakhtiari province (Southwestern Iran). Microbial tests and chemical characteristics (fat and acidity level) were done on 228 cream-filled pastries samples that were collected randomly from various confectioneries. After microbial tests, it was found that 33.33% of all samples were contaminated by microbial agents. The microbial tests showed that Shahrekord (10.09%) and Broujen (9.21%) cities had high levels of contamination and in Koohrang (1.31%) it was low compared with the other four cities. High contamination of coliforms (61.84%), staphylococci (48.68%), and yeast (27.63%) were observed in almost all samples. The chemical analysis showed maximum amounts of fat content and titratable acidity in cream-filled pastry samples obtained from Lordegan and Shahrekord cities, respectively. The findings of the present work demonstrated that the microbial contamination and chemical quality of cream-filled pastries produced in confectionaries of Chaharmahal Va Bakhtiari province were not in acceptable ranges. These problems may be related to fecal contamination of cream samples or lack of hygiene by handlers and it is necessary to observe the standards of hygiene and to develop safe food handling techniques and aseptic pastry manufacturing systems in some confectioneries of Chaharmahal Va Bakhtiari province.

  8. Fecal zonulin is elevated in Crohn’s disease and in cigarette smokers

    OpenAIRE

    Malíčková, Karin; Francová, Irena; Lukáš, Milan; Kolář, Martin; Králíková, Eva; Bortlík, Martin; Ďuricová, Dana; Štěpánková, Lenka; Zvolská, Kamila; Pánková, Alexandra; Zima, Tomáš

    2017-01-01

    Objectives: Human zonulin is a protein that increases permeability in the epithelial layer of the small intestine by reversibly modulating the intercellular tight junctions. There is not sufficient information available about zonulin's participation in inflammatory bowel diseases (IBD). The aim of this study was therefore to investigate fecal and serum zonulin in IBD patients and its relation to the disease localization, behavior and smoking status. Design and methods: Forty IBD patients and ...

  9. Changes in Escherichia coli to Cryptosporidium ratios for various fecal pollution sources and drinking water intakes.

    Science.gov (United States)

    Lalancette, Cindy; Papineau, Isabelle; Payment, Pierre; Dorner, Sarah; Servais, Pierre; Barbeau, Benoit; Di Giovanni, George D; Prévost, Michèle

    2014-05-15

    Assessing the presence of human pathogenic Cryptosporidium oocysts in surface water remains a significant water treatment and public health challenge. Most drinking water suppliers rely on fecal indicators, such as the well-established Escherichia coli (E. coli), to avoid costly Cryptosporidium assays. However, the use of E. coli has significant limitations in predicting the concentration, the removal and the transport of Cryptosporidium. This study presents a meta-analysis of E. coli to Cryptosporidium concentration paired ratios to compare their complex relationships in eight municipal wastewater sources, five agricultural fecal pollution sources and at 13 drinking water intakes (DWI) to a risk threshold based on US Environmental Protection Agency (USEPA) regulations. Ratios lower than the USEPA risk threshold suggested higher concentrations of oocysts in relation to E. coli concentrations, revealing an underestimed risk for Cryptosporidium based on E. coli measurements. In raw sewage (RS), high ratios proved E. coli (or fecal coliforms) concentrations were a conservative indicator of Cryptosporidium concentrations, which was also typically true for secondary treated wastewater (TWW). Removals of fecal indicator bacteria (FIB) and parasites were quantified in WWTPs and their differences are put forward as a plausible explanation of the sporadic ratio shift. Ratios measured from agricultural runoff surface water were typically lower than the USEPA risk threshold and within the range of risk misinterpretation. Indeed, heavy precipitation events in the agricultural watershed led to high oocyst concentrations but not to E. coli or enterococci concentrations. More importantly, ratios established in variously impacted DWI from 13 Canadian drinking water plants were found to be related to dominant fecal pollution sources, namely municipal sewage. In most cases, when DWIs were mainly influenced by municipal sewage, E. coli or fecal coliforms concentrations agreed with

  10. Microbial glycoproteomics

    DEFF Research Database (Denmark)

    Halim, Adnan; Anonsen, Jan Haug

    2017-01-01

    Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

  11. Distinguishing bovine fecal matter on spinach leaves using field spectroscopy

    Science.gov (United States)

    Detection of fecal contaminants on leafy greens in the field will allow for decreasing cross-contamination of produce during and post-harvest. Fecal contamination of leafy greens has been associated with E.coli O157:H7 outbreaks and foodbourne illnesses. In this study passive field spectroscopy, mea...

  12. Effects of supplementing lactic acid bacteria on fecal microbiota ...

    African Journals Online (AJOL)

    Results: The results indicated that Lactobacillus plantarum strain L.p X3-2B increased fecal lactic acid bacteria(LAB) and Bifidobacterium while resisting the growth of harmful bacteria. Viable counts of LAB and Bifidobacterium reached 8 log cfu/mL after feeding for 14 days. Fecal pH in the control group was high in ...

  13. Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon.

    Science.gov (United States)

    Fehlbaum, Sophie; Chassard, Christophe; Haug, Martina C; Fourmestraux, Candice; Derrien, Muriel; Lacroix, Christophe

    2015-01-01

    In vitro gut modeling is a useful approach to investigate some factors and mechanisms of the gut microbiota independent of the effects of the host. This study tested the use of immobilized fecal microbiota to develop different designs of continuous colonic fermentation models mimicking elderly gut fermentation. Model 1 was a three-stage fermentation mimicking the proximal, transverse and distal colon. Models 2 and 3 were based on the new PolyFermS platform composed of an inoculum reactor seeded with immobilized fecal microbiota and used to continuously inoculate with the same microbiota different second-stage reactors mounted in parallel. The main gut bacterial groups, microbial diversity and metabolite production were monitored in effluents of all reactors using quantitative PCR, 16S rRNA gene 454-pyrosequencing, and HPLC, respectively. In all models, a diverse microbiota resembling the one tested in donor's fecal sample was established. Metabolic stability in inoculum reactors seeded with immobilized fecal microbiota was shown for operation times of up to 80 days. A high microbial and metabolic reproducibility was demonstrated for downstream control and experimental reactors of a PolyFermS model. The PolyFermS models tested here are particularly suited to investigate the effects of environmental factors, such as diet and drugs, in a controlled setting with the same microbiota source.

  14. Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon.

    Directory of Open Access Journals (Sweden)

    Sophie Fehlbaum

    Full Text Available In vitro gut modeling is a useful approach to investigate some factors and mechanisms of the gut microbiota independent of the effects of the host. This study tested the use of immobilized fecal microbiota to develop different designs of continuous colonic fermentation models mimicking elderly gut fermentation. Model 1 was a three-stage fermentation mimicking the proximal, transverse and distal colon. Models 2 and 3 were based on the new PolyFermS platform composed of an inoculum reactor seeded with immobilized fecal microbiota and used to continuously inoculate with the same microbiota different second-stage reactors mounted in parallel. The main gut bacterial groups, microbial diversity and metabolite production were monitored in effluents of all reactors using quantitative PCR, 16S rRNA gene 454-pyrosequencing, and HPLC, respectively. In all models, a diverse microbiota resembling the one tested in donor's fecal sample was established. Metabolic stability in inoculum reactors seeded with immobilized fecal microbiota was shown for operation times of up to 80 days. A high microbial and metabolic reproducibility was demonstrated for downstream control and experimental reactors of a PolyFermS model. The PolyFermS models tested here are particularly suited to investigate the effects of environmental factors, such as diet and drugs, in a controlled setting with the same microbiota source.

  15. Fecal corticosterone reflects serum corticosterone in Florida sandhill cranes.

    Science.gov (United States)

    Ludders, J W; Langenberg, J A; Czekala, N M; Erb, H N

    2001-07-01

    Florida sandhill cranes (Grus canadensis pratensis) were conditioned to confinement 6 hr/day for 7 days. On day 8, each bird's jugular vein was catheterized, blood samples were drawn, and each crane was confined for 6 hr. Using a randomized, restricted cross-over design, cranes were injected intravenously with either 0.9% NaCl solution or ACTH (cosyntropin; Cortrosyn; 0.25 mg). During the 6 hr of confinement, fecal samples (feces and urine) were collected from each of five cranes immediately after defecation. Individual fecal samples were collected approximately at hourly intervals and assayed for corticosterone. We showed previously that serum corticosterone did not vary significantly following saline injection, but peaked significantly 60 min after ACTH injection. Maximal fecal corticosterone concentrations (ng/g) were greater (P cranes under controlled conditions, fecal corticosterone concentration reflects serum corticosterone levels, fecal corticosterone, Grus canadensis pratensis, sandhill cranes, serum corticosterone levels.

  16. Expression of IL-8, IL-6 and IL-1β in Tears as a Main Characteristic of the Immune Response in Human Microbial Keratitis

    Science.gov (United States)

    Santacruz, Concepcion; Linares, Marisela; Garfias, Yonathan; Loustaunau, Luisa M.; Pavon, Lenin; Perez-Tapia, Sonia Mayra; Jimenez-Martinez, Maria C.

    2015-01-01

    Corneal infections are frequent and potentially vision-threatening diseases, and despite the significance of the immunological response in animal models of microbial keratitis (MK), it remains unclear in humans. The aim of this study was to describe the cytokine profile of tears in patients with MK. Characteristics of ocular lesions such as size of the epithelial defect, stromal infiltration, and hypopyon were analyzed. Immunological evaluation included determination of interleukine (IL)-1β, IL-6, IL-8, IL-10, IL-12 and tumor necrosis factor (TNF)-α in tear samples obtained from infected eyes of 28 patients with MK and compared with their contralateral non-infected eyes. Additionally, frequency of CD4+, CD8+, CD19+ and CD3−CD56+ cells was also determined in peripheral blood mononuclear cells in patients with MK, and compared with 48 healthy controls. Non-significant differences were observed in the size of the epithelial defect, stromal infiltration, and hypopyon. Nevertheless, we found an immunological profile apparently related to MK etiology. IL-8 > IL-6 in patients with bacterial keratitis; IL-8 > IL-6 > IL-1β and increased frequency of circulating CD3−CD56+ NK cells in patients with gram-negative keratitis; and IL-8 = IL-6 > IL-1β in patients with fungal keratitis. Characterization of tear cytokines from patients with MK could aid our understanding of the immune pathophysiological mechanisms underlying corneal damage in