DOCSLIB.ORG

Chronic Diarrhea, Bile Acids, and Clostridia

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chronic Diarrhea, Bile Acids, and Clostridia Chronic diarrhea, bile acids, and Clostridia Julian R.F. Walters, Julian R. Marchesi J Clin Invest. 2020;130(1):77-79. https://doi.org/10.1172/JCI133117. Commentary Excessive fecal bile acid (BA) loss causes symptoms in a large proportion of people diagnosed with irritable bowel syndrome with diarrhea, a common functional bowel disorder. This BA diarrhea (BAD) results from increased hepatic synthesis of BAs, with impaired negative feedback regulation by the ileal hormone fibroblast growth factor 19 (FGF19). In this issue of the JCI, Zhao et al. investigated BA metabolism, including fecal BAs, serum BAs, and FGF19, in patients and controls. They identified associations between fecal bacterial BA metabolism and specific microbiota, especially Clostridium scindens. These findings have been tested in a mouse model using microbiota transplants and antibiotic treatment. This group of organisms has potential as a biomarker for BAD and to be a target for therapy. Find the latest version: https://jci.me/133117/pdf The Journal of Clinical Investigation COMMENTARY Chronic diarrhea, bile acids, and Clostridia Julian R.F. Walters1,2 and Julian R. Marchesi1,3 1Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom. 2Gastroenterology, Division of Medicine and Integrated Care, Imperial College Healthcare NHS Trust, London, United Kingdom. 3School of Biosciences, Cardiff University, Cardiff, United Kingdom. A possible cause of PBAD Excessive fecal bile acid (BA) loss causes symptoms in a large proportion In this issue of the JCI, Zhao et al. investi- gated the relevance of the BA/FXR signal- of people diagnosed with irritable bowel syndrome with diarrhea, a ing pathway and the effects of microbial common functional bowel disorder. This BA diarrhea (BAD) results from metabolism of BAs in relation to the pos- increased hepatic synthesis of BAs, with impaired negative feedback sible cause of PBAD (16). Starting with regulation by the ileal hormone fibroblast growth factor 19 (FGF19). In an unselected population of 345 Chinese this issue of the JCI, Zhao et al. investigated BA metabolism, including adults who met Rome IV diagnostic cri- fecal BAs, serum BAs, and FGF19, in patients and controls. They identified teria for IBS-D (1), the authors identified associations between fecal bacterial BA metabolism and specific approximately 25% of these with excess microbiota, especially Clostridium scindens. These findings have been total fecal BAs (called the BA+IBS-D group tested in a mouse model using microbiota transplants and antibiotic by Zhao et al.). This figure is a similar pro- treatment. This group of organisms has potential as a biomarker for BAD portion to the IBS-D patients reported else- and to be a target for therapy. where with PBAD (8–10). Importantly, the authors showed that the BA- positive group, when compared with the BA-negative group, also showed raised serum C4 and Pathophysiology of the The precise causes of this idiopathic, pri- total BA levels, with lower FGF19. Total functional bowel disorders mary BAD (PBAD) have largely been unclear. fecal BAs were associated with increased Bile acids (BAs) are increasingly recog- BAs are mostly reabsorbed in the ileum and symptom severity, increased BA synthesis, nized as major factors in the pathophysiol- undergo enterohepatic circulation. BA mal- and impaired FGF19 feedback, making the ogy of the functional bowel disorders with absorption, which is clearly present in ileal Zhao et al. study patients representative of diarrhea (1, 2). Recent guidelines recom- Crohn’s disease or resection, is usually not those studied previously (16). mend investigation of patients with chronic found in PBAD. An alternative cause for BA profile differences in serum and fecal diarrhea to detect the presence of BA the excess fecal BA loss is increased hepatic samples of the BA-positive group suggest that diarrhea (BAD) (3, 4). Such patients may BA synthesis (6, 11). BAs are synthesized there are differences in the BA- transforming meet the diagnostic criteria for irritable from cholesterol by the enzyme cholesterol microbiota in PBAD. In the serum, BAs con- bowel syndrome with predominant diar- 7α-hydroxylase (CYP7A1). Raised levels of jugated with glycine or taurine and the free rhea (IBS-D) or functional diarrhea (FD), the BA intermediate 7α-OH-4-cholesten-3- unconjugated liver-derived (primary) BAs, depending on how they report abdominal one (C4) demonstrate the increased activity cholic acid (CA) and chenodeoxycholic acid pain (1), but they all experience frequent, of the classical synthesis pathway, where (CDCA), predominated. CDCA and gly- soft or liquid stools, with urgency and CYP7A1 is rate limiting. This enzyme is reg- cochenodeoxycholic acid (GCDCA) were often fecal incontinence, with a response ulated via negative feedback by the ileal hor- increased, and the secondary BA, ursode- to BA sequestrants (5). Diagnostic delay mone fibroblast growth factor 19 (FGF19). oxycholic acid (UDCA) and its conjugated is common, as the recognition of BAD by Serum FGF19 levels are usually low in PBAD, form, glycoursodeoxycholic acid (GUDCA), physicians is poor, and there is limited and are inversely correlated with C4 (12). In were also particularly higher in the BA- availability of diagnostic tests, such as the ileal tissue, BA and other agonists bind to positive group. Similarly, in feces, increases nuclear medicine 75Se–homocholic acid the farnesoid X receptor (FXR) to stimulate in the total of most BAs, and the proportions taurine (SeHCAT) test (4, 6). SeHCAT is FGF19 transcription (13). In PBAD, there is of CA, CDCA, UDCA, and 7-ketodeoxycho- unavailable in the US, which has led to the evidence for impaired FGF19 production lic acid (7-KDCA) were found. Relevantly, development of alternative blood or fecal from the ileum (14). Further, PBAD is asso- identifying raised levels of unconjugated tests (7). The frequency of BAD is estimat- ciated with certain polymorphisms in genes primary BAs (CA and CDCA) in fecal sam- ed at 28% in IBS-D or FD, giving a popula- (FGFR4 and KLB) that affect the hepatic ples has been proposed as a novel diagnostic tion prevalence of 1% (8–10). response to FGF19 (15). method to identify PBAD (7). Intestinal bacteria possess special- ized BA-modifying enzymes, and conse- Related Article: p. 438 quently are integral to BA metabolism. Deconjugation, i.e., removing glycine or Conflict of interest: The authors have declared that no conflict of interest exists. Copyright: © 2020, American Society for Clinical Investigation. taurine, by choloylglycine hydrolase (also Reference information: J Clin Invest. 2020;130(1):77–79. https://doi.org/10.1172/JCI133117. known as bile salt hydrolase) encoded jci.org Volume 130 Number 1 January 2020 77 COMMENTARY The Journal of Clinical Investigation FGF15 at both transcript and protein lev- els. Conversely, vancomycin increased ileal Fgf15 and inhibited hepatic Cyp7a1 gene expression (16). Cell-line studies were performed to add to these findings. In the hepatocyte L-02 cell line, vancomycin or C. scindens failed to produce direct effects on CYP7A1 expression. In NCI-H716 cells, which have an enterocyte-like phenotype, CDCA stim- ulated FGF19 expression, as previously demonstrated in similar cells (17), confirm- ing findings with human ileal tissue that FXR agonists potently regulate this gene (13). Further, coincubating the cells with other BAs, including GUDCA, GCDCA, GCA, UDCA, or 7-KDCA, inhibited the CDCA-stimulated FGF19 (16). Other research has suggested that certain modified, secondary BAs can have actions as FXR antagonists. For example, tauro-β-muricholic acid was shown to act as an antagonist (18), but humans, unlike mice, have very low lev- els of this BA. In the Zhao et al. study, the related metabolite, ω-muricholic Figure 1. Factors contributing to BA diarrhea. The key physiological steps in BA metabolism produce or interact with specific factors that can contribute to the pathophysiology of altered BA metabolism acid, was detected at higher levels in and thus result in chronic diarrhea. Bacterial species influence various BA proportions (gold arrows feces of BA-positive patients. GUDCA with varying width) and influence FGF19 signaling (purple arrow). also has FXR-antagonist effects, and is increased by metformin, which decreases a specific Bacteroides species and can by the cgh gene, and 7-dehydroxylation/ into pseudo-germ-free mice, and after one also cause BAD (19, 20). dehydrogenation enzymes encoded by week, those that had received feces from bais (7-dehydroxylase) and hdhA (7α-hy- the group of BA-positive patients had cecal Clinical implications droxysteroid dehydrogenase, 7-HSDH) microbiota with decreased deconjugating The findings in Zhao et al. are significant are key to the production of the sec- ability and increased 7-HSDH and 7α–dehy- and important, advancing our understand- ondary, modified BAs. Using shotgun droxylating levels. They also had pathophys- ing of the role of the gut microbiota and BAs metagenomics and DNA extracted from iologic differences, increased fecal water in IBS-D. They will need to be confirmed the feces of the study group, Zhao et and BA, increased serum C4 and hepatic in other defined groups of PBAD, such al. found reduced Bacteroidetes, with BA-synthesizing enzyme activity, and as those diagnosed by reduced Se HCAT decreased abundances of Alistipes and decreased ileal FGF15 (the mouse homolog retention, blood tests, or by raised fecal Bacteroides, which express cgh, contrib- of human FGF19). No differences in ileal BA total or primary BAs (6, 7). They add to pre- uting to the reduced activity, and less BA transporters or hepatic receptors were iden- vious PBAD mechanistic studies, where deconjugation in the BA-positive patients tified. The Firmicutes/Bacteroidetes ratio was overproduction of BAs with raised C4, due (the BA+IBS-D group). This group had higher, and increases in Clostridium cluster to impaired FGF19-related negative feed- an increase in their microbiota in Firmi­ XIVa and C.
Load more

Recommended publications
  • Uneven Distribution of Cobamide Biosynthesis and Dependence in Bacteria Predicted By
    bioRxiv preprint doi: https://doi.org/10.1101/342006; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by 2 comparative genomics 3 4 Running title: Cobamide biosynthesis predictions 5 6 Amanda N. Shelton1, Erica C. Seth1, Kenny C. Mok1, Andrew W. Han2, Samantha N. Jackson3,4, 7 David R. Haft3, Michiko E. Taga1* 8 9 1 Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 10 USA 11 2 Second Genome, Inc., South San Francisco, CA, USA 12 3 J. Craig Venter Institute, Rockville, MD, USA 13 4 Current address: Department of Biological & Environmental Engineering, Cornell University, 14 Ithaca, NY, USA 15 16 * Address correspondence to Michiko E. Taga, [email protected] 17 18 19 -- 20 Abstract 21 22 The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial 23 metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent 1 bioRxiv preprint doi: https://doi.org/10.1101/342006; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 24 and distribution of cobamide production and use across bacteria.
    [Show full text]
  • Supporting Information
    Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs.
    [Show full text]
  • The Isolation of Novel Lachnospiraceae Strains and the Evaluation of Their Potential Roles in Colonization Resistance Against Clostridium Difficile
    The isolation of novel Lachnospiraceae strains and the evaluation of their potential roles in colonization resistance against Clostridium difficile Diane Yuan Wang Honors Thesis in Biology Department of Ecology and Evolutionary Biology College of Literature, Science, & the Arts University of Michigan, Ann Arbor April 1st, 2014 Sponsor: Vincent B. Young, M.D., Ph.D. Associate Professor of Internal Medicine Associate Professor of Microbiology and Immunology Medical School Co-Sponsor: Aaron A. King, Ph.D. Associate Professor of Ecology & Evolutionary Associate Professor of Mathematics College of Literature, Science, & the Arts Reader: Blaise R. Boles, Ph.D. Assistant Professor of Molecular, Cellular and Developmental Biology College of Literature, Science, & the Arts 1 Table of Contents Abstract 3 Introduction 4 Clostridium difficile 4 Colonization Resistance 5 Lachnospiraceae 6 Objectives 7 Materials & Methods 9 Sample Collection 9 Bacterial Isolation and Selective Growth Conditions 9 Design of Lachnospiraceae 16S rRNA-encoding gene primers 9 DNA extraction and 16S ribosomal rRNA-encoding gene sequencing 10 Phylogenetic analyses 11 Direct inhibition 11 Bile salt hydrolase (BSH) detection 12 PCR assay for bile acid 7α-dehydroxylase detection 12 Tables & Figures Table 1 13 Table 2 15 Table 3 21 Table 4 25 Figure 1 16 Figure 2 19 Figure 3 20 Figure 4 24 Figure 5 26 Results 14 Isolation of novel Lachnospiraceae strains 14 Direct inhibition 17 Bile acid physiology 22 Discussion 27 Acknowledgments 33 References 34 2 Abstract Background: Antibiotic disruption of the gastrointestinal tract’s indigenous microbiota can lead to one of the most common nosocomial infections, Clostridium difficile, which has an annual cost exceeding $4.8 billion dollars.
    [Show full text]
  • Uneven Distribution of Cobamide Biosynthesis and Dependence in Bacteria Predicted by Comparative Genomics
    The ISME Journal (2018) 13:789–804 https://doi.org/10.1038/s41396-018-0304-9 ARTICLE Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics 1 1 1 1,2 3,4 3 Amanda N. Shelton ● Erica C. Seth ● Kenny C. Mok ● Andrew W. Han ● Samantha N. Jackson ● David R. Haft ● Michiko E. Taga1 Received: 7 June 2018 / Revised: 14 September 2018 / Accepted: 4 October 2018 / Published online: 14 November 2018 © The Author(s) 2018. This article is published with open access Abstract The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced 1234567890();,: 1234567890();,: by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway.
    [Show full text]
  • Characterization of an Endolysin Targeting Clostridioides Difficile
    International Journal of Molecular Sciences Article Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth Shakhinur Islam Mondal 1,2 , Arzuba Akter 3, Lorraine A. Draper 1,4 , R. Paul Ross 1 and Colin Hill 1,4,* 1 APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; [email protected] (S.I.M.); [email protected] (L.A.D.); [email protected] (R.P.R.) 2 Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh 3 Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh; [email protected] 4 School of Microbiology, University College Cork, T12 K8AF Cork, Ireland * Correspondence: [email protected] Abstract: Clostridioides difficile is a spore-forming enteric pathogen causing life-threatening diarrhoea and colitis. Microbial disruption caused by antibiotics has been linked with susceptibility to, and transmission and relapse of, C. difficile infection. Therefore, there is an urgent need for novel therapeutics that are effective in preventing C. difficile growth, spore germination, and outgrowth. In recent years bacteriophage-derived endolysins and their derivatives show promise as a novel class of antibacterial agents. In this study, we recombinantly expressed and characterized a cell wall hydrolase (CWH) lysin from C. difficile phage, phiMMP01. The full-length CWH displayed lytic activity against selected C. difficile strains. However, removing the N-terminal cell wall binding domain, creating CWH351—656, resulted in increased and/or an expanded lytic spectrum of activity. C. difficile specificity was retained versus commensal clostridia and other bacterial species.
    [Show full text]
  • The Mechanisms of in Vivo Commensal Control of C
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.04.894915; this version posted January 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The mechanisms of in vivo commensal control of C. difficile virulence Title: The mechanisms of in vivo commensal control of Clostridioides difficile virulence Authors: Girinathan BP1*, DiBenedetto N1*, Worley J1,2, Peltier J3§, Lavin R4, Delaney ML1,5, Cummins C1, Onderdonk AB1,5, Gerber GK1,6,, Dupuy B3, Sonenshein AL4, Bry L1,5,** Abstract: We define multiple mechanisms by which commensals protect against or worsen Clostridioides difficile infection. Using a systems-level approach we show how two species of Clostridia with distinct metabolic capabilities modulate the pathogen’s virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Clostridium bifermentans survived infection, while colonization with the butyrate-producer, Clostridium sardiniense, more rapidly succumbed. Systematic in vivo analyses revealed how each commensal altered the pathogen’s carbon source metabolism, cellular machinery, stress responses, and toxin production. Protective effects were replicated in infected conventional mice receiving C. bifermentans as an oral bacteriotherapeutic that prevented lethal infection. Leveraging a systematic and organism-level approach to host-commensal- pathogen interactions in vivo, we lay the groundwork for mechanistically-informed therapies to treat and prevent this disease. Author Affiliations: 1. Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 2.
    [Show full text]
  • Depression and Microbiome—Study on the Relation and Contiguity Between Dogs and Humans
    applied sciences Article Depression and Microbiome—Study on the Relation and Contiguity between Dogs and Humans Elisabetta Mondo 1,*, Alessandra De Cesare 1, Gerardo Manfreda 2, Claudia Sala 3 , Giuseppe Cascio 1, Pier Attilio Accorsi 1, Giovanna Marliani 1 and Massimo Cocchi 1 1 Department of Veterinary Medical Science, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Italy; [email protected] (A.D.C.); [email protected] (G.C.); [email protected] (P.A.A.); [email protected] (G.M.); [email protected] (M.C.) 2 Department of Agricultural and Food Sciences, University of Bologna, Via del Florio 2, 40064 Ozzano Emilia, Italy; [email protected] 3 Department of Physics and Astronomy, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-051-209-7329 Received: 22 November 2019; Accepted: 7 January 2020; Published: 13 January 2020 Abstract: Behavioral studies demonstrate that not only humans, but all other animals including dogs, can suffer from depression. A quantitative molecular evaluation of fatty acids in human and animal platelets has already evidenced similarities between people suffering from depression and German Shepherds, suggesting that domestication has led dogs to be similar to humans. In order to verify whether humans and dogs suffering from similar pathologies also share similar microorganisms at the intestinal level, in this study the gut-microbiota composition of 12 German Shepherds was compared to that of 15 dogs belonging to mixed breeds which do not suffer from depression. Moreover, the relation between the microbiota of the German Shepherd’s group and that of patients with depression has been investigated.
    [Show full text]
  • Updates on the Sporulation Process in Clostridium Species
    Updates on the sporulation process in Clostridium species Talukdar, P. K., Olguín-Araneda, V., Alnoman, M., Paredes-Sabja, D., & Sarker, M. R. (2015). Updates on the sporulation process in Clostridium species. Research in Microbiology, 166(4), 225-235. doi:10.1016/j.resmic.2014.12.001 10.1016/j.resmic.2014.12.001 Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse *Manuscript 1 Review article for publication in special issue: Genetics of toxigenic Clostridia 2 3 Updates on the sporulation process in Clostridium species 4 5 Prabhat K. Talukdar1, 2, Valeria Olguín-Araneda3, Maryam Alnoman1, 2, Daniel Paredes-Sabja1, 3, 6 Mahfuzur R. Sarker1, 2. 7 8 1Department of Biomedical Sciences, College of Veterinary Medicine and 2Department of 9 Microbiology, College of Science, Oregon State University, Corvallis, OR. U.S.A; 3Laboratorio 10 de Mecanismos de Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de 11 Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. 12 13 14 Running Title: Clostridium spore formation. 15 16 17 Key Words: Clostridium, spores, sporulation, Spo0A, sigma factors 18 19 20 Corresponding author: Dr. Mahfuzur Sarker, Department of Biomedical Sciences, College of 21 Veterinary Medicine, Oregon State University, 216 Dryden Hall, Corvallis, OR 97331. Tel: 541- 22 737-6918; Fax: 541-737-2730; e-mail: [email protected] 23 1 24 25 Abstract 26 Sporulation is an important strategy for certain bacterial species within the phylum Firmicutes to 27 survive longer periods of time in adverse conditions. All spore-forming bacteria have two phases 28 in their life; the vegetative form, where they can maintain all metabolic activities and replicate to 29 increase numbers, and the spore form, where no metabolic activities exist.
    [Show full text]
  • Functional Genomic Examinations of Interactions Between Common Members of the Umh an Gut Microbiota Michael Mahowald Washington University in St
    Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) January 2010 Functional Genomic Examinations Of Interactions Between Common Members Of The umH an Gut Microbiota Michael Mahowald Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Mahowald, Michael, "Functional Genomic Examinations Of Interactions Between Common Members Of The umH an Gut Microbiota" (2010). All Theses and Dissertations (ETDs). 222. https://openscholarship.wustl.edu/etd/222 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY Division of Biology and Biomedical Sciences Molecular Microbiology and Microbial Pathogenesis Dissertation Examination Committee: Jeffrey I. Gordon, Chair Douglas E. Berg Michael G. Caparon Daniel E. Goldberg Elaine R. Mardis Clay F. Semenkovich FUNCTIONAL GENOMIC EXAMINATIONS OF INTERACTIONS BETWEEN COMMON MEMBERS OF THE HUMAN GUT MICROBIOTA by Michael Anthony Mahowald A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2010 Saint Louis, Missouri Copyright by Michael Anthony Mahowald 2010 Dedication To my parents, Anthony P. and Mary Briody Mahowald ii ABSTRACT OF THE DISSERTATION Functional genomic examinations of interactions between common members of the human gut microbiota by Michael Anthony Mahowald Doctor of Philosophy in Biology and Biomedical Sciences (Molecular Microbiology and Microbial Pathogenesis) Washington University in St.
    [Show full text]
  • Assignment of Eubacterium Sp. VPI 12708
    International Journal of Systematic and Evolutionary Microbiology (2000), 50, 971–978 Printed in Great Britain Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7α- dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces Maki Kitahara,1 Fusae Takamine,2 Teisuke Imamura2 and Yoshimi Benno1 Author for correspondence: Maki Kitahara. Tel: j81 48 4679562. Fax: j81 48 462 4619. e-mail: kitahara!jcm.riken.go.jp 1 Japan Collection of Unknown Eubacterium-like organisms VPI 12708 and five strains (Y-1113, I-10, Microorganisms, RIKEN, M-18, TH-82 and 36S) had high bile acid 7α-dehydroxylating activity; the Wako, Saitama 351-0198, T Japan unknown Clostridium-like organisms TN-271 and TN-272 also had the same activity. Analysis of their 16S rDNA sequences demonstrated that all strains 2 Laboratory of Microbiology, School of belong to cluster XIVa of the genus Clostridium (Collins et al., 1994). Strain VPI Health Sciences, Faculty of 12708 and five other strains (Y-1113, I-10, M-18, TH-82 and 36S) formed a single Medicine, University of the cluster and strains TN-271T and TN-272 formed another single cluster. Ryukyus, Okinawa T 903-0215, Japan Clostridium scindens JCM 6567 was the most closely related species for two clusters in the phylogenetic tree. Values for DNA–DNA similarities among C. scindens JCM 6567T, strain VPI 12708 and the other five strains were greater than 70%, showing that these micro-organisms were a single species. Therefore, we identified strain VPI 12708 and the five other strains as C.
    [Show full text]
  • Staff Advice Report
    Staff Advice Report 11 January 2021 Advice to the Decision-making Committee to determine the new organism status of 18 gut bacteria species Application code: APP204098 Application type and sub-type: Statutory determination Applicant: PSI-CRO Date application received: 4 December 2020 Purpose of the Application: Information to support the consideration of the determination of 18 gut bacteria species Executive Summary On 4 December 2020, the Environmental Protection Authority (EPA) formally received an application from PSI-CRO requesting a statutory determination of 18 gut bacteria species, Anaerotruncus colihominis, Blautia obeum (aka Ruminococcus obeum), Blautia wexlerae, Enterocloster aldenensis (aka Clostridium aldenense), Enterocloster bolteae (aka Clostridium bolteae), Clostridium innocuum, Clostridium leptum, Clostridium scindens, Clostridium symbiosum, Eisenbergiella tayi, Emergencia timonensis, Flavonifractor plautii, Holdemania filiformis, Intestinimonas butyriciproducens, Roseburia hominis, ATCC PTA-126855, ATCC PTA-126856, and ATCC PTA-126857. In absence of publicly available data on the gut microbiome from New Zealand, the applicant provided evidence of the presence of these bacteria in human guts from the United States, Europe and Australia. The broad distribution of the species in human guts supports the global distribution of these gut bacteria worldwide. After reviewing the information provided by the applicant and found in scientific literature, EPA staff recommend the Hazardous Substances and New Organisms (HSNO) Decision-making Committee (the Committee) to determine that the 18 bacteria are not new organisms for the purpose of the HSNO Act. Recommendation 1. Based on the information available, the bacteria appear to be globally ubiquitous and commonly identified in environments that are also found in New Zealand (human guts). 2.
    [Show full text]
  • Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy Vogel, Catherine Larose
    Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy Vogel, Catherine Larose To cite this version: Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy Vogel, Catherine Larose. Do Or- ganic Substrates Drive Microbial Community Interactions in Arctic Snow?. Frontiers in Microbiology, Frontiers Media, 2019, 10, 10.3389/fmicb.2019.02492. hal-02415106 HAL Id: hal-02415106 https://hal.archives-ouvertes.fr/hal-02415106 Submitted on 8 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-10-02492 October 30, 2019 Time: 16:16 # 1 ORIGINAL RESEARCH published: 31 October 2019 doi: 10.3389/fmicb.2019.02492 Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? Benoît Bergk Pinto1*, Lorrie Maccario1†, Aurélien Dommergue2, Timothy M. Vogel1 and Catherine Larose1* 1 Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, UMR CNRS 5005, Université de Lyon, Lyon, France, 2 Univ Grenoble Alpes, CNRS, IRD, Grenoble INP, Institut des Géosciences de l’Environnement, Grenoble, France The effect of nutrients on microbial interactions, including competition and collaboration, has mainly been studied in laboratories, but their potential application to complex ecosystems is unknown.
    [Show full text]