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Park MY, Kim S, Ko E, Ahn SH, Seo H, Sung MK. Gut microbiota-associated bile acid deconjugation accelerates hepatic steatosis in ob/ob mice. J Appl Microbiol 2016; 121:800-10. [DOI: 10.1111/jam.13158] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/14/2016] [Accepted: 04/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- M.-Y. Park
- Department of Food and Nutrition Education; Graduate School of Education; Soonchunhyang University; Asan Chungnam Korea
| | - S.J. Kim
- Department of Food and Nutrition; Sookmyung Women's University; Seoul Korea
| | - E.K. Ko
- Department of Food and Nutrition; Sookmyung Women's University; Seoul Korea
| | - S.-H. Ahn
- Collage of Pharmacy; Kangwon National University; Chuncheon Korea
| | - H. Seo
- Department of Drug Discovery Platform Technology; Korea Research Institute of Chemical Technology; Daejeon Korea
| | - M.-K. Sung
- Department of Food and Nutrition; Sookmyung Women's University; Seoul Korea
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52
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Torres J, Bao X, Goel A, Colombel JF, Pekow J, Jabri B, Williams K, Castillo A, Odin J, Meckel K, Fasihuddin F, Peter I, Itzkowitz S, Hu J. The features of mucosa-associated microbiota in primary sclerosing cholangitis. Aliment Pharmacol Ther 2016; 43:790-801. [PMID: 26857969 PMCID: PMC5177987 DOI: 10.1111/apt.13552] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/12/2015] [Accepted: 01/18/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Little is known about the role of the microbiome in primary sclerosing cholangitis. AIM To explore the mucosa-associated microbiota in primary sclerosing cholangitis (PSC) patients across different locations in the gut, and to compare it with inflammatory bowel disease (IBD)-only patients and healthy controls. METHODS Biopsies from the terminal ileum, right colon, and left colon were collected from patients and healthy controls undergoing colonoscopy. Microbiota profiling using bacterial 16S rRNA sequencing was performed on all biopsies. RESULTS Forty-four patients were recruited: 20 with PSC (19 with PSC-IBD and one with PSC-only), 15 with IBD-only and nine healthy controls. The overall microbiome profile was similar throughout different locations in the gut. No differences in the global microbiome profile were found. However, we observed significant PSC-associated enrichment in Barnesiellaceae at the family level, and in Blautia and an unidentified Barnesiellaceae at the genus level. At the operational taxa unit level, most shifts in PSC were observed in Clostridiales and Bacteroidales orders, with approximately 86% of shifts occurring within the former order. CONCLUSIONS The overall microbiota profile was similar across multiple locations in the gut from the same individual regardless of disease status. In this study, the mucosa associated-microbiota of patients with primary sclerosing cholangitis was characterised by enrichment of Blautia and Barnesiellaceae and by major shifts in operational taxa units within Clostridiales order.
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Affiliation(s)
- Joana Torres
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Xiuliang Bao
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Aparna Goel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joel Pekow
- Section of Gastroenterology, Hepatology, and Nutrition University of Chicago, Chicago, Illinois, USA
| | - Bana Jabri
- Section of Gastroenterology, Hepatology, and Nutrition University of Chicago, Chicago, Illinois, USA
| | - Kelli Williams
- Section of Gastroenterology, Hepatology, and Nutrition University of Chicago, Chicago, Illinois, USA
| | - Anabella Castillo
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joseph Odin
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Katherine Meckel
- Section of Gastroenterology, Hepatology, and Nutrition University of Chicago, Chicago, Illinois, USA
| | - Farah Fasihuddin
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Steven Itzkowitz
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
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Abstract
Colorectal cancer (CRC) is one of the most frequent causes of cancer death worldwide and is associated with adoption of a diet high in animal protein and saturated fat. Saturated fat induces increased bile secretion into the intestine. Increased bile secretion selects for populations of gut microbes capable of altering the bile acid pool, generating tumor-promoting secondary bile acids such as deoxycholic acid and lithocholic acid. Epidemiological evidence suggests CRC is associated with increased levels of DCA in serum, bile, and stool. Mechanisms by which secondary bile acids promote CRC are explored. Furthermore, in humans bile acid conjugation can vary by diet. Vegetarian diets favor glycine conjugation while diets high in animal protein favor taurine conjugation. Metabolism of taurine conjugated bile acids by gut microbes generates hydrogen sulfide, a genotoxic compound. Thus, taurocholic acid has the potential to stimulate intestinal bacteria capable of converting taurine and cholic acid to hydrogen sulfide and deoxycholic acid, a genotoxin and tumor-promoter, respectively.
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Affiliation(s)
- Jason M. Ridlon
- Carl R. Woese Institute for Genome Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Carl R. Woese Institute for Genome Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - H. Rex Gaskins
- Carl R. Woese Institute for Genome Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA,University of Illinois Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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54
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Yamada T, Takahashi D, Hase K. The diet-microbiota-metabolite axis regulates the host physiology. J Biochem 2016; 160:1-10. [PMID: 26970281 DOI: 10.1093/jb/mvw022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/24/2016] [Indexed: 12/27/2022] Open
Abstract
The intestinal microbiota has been implicated in a wide range of diseases, including inflammatory bowel disease, obesity and cancer. Food ingredients are considered a major determinant of gut microbial composition, as exemplified by high-fat diet-induced dysbiosis that can affect host physiology. Accumulating studies show that microbial metabolites are key regulators of the intestinal epithelial barrier and gut immunity. In particular, short-chain fatty acids produced by bacterial fermentation of indigestible polysaccharides have profound impacts on host physiology beyond the gut. In this review, we describe the influences of the diet-microbiota-metabolite axis on host physiology, and especially on the immune and metabolic systems.
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Affiliation(s)
- Takahiro Yamada
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Daisuke Takahashi
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan Division of Mucosal Barriology, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science the University of Tokyo, Tokyo 108-8639, Japan
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Ridlon JM, Harris SC, Bhowmik S, Kang DJ, Hylemon PB. Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes 2016; 7:22-39. [PMID: 26939849 PMCID: PMC4856454 DOI: 10.1080/19490976.2015.1127483] [Citation(s) in RCA: 623] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Emerging evidence strongly suggest that the human "microbiome" plays an important role in both health and disease. Bile acids function both as detergents molecules promoting nutrient absorption in the intestines and as hormones regulating nutrient metabolism. Bile acids regulate metabolism via activation of specific nuclear receptors (NR) and G-protein coupled receptors (GPCRs). The circulating bile acid pool composition consists of primary bile acids produced from cholesterol in the liver, and secondary bile acids formed by specific gut bacteria. The various biotransformation of bile acids carried out by gut bacteria appear to regulate the structure of the gut microbiome and host physiology. Increased levels of secondary bile acids are associated with specific diseases of the GI system. Elucidating methods to control the gut microbiome and bile acid pool composition in humans may lead to a reduction in some of the major diseases of the liver, gall bladder and colon.
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Affiliation(s)
- Jason M. Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Spencer C. Harris
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Shiva Bhowmik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dae-Joong Kang
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
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Hay AJ, Zhu J. In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut. ADVANCES IN APPLIED MICROBIOLOGY 2016; 96:43-64. [PMID: 27565580 DOI: 10.1016/bs.aambs.2016.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Colonization of a human host with a commensal microbiota has a complex interaction in which bacterial communities provide numerous health benefits to the host. An equilibrium between host and microbiota is kept in check with the help of biliary secretions by the host. Bile, composed primarily of bile salts, promotes digestion. It also provides a barrier between host and bacteria. After bile salts are synthesized in the liver, they are stored in the gallbladder to be released after food intake. The set of host-secreted bile salts is modified by the resident bacteria. Because bile salts are toxic to bacteria, an equilibrium of modified bile salts is reached that allows commensal bacteria to survive, yet rebuffs invading pathogens. In addition to direct toxic effects on cells, bile salts maintain homeostasis as signaling molecules, tuning the immune system. To cause disease, gram-negative pathogenic bacteria have shared strategies to survive this harsh environment. Through exclusion of bile, efflux of bile, and repair of bile-induced damage, these pathogens can successfully disrupt and outcompete the microbiota to activate virulence factors.
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Affiliation(s)
- A J Hay
- University of Pennsylvania, Philadelphia, PA, United States
| | - J Zhu
- University of Pennsylvania, Philadelphia, PA, United States
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Selwyn FP, Csanaky IL, Zhang Y, Klaassen CD. Importance of Large Intestine in Regulating Bile Acids and Glucagon-Like Peptide-1 in Germ-Free Mice. Drug Metab Dispos 2015. [PMID: 26199423 DOI: 10.1124/dmd.115.065276] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
It is known that 1) elevated serum bile acids (BAs) are associated with decreased body weight, 2) elevated glucagon-like peptide-1 (GLP-1) levels can decrease body weight, and 3) germ-free (GF) mice are resistant to diet-induced obesity. The purpose of this study was to test the hypothesis that a lack of intestinal microbiota results in more BAs in the body, resulting in increased BA-mediated transmembrane G protein-coupled receptor 5 (TGR5) signaling and increased serum GLP-1 as a mechanism of resistance of GF mice to diet-induced obesity. GF mice had 2- to 4-fold increased total BAs in the serum, liver, bile, and ileum. Fecal excretion of BAs was 63% less in GF mice. GF mice had decreased secondary BAs and increased taurine-conjugated BAs, as anticipated. Surprisingly, there was an increase in non-12α-OH BAs, namely, β-muricholic acid, ursodeoxycholic acid (UDCA), and their taurine conjugates, in GF mice. Further, in vitro experiments confirmed that UDCA is a primary BA in mice. There were minimal changes in the mRNA of farnesoid X receptor target genes in the ileum (Fibroblast growth factor 15, small heterodimer protein, and ileal bile acid-binding protein), in the liver (small heterodimer protein, liver receptor homolog-1, and cytochrome P450 7a1), and BA transporters (apical sodium dependent bile acid transporter, organic solute transporter α, and organic solute transporter β) in the ileum of GF mice. Surprisingly, there were marked increases in BA transporters in the large intestine. Increased GLP-1 levels and gallbladder size were observed in GF mice, suggesting activation of TGR5 signaling. In summary, the GF condition results in increased expression of BA transporters in the colon, resulting in 1) an increase in total BA concentrations in tissues, 2) a change in BA composition to favor an increase in non-12α-OH BAs, and 3) activation of TGR5 signaling with increased gallbladder size and GLP-1.
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Affiliation(s)
- Felcy Pavithra Selwyn
- Departments of Pharmacology, Toxicology, and Therapeutics (F.P.S., Y.Z.) and Internal Medicine (I.L.C., C.D.K.), University of Kansas Medical Center, Kansas City, Kansas
| | - Iván L Csanaky
- Departments of Pharmacology, Toxicology, and Therapeutics (F.P.S., Y.Z.) and Internal Medicine (I.L.C., C.D.K.), University of Kansas Medical Center, Kansas City, Kansas
| | - Youcai Zhang
- Departments of Pharmacology, Toxicology, and Therapeutics (F.P.S., Y.Z.) and Internal Medicine (I.L.C., C.D.K.), University of Kansas Medical Center, Kansas City, Kansas
| | - Curtis D Klaassen
- Departments of Pharmacology, Toxicology, and Therapeutics (F.P.S., Y.Z.) and Internal Medicine (I.L.C., C.D.K.), University of Kansas Medical Center, Kansas City, Kansas.
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Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 2015; 161:264-76. [PMID: 25860609 PMCID: PMC4393509 DOI: 10.1016/j.cell.2015.02.047] [Citation(s) in RCA: 2063] [Impact Index Per Article: 229.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/16/2014] [Accepted: 02/18/2015] [Indexed: 01/16/2023]
Abstract
The gastrointestinal (GI) tract contains much of the body's serotonin (5-hydroxytryptamine, 5-HT), but mechanisms controlling the metabolism of gut-derived 5-HT remain unclear. Here, we demonstrate that the microbiota plays a critical role in regulating host 5-HT. Indigenous spore-forming bacteria (Sp) from the mouse and human microbiota promote 5-HT biosynthesis from colonic enterochromaffin cells (ECs), which supply 5-HT to the mucosa, lumen, and circulating platelets. Importantly, microbiota-dependent effects on gut 5-HT significantly impact host physiology, modulating GI motility and platelet function. We identify select fecal metabolites that are increased by Sp and that elevate 5-HT in chromaffin cell cultures, suggesting direct metabolic signaling of gut microbes to ECs. Furthermore, elevating luminal concentrations of particular microbial metabolites increases colonic and blood 5-HT in germ-free mice. Altogether, these findings demonstrate that Sp are important modulators of host 5-HT and further highlight a key role for host-microbiota interactions in regulating fundamental 5-HT-related biological processes.
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Affiliation(s)
- Jessica M Yano
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kristie Yu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gregory P Donaldson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gauri G Shastri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Phoebe Ann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Liang Ma
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cathryn R Nagler
- Department of Pathology and Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elaine Y Hsiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C, Wang J. Gut microbiome development along the colorectal adenoma–carcinoma sequence. Nat Commun 2015; 6:6528. [DOI: 10.1038/ncomms7528] [Citation(s) in RCA: 718] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
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Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014; 38:996-1047. [PMID: 24861948 PMCID: PMC4262072 DOI: 10.1111/1574-6976.12075] [Citation(s) in RCA: 716] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023] Open
Abstract
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of BelgradeBelgrade, Serbia
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
- Departments of Bacteriology and Immunology, and Veterinary Biosciences, University of HelsinkiHelsinki, Finland
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Walker A, Pfitzner B, Neschen S, Kahle M, Harir M, Lucio M, Moritz F, Tziotis D, Witting M, Rothballer M, Engel M, Schmid M, Endesfelder D, Klingenspor M, Rattei T, Castell WZ, de Angelis MH, Hartmann A, Schmitt-Kopplin P. Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet. ISME JOURNAL 2014; 8:2380-96. [PMID: 24906017 DOI: 10.1038/ismej.2014.79] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/25/2014] [Accepted: 04/07/2014] [Indexed: 01/06/2023]
Abstract
A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. This study focused on gut and liver metabolomics of two different mouse strains, the C57BL/6J (C57J) and the C57BL/6N (C57N) fed with high-fat diet (HFD) for 3 weeks, causing diet-induced obesity in C57N, but not in C57J mice. Furthermore, a 16S-ribosomal RNA comparative sequence analysis using 454 pyrosequencing detected significant differences between the microbiome of the two strains on phylum level for Firmicutes, Deferribacteres and Proteobacteria that propose an essential role of the microbiome in obesity susceptibility. Gut microbial and liver metabolomics were followed by a combinatory approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography time of tlight MS/MS with subsequent multivariate statistical analysis, revealing distinctive host and microbial metabolome patterns between the C57J and the C57N strain. Many taurine-conjugated bile acids (TBAs) were significantly elevated in the cecum and decreased in liver samples from the C57J phenotype likely displaying different energy utilization behavior by the bacterial community and the host. Furthermore, several metabolite groups could specifically be associated with the C57N phenotype involving fatty acids, eicosanoids and urobilinoids. The mass differences based metabolite network approach enabled to extend the range of known metabolites to important bile acids (BAs) and novel taurine conjugates specific for both strains. In summary, our study showed clear alterations of the metabolome in the gastrointestinal tract and liver within a HFD-induced obesity mouse model in relation to the host-microbial nutritional adaptation.
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Affiliation(s)
- Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Pfitzner
- Research Unit Microbe-Plant Interactions, Research Group Molecular Microbial Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Neschen
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Kahle
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dimitrios Tziotis
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Rothballer
- Research Unit Microbe-Plant Interactions, Research Group Molecular Microbial Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marion Engel
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schmid
- Research Unit Microbe-Plant Interactions, Research Group Molecular Microbial Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - David Endesfelder
- Scientific Computing Research Unit, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Klingenspor
- Technische Universität München, Molecular Nutritional Medicine, Else Kröner-Fresenius Center and ZIEL Research Center for Nutrition and Food Sciences, Freising-Weihenstephan, Germany
| | - Thomas Rattei
- Department of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfgang Zu Castell
- Scientific Computing Research Unit, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabé de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Research Group Molecular Microbial Ecology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Philippe Schmitt-Kopplin
- 1] Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany [2] Technische Universität München, Chair of Analytical Food Chemistry, Freising-Weihenstephan, Germany
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van der Wulp MYM, Derrien M, Stellaard F, Wolters H, Kleerebezem M, Dekker J, Rings EHHM, Groen AK, Verkade HJ. Laxative treatment with polyethylene glycol decreases microbial primary bile salt dehydroxylation and lipid metabolism in the intestine of rats. Am J Physiol Gastrointest Liver Physiol 2013; 305:G474-82. [PMID: 23868407 DOI: 10.1152/ajpgi.00375.2012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polyethylene glycol (PEG) is a frequently used osmotic laxative that accelerates gastrointestinal transit. It has remained unclear, however, whether PEG affects intestinal functions. We aimed to determine the effect of PEG treatment on intestinal sterol metabolism. Rats were treated with PEG in drinking water (7%) for 2 wk or left untreated (controls). We studied the enterohepatic circulation of the major bile salt (BS) cholate with a plasma stable isotope dilution technique and determined BS profiles and concentrations in bile, intestinal lumen contents, and feces. We determined the fecal excretion of cholesterol plus its intestinally formed metabolites. Finally, we determined the cytolytic activity of fecal water (a surrogate marker of colorectal cancer risk) and the amount and composition of fecal microbiota. Compared with control rats, PEG treatment increased the pool size (+51%; P < 0.01) and decreased the fractional turnover of cholate (-32%; P < 0.01). PEG did not affect the cholate synthesis rate, corresponding with an unaffected fecal primary BS excretion. PEG reduced fecal excretion of secondary BS and of cholesterol metabolites (each P < 0.01). PEG decreased the cytolytic activity of fecal water [54 (46-62) vs. 87 (85-92)% erythrocyte potassium release in PEG-treated and control rats, respectively; P < 0.01]. PEG treatment increased the contribution of Verrucomicrobia (P < 0.01) and decreased that of Firmicutes (P < 0.01) in fecal flora. We concluded that PEG treatment changes the intestinal bacterial composition, decreases the bacterial dehydroxylation of primary BS and the metabolism of cholesterol, and increases the pool size of the primary BS cholate in rats.
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Affiliation(s)
- Mariëtte Y M van der Wulp
- Univ. Medical Center Groningen, Beatrix Children's Hospital, Div. Pediatric Gastroenterology and Hepatology, P.O. Box 30.001, 9700 RB Groningen, The Netherlands.
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Zhao Y, Wu J, Li JV, Zhou NY, Tang H, Wang Y. Gut microbiota composition modifies fecal metabolic profiles in mice. J Proteome Res 2013; 12:2987-99. [PMID: 23631562 DOI: 10.1021/pr400263n] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The gut microbiome is known to be extensively involved in human health and disease. In order to reveal the metabolic relationship between host and microbiome, we monitored recovery of the gut microbiota composition and fecal profiles of mice after gentamicin and/or ceftriaxone treatments. This was performed by employing (1)H nuclear magnetic resonance (NMR)-based metabonomics and denaturing gradient gel electrophoresis (DGGE) fingerprint of gut microbiota. The common features of fecal metabolites postantibiotic treatment include decreased levels of short chain fatty acids (SCFAs), amino acids and primary bile acids and increased oligosaccharides, d-pinitol, choline and secondary bile acids (deoxycholic acid). This suggests suppressed bacterial fermentation, protein degradation and enhanced gut microbial modification of bile acids. Barnesiella, Prevotella, and Alistipes levels were shown to decrease as a result of the antibiotic treatment, whereas levels of Bacteroides, Enterococcus and Erysipelotrichaceae incertae sedis, and Mycoplasma increased after gentamicin and ceftriaxone treatment. In addition, there was a strong correlation between fecal profiles and levels of Bacteroides, Barnesiella, Alistipes and Prevotella. The integration of metabonomics and gut microbiota profiling provides important information on the changes of gut microbiota and their impact on fecal profiles during the recovery after antibiotic treatment. The correlation between gut microbiota and fecal metabolites provides important information on the function of bacteria, which in turn could be important in optimizing therapeutic strategies, and developing potential microbiota-based disease preventions and therapeutic interventions.
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Affiliation(s)
- Ying Zhao
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
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64
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Rajilić-Stojanović M. Function of the microbiota. Best Pract Res Clin Gastroenterol 2013; 27:5-16. [PMID: 23768548 DOI: 10.1016/j.bpg.2013.03.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/28/2013] [Accepted: 03/14/2013] [Indexed: 02/07/2023]
Abstract
The gut microbiota of humans is complex but stable in composition and function. Metabolic conversions performed by the members of the microbiota yield both beneficial and hazardous compounds, and have a systematic impact on human health. Comparative studies have shown that the microbiota of patients, suffering from a number of diseases, is in dysbiosis, which is characterized by a distinct composition. Compositional differences have also been noted between members of geographically distant healthy populations. To be able to identify which compositional changes promote compromised health, it is of interest to identify members of the microbiota that perform essential metabolic transformations. This review provides an insight into the microbial contribution to the metabolism of carbohydrates, proteins and bile acids, and focuses on the link between diversity and function.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000 Belgrade, Serbia.
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Rath CM, Alexandrov T, Higginbottom SK, Song J, Milla M, Fischbach M, Sonnenburg JL, Dorrestein PC. Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations. Anal Chem 2012; 84:9259-67. [PMID: 23009651 PMCID: PMC3711173 DOI: 10.1021/ac302039u] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The communities constituting our microbiotas are emerging as mediators of the health-disease continuum. However, deciphering the functional impact of microbial communities on host pathophysiology represents a formidable challenge, due to the heterogeneous distribution of chemical and microbial species within the gastrointestinal (GI) tract. Herein, we apply imaging mass spectrometry (IMS) to localize metabolites from the interaction between the host and colonizing microbiota. This approach complements other molecular imaging methodologies in that analytes need not be known a priori, offering the possibility of untargeted analysis. Localized molecules within the GI tract were then identified in situ by surface sampling with nanodesorption electrospray ionization Fourier transform ion cyclotron resonance-mass spectrometry (nanoDESI FTICR-MS). Products from diverse structural classes were identified including cholesterol-derived lipids, glycans, and polar metabolites. Specific chemical transformations performed by the microbiota were validated with bacteria in culture. This study illustrates how untargeted spatial characterization of metabolites can be applied to the molecular dissection of complex biology in situ.
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Affiliation(s)
- Christopher M. Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, San Diego, CA 92093, United States
| | - Theodore Alexandrov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, San Diego, CA 92093, United States
- Center for Industrial Mathematics, University of Bremen, Breman, Germany
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Jiao Song
- Janssen, San Diego, CA 92121, United States
| | | | - Michael Fischbach
- Department of Bioengineering and Therapeutic Sciences University of California at San Francisco, San Francisco, CA 94143, United States
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, San Diego, CA 92093, United States
- Department of Chemistry and Biochemistry, University of California at San Diego, San Diego, CA 92093, United States
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66
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Flores R, Shi J, Gail MH, Ravel J, Goedert JJ. Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities. Eur J Clin Invest 2012; 42:848-54. [PMID: 22409163 PMCID: PMC3399928 DOI: 10.1111/j.1365-2362.2012.02660.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The intestinal microbial community has major effects on human health, but optimal research methods are unsettled. To facilitate epidemiologic and clinical research, we sought to optimize conditions and to assess reproducibility of selected core functions of the distal gut microbiota, β-glucuronidase and β-glucosidase bioactivities. METHODS AND RESULTS A colorimetric kinetic method was optimized and used to quantify activities of β-glucuronidase and β-glucosidase in human faeces. Enzyme detection was optimal with neutral pH, snap freezing in liquid nitrogen and rapid thawing to 37 °C before protein extraction. Enzymatic stability was assessed by delayed freezing for 2-48 h to mimic field settings. Activities decayed approximately 20% within 2 h and 40% within 4 h at room temperature. To formally assess reproducibility, 51 volunteers (25 men; mean age 39) used two devices to self-collect and rapidly chill four replicates of a stool. Devices were compared for mean enzymatic activities and intraclass correlation coefficients (ICC) in paired replicates of the self-collected specimens. Reproducibility was excellent with both devices for β-glucuronidase (ICC 0·92). The larger collection device had significantly higher reproducibility for β-glucosidase (ICC 0·92 vs. 0·76, P < 0·0001) and higher mean activities for both enzymes (P < 0·0001). CONCLUSIONS Optimal measurement of these core activities of the microbiota required a sufficient quantity of rapidly chilled or frozen specimens collected in phosphate buffered saline at pH7·0. Application of these methods to clinical and epidemiologic research could provide insights on how the intestinal microbiota affects human health.
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Affiliation(s)
- Roberto Flores
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA.
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67
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Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. The mind-body-microbial continuum. DIALOGUES IN CLINICAL NEUROSCIENCE 2011. [PMID: 21485746 PMCID: PMC3139398 DOI: 10.31887/dcns.2011.13.1/agonzalez] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent "metagenomic" techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A central question in psychiatry is the relative role of genes and environment in shaping behavior. The human microbiome serves as the interface between our genes and our history of environmental exposures; explorations of our microbiomes thus offer the possibility of providing new insights into our neurodevelopment and our behavioral phenotypes by affecting complex processes such as inter- and intra personal variations in cognition, personality, mood, sleep, and eating behavior, and perhaps even a variety of neuropsychiatric diseases ranging from affective disorders to autism. Better understanding of microbiome-encoded pathways for xenobiotic metabolism also has important implications for improving the efficacy of pharmacologic interventions with neuromodulatory agents.
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Affiliation(s)
- Antonio Gonzalez
- Department of Computer Science, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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68
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Ridlon JM, Kang DJ, Hylemon PB. Isolation and characterization of a bile acid inducible 7alpha-dehydroxylating operon in Clostridium hylemonae TN271. Anaerobe 2010; 16:137-46. [PMID: 19464381 PMCID: PMC6262846 DOI: 10.1016/j.anaerobe.2009.05.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 05/12/2009] [Indexed: 12/29/2022]
Abstract
Primary bile acids are synthesized from cholesterol in the liver, conjugated to either glycine or taurine and secreted into bile. Bile salts undergo enterohepatic circulation several times each day. During this process, they are biotransformed into a variety of metabolites by gut bacteria. The major biotransformation is the 7alpha-dehydroxylation of cholic acid and chenodeoxycholic acid yielding deoxycholic acid and lithocholic acid, respectively. 7alpha-Dehydroxylation is a multi-step pathway. The genes encoding enzymes in this pathway have been identified in two species of "high" activity strains of clostridia. Here, we report the isolation and characterization of a bile acid inducible (bai) operon in Clostridium hylemonae, a "low" activity 7alpha-dehydroxylating strain. The gene organization and sequence of the baiBCDEFGHI operon was highly conserved between C. hylemonae and "high" activity strains. Surprisingly, the baiA gene was missing from the bai operon of C. hylemonae. The baiA gene was isolated using PCR and degenerate oligonucleotide primers. The mRNA start site for the large bai operon was determined and shown to be only 11bp from the initiation codon of the first gene. It was also discovered that allocholic acid (5alpha) induced the bai operon and stimulated the conversion of [24-(14)C] cholic acid to [24-(14)C] allodeoxycholic acid in cultures of C. scindens and C. hylemonae allodeoxycholic acid. Finally, it was discovered that the addition of testosterone to the growth medium markedly increased 7alpha-dehydroxylation of cholic acid in Clostridium scindens and C. hylemonae. We hypothesize that testosterone may be a gratuitous inducer of genes involved in the reductive arm of the bile acid 7alpha-dehydroxylation pathway.
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Affiliation(s)
- Jason M Ridlon
- Department of Microbiology and Immunology, Medical College of Virginia Campus, Box 980678, Virginia Commonwealth University, Richmond, Virginia 23298 0678, USA.
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69
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The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm 2008; 363:1-25. [DOI: 10.1016/j.ijpharm.2008.07.009] [Citation(s) in RCA: 446] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 12/23/2022]
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Abstract
In their intestine, humans possess an "extended genome" of millions of microbial genes-the microbiome. Because this complex symbiosis influences host metabolism, physiology, and gene expression, it has been proposed that humans are complex biologic "superorganisms." Advances in microbiologic analysis and systems biology are now beginning to implicate the gut microbiome in the etiology of localized intestinal diseases such as the irritable bowel syndrome, inflammatory bowel disease, and colon cancer. These approaches also suggest possible links between the gut and previously unassociated systemic conditions such as type 2 diabetes and obesity. The elucidation of the intestinal microbiome is therefore likely to underpin future disease prevention strategies, personalized health care regimens, and the development of novel therapeutic interventions. This review summarizes the research that is defining our understanding of the intestinal microbiome and highlights future areas of research in gastroenterology and human health in which the intestinal microbiome will play a significant role.
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Hydrogen as an energy source for the human pathogen Bilophila wadsworthia. Antonie van Leeuwenhoek 2007; 93:381-90. [PMID: 18066702 DOI: 10.1007/s10482-007-9215-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 11/29/2007] [Indexed: 02/08/2023]
Abstract
The gram-negative anaerobic gut bacterium Bilophila wadsworthia is the third most common isolate in perforated and gangrenous appendicitis, being also found in a variety of other infections. This organism performs a unique kind of anaerobic respiration in which taurine, a major organic solute in mammals, is used as a source of sulphite that serves as terminal acceptor for the electron transport chain. We show here that molecular hydrogen, one of the major products of fermentative bacteria in the colon, is an excellent growth substrate for B. wadsworthia. We have quantified the enzymatic activities associated with the oxidation of H(2), formate and pyruvate for cells obtained in different growth conditions. The cell extracts present high levels of hydrogenase activity, and up to five different hydrogenases can be expressed by this organism. One of the hydrogenases appears to be constitutive, whereas the others show differential expression in different growth conditions. Two of the hydrogenases are soluble and are recognised by antibodies against a [FeFe] hydrogenase of a sulphate reducing bacterium. One of these hydrogenases is specifically induced during fermentative growth on pyruvate. Another two hydrogenases are membrane-bound and show increased expression in cells grown with hydrogen. Further work should be carried out to reveal whether oxidation of hydrogen contributes to the virulence of B. wadsworthia.
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