DOCSLIB.ORG

Noncontiguous Finished Genome Sequence and Description of Intestinimonas Massilien Sis Sp

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Noncontiguous Finished Genome Sequence and Description of Intestinimonas Massilien Sis Sp Noncontiguous finished genome sequence and description of Intestinimonas massilien sis sp. nov strain GD2 T , the second Intestinimonas species cultured from the human gut Pamela Afouda, Guillaume Durand, Jean-Christophe Lagier, Noemie Labas, Frederic Cadoret, Nicholas Armstrong, Didier Raoult, Gregory Dubourg To cite this version: Pamela Afouda, Guillaume Durand, Jean-Christophe Lagier, Noemie Labas, Frederic Cadoret, et al.. Noncontiguous finished genome sequence and description of Intestinimonas massilien sis sp. nov strain GD2 T , the second Intestinimonas species cultured from the human gut. MicrobiologyOpen, Wiley, 2019, 8 (1), pp.e00621. 10.1002/mbo3.621. hal-02009953 HAL Id: hal-02009953 https://hal.archives-ouvertes.fr/hal-02009953 Submitted on 10 Dec 2019 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. Distributed under a Creative Commons Attribution| 4.0 International License Received: 21 November 2017 | Revised: 15 February 2018 | Accepted: 19 February 2018 DOI: 10.1002/mbo3.621 ORIGINAL RESEARCH Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2T, the second Intestinimonas species cultured from the human gut Pamela Afouda | Guillaume A. Durand | Jean-Christophe Lagier | Noémie Labas | Fréderic Cadoret | Nicholas Armstrong | Didier Raoult | Grégory Dubourg Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM Abstract 63, CNRS 7278, IRD 198, Inserm 1095, IHU Intestinimonas massiliensis sp. nov strain GD2T is a new species of the genus - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France Intestinimonas (the second, following Intestinimonas butyriciproducens gen. nov., sp. nov). First isolated from the gut microbiota of a healthy subject of French origin using Correspondence Grégory Dubourg, IHU Méditerranée a culturomics approach combined with taxono- genomics, it is strictly anaerobic, Infection, Marseille, France. nonspore- forming, rod- shaped, with catalase- and oxidase- negative reactions. Its Email: [email protected] growth was observed after preincubation in an anaerobic blood culture enriched Funding information with sheep blood (5%) and rumen fluid (5%), incubated at 37°C. Its phenotypic and This study was supported by Méditerranée Infection and the National Research Agency genotypic descriptions are presented in this paper with a full annotation of its ge- under the program « Investissements d’ave- nome sequence. This genome consists of 3,104,261 bp in length and contains 3,074 nir », reference ANR-10-IAHU-03. predicted genes, including 3,012 protein-coding genes and 62 RNA-coding genes. Strain GD2T significantly produces butyrate and is frequently found among available 16S rRNA gene amplicon datasets, which leads consideration of Intestinimonas massil- iensis as an important human gut commensal. KEYWORDS anaerobe, butyrate, culturomics, new species, taxono-genomics 1 | INTRODUCTION several limitations of these methods have been extensively dis- cussed (Poretsky, Rodriguez-R, Luo, Tsementzi, & Konstantinidis, The description of the human microbiome has become one the most 2014). Among these, 16S rRNA gene sequences may not match to exciting challenges of the 21st century in the field of microbiology, a corresponding species in the database, which can potentially lead as reflected by the Human Microbiome Project (HMP) (Turnbaugh to missed and unknown taxa of great interest. Recently, Lagier et al. et al., 2007). In particular, alterations in the composition of the human (2012, 2016) have shown that extensive bacterial culture, referred gut microbiota have been associated with several diseases, including to as culturomics, can fill in the blanks of metagenomic data through obesity and inflammatory bowel disease. More recently, specific the discovery of hundreds of new bacterial species associated with microbial signatures were predictive of the response to anticancer humans. therapy in lung cancer (Vétizou et al., 2015). While high- throughput Considering the limitations of the traditional combination of sequencing techniques have enabled substantial advances in under- phenotypic and genotypic characteristics to describe these new standing the role exerted by the gut microbiota in human health, species (Kim, Oh, Park, & Chun, 2014; Rosselló- Mora, 2006; Tindall, This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. MicrobiologyOpen. 2019;8:e621. www.MicrobiologyOpen.com | 1 of 11 https://doi.org/10.1002/mbo3.621 2 of 11 | AFOUDA ET AL. Rosselló- Móra, Busse, Ludwig, & Kämpfer, 2010; Wayne et al., 1987), the sequences of different species (Thompson, Higgins, & Gibson, we also proposed using genomic information to help define and de- 1994) and the Kimura two- parameter model was used to calculate scribe new bacterial species (Fournier, Lagier, Dubourg, & Raoult, evolutionary distance (Kimura, 1980). 2015). We isolated a species belonging to the Intestinimonas genus as part of a culturomics study, using an anaerobic culture applied to a 2.3 | Physiological and phenotypic characteristics stool sample from a healthy subject. The genus Intestinimonas, which belongs to the Firmicutes phylum, was created in 2013. To date, this The strain was tested for growth in anaerobic conditions at varying genus contains only Intestinimonas butyriciproducens gen. nov, sp. nov, temperatures: 28°C, 37°C, 45°C, and 56°C. Growth under aerobic which was first isolated from mice (Kläring et al., 2013). It has also and microaerophilic conditions was also assessed. To determine the been cultured from the human gut (Bui et al., 2015). Furthermore, biochemical characteristics of the strain, API ZYM (bioMérieux), it has recently been abundantly detected in human colonic samples API Rapid ID 20 NE (bioMérieux), and API 50 CH (bioMérieux) (Bui et al., 2015), with a particular focus on butyrate production. In were used, following the instructions of the manufacturer. Catalase this paper, we present a summary of the classification and set of fea- and oxidase activities were also tested. Gram staining and motil- tures for Intestinimonas massiliensis sp. nov. strain GD2T, together ity were determined using the light microscope DM1000 (Leica with a description of its complete genomic sequencing and annota- Microsystems, Nanterre, France). Cell morphology was determined tion. These characteristics enable the creation of the Intestinimonas using Tecnai G20 transmission electron microscopy (FEI Company, massiliensis species, which represents the second Intestinimonas spe- Limeil- Brévannes, France), after negative staining of the bacteria cies and the first cultured from the human gut microbiota. and elements determining the gram- stain characteristics of the bacteria were evaluated using the Morgagni 268D TEM (Philips). For preparation for transmission electron microscopy (TEM), bac- 2 | MATERIAL AND METHODS teria were recovered and pelleted for 10 min at 5,000 g. The pel- let was resuspended in 1 ml of phosphate- buffered saline (PBS) 2.1 | Sample information with 2.5% glutaraldehyde in a 0.1mol/L sodium cacodylate buffer The specimen was sampled from a healthy 28- year- old male of and incubated for at least 1 hr at 4°C. The pellet was then washed French origin, with a body mass index of 23.4 kg/m2. Consent was three times with 0.1mol/L cacodylate- saccharose and resuspended obtained, and the study was approved by the Institut Fédératif de in the same buffer. After repelleting, the sample was embedded in Recherche 48 (Faculty of Medicine, Marseille, France), under agree- Epon resin using a standard method, as follows: 1 hr of fixation in ment Number 09- 022. 1% osmium tetroxide, two washes in distilled water, dehydration in increasing ethanol concentrations (30%, 50%, 70%, 96%, and 100% ethanol), and embedding in Epon- 812. Ultrathin sections of 70 nm 2.2 | Strain identification and phylogenetic were poststained with 5% uranyl acetate and lead citrate following classification the Reynolds method (Reynolds, 1963). Samples were then observed Strain GD2T was isolated in February 2015 from a stool stored using a Morgagni 268D TEM (Philips) operating at 60 keV. To deter- 10 days at −20°C after preincubation 72 hr and subculture under mine sporulation, thermal shock was carried out on the bacteria at strict anaerobic conditions in the presence of sheep blood (5%) 80°C for 20 min, which were then seeded on Colombia blood agar. and rumen fluid (5%). Identification was performed using MALDI- Plates were then incubated for 48 hr under anaerobic conditions. TOF mass spectrometry and by sequencing of the 16S rRNA gene. We determined antibiotic susceptibility using the E- test gradient DNA extraction was realized using an EZ1 DNA Tissue Kit (Qiagen, strip method (bioMérieux) to define the minimal inhibitory concen- Courtaboeuf, France). The
Load more

Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • Doctoral Dissertation Template
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By QICHAO TU Norman, Oklahoma 2014 METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Jizhong Zhou, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Fengxia (Felicia) Qi ______________________________ Dr. Michael McInerney ______________________________ Dr. Bradley Stevenson © Copyright by QICHAO TU 2014 All Rights Reserved. Acknowledgements At this special moment approaching the last stage for this degree, I would like to express my gratitude to all the people who encouraged me and helped me out through the past years. Dr. Jizhong Zhou, my advisor, is no doubt the most influential and helpful person in pursuing my academic goals. In addition to continuous financial support for the past six years, he is the person who led me into the field of environmental microbiology, from a background of bioinformatics and plant molecular biology. I really appreciated the vast training I received from the many interesting projects I got involved in, without which I would hardly develop my broad experienced background from pure culture microbial genomics to complex metagenomics. Dr. Zhili He, who played a role as my second advisor, is also the person I would like to thank most. Without his help, I could be still struggling working on those manuscripts lying in my hard drive. I definitely learned a lot from him in organizing massed results into logical scientific work—skills that will benefit me for life.
    [Show full text]
  • Clostridium Amazonitimonense, Clostridium Me
    ORIGINAL ARTICLE Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’, ‘Clostridium merdae’, ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’ M. T. Alou1, S. Ndongo1, L. Frégère1, N. Labas1, C. Andrieu1, M. Richez1, C. Couderc1, J.-P. Baudoin1, J. Abrahão2, S. Brah3, A. Diallo1,4, C. Sokhna1,4, N. Cassir1, B. La Scola1, F. Cadoret1 and D. Raoult1,5 1) Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France, 2) Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 3) Hopital National de Niamey, BP 247, Niamey, Niger, 4) Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal and 5) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2T, ‘Clostridium massilidielmoense’ strain MT26T, ‘Clostridium nigeriense’ strain Marseille-P2414T and ‘Clostridium merdae’ strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation. © 2017 Published by Elsevier Ltd. Keywords: ‘Clostridium amazonitimonense’, ‘Clostridium massilidielmoense’, ‘Clostridium merdae’, ‘Clostridium nigeriense’, culturomics, emerging bacteria, human microbiota, taxonogenomics Original Submission: 18 August 2017; Revised Submission: 9 November 2017; Accepted: 16 November 2017 Article published online: 22 November 2017 intestine [1,4–6].
    [Show full text]
  • Crowdsourced Study of Children with Autism and Their Typically
    bioRxiv preprint doi: https://doi.org/10.1101/319236; this version posted May 10, 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 4.0 International license. 1 Crowdsourced study of children with autism and their typically 2 developing siblings identifies differences in taxonomic and predicted 3 function for stool-associated microbes using exact sequence variant 4 analysis. 5 Maude M David1,2, Christine Tataru1, Jena Daniels1, Jessey Schwartz1, Jessica Keating1, Jarrad Hampton-Marcell3, Neil 6 Gottel4, Jack A. Gilbert3,4, Dennis P. Wall1,5* 7 1 Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA 8 2 Department of Microbiology, Oregon State University, Corvallis, OR, USA 9 3 Bioscience Division, The Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA 10 4 Department of Surgery, The Microbiome Center, University of Chicago, Chicago, Illinois, USA 11 5 Department of Biomedical Data Science, Stanford University, Stanford, CA, USA 12 *Corresponding Author: 13 Dennis P. Wall, Ph.D. 14 Department of Pediatrics, Division of Systems Medicine 15 Stanford University 16 1265 Welch Rd, Suite X141, Stanford, CA 94305 17 P: 650-497-0921 18 E: [email protected] 19 20 Keywords 21 Autism spectrum disorder, microbiome, crowdsource, 16S ribosomal sequencing, Clostridiales, Lachnospiraceae, butyrate 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/319236; this version posted May 10, 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.
    [Show full text]
  • Interactions Between Host Genetics and Gut Microbiota Determine Susceptibility to CNS Autoimmunity
    Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity Theresa L. Montgomerya,1, Axel Künstnerb,c,1, Josephine J. Kennedya, Qian Fangd, Lori Asariand, Rachel Culp-Hille, Angelo D’Alessandroe, Cory Teuscherd, Hauke Buschb,c, and Dimitry N. Krementsova,2 aDepartment of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401; bMedical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; cInstitute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; dDepartment of Medicine, Immunobiology Division, University of Vermont, Burlington, VT 05401; and eDepartment of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045 Edited by Dennis L. Kasper, Harvard Medical School, Boston, MA, and approved August 26, 2020 (received for review February 23, 2020) Multiple sclerosis (MS) is an autoimmune disease of the central circulation to directly impact distal sites, including the brain (11, nervous system. The etiology of MS is multifactorial, with disease 12). With regard to MS, a number of recent case-control studies risk determined by genetics and environmental factors. An emerg- have demonstrated that the gut microbiome of MS patients differs ing risk factor for immune-mediated diseases is an imbalance from that of their healthy control counterparts. Some broad fea- in the gut microbiome. However, the identity of gut microbes as- tures, such as decreased abundance of putative short-chain fatty sociated with disease risk, their mechanisms of action, and the acid (SCFA)-producing bacteria and expansion of Akkermansia, interactions with host genetics remain obscure. To address these have been observed consistently across several studies (13–19).
    [Show full text]
  • MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
    BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ...........................................................................................................
    [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 Comparison of Bacteria from the Human Gut and Closely
    Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte To cite this version: Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte. Functional comparison of bacteria from the human gut and closely related non-gut bacte- ria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment. PLoS ONE, Public Library of Science, 2016, 11 (7), pp.e0159030. 10.1371/jour- nal.pone.0159030. hal-01353535 HAL Id: hal-01353535 https://hal.archives-ouvertes.fr/hal-01353535 Submitted on 11 Aug 2016 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. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals
    [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]
  • An Exploration of the Gut Bacteria in a Mouse Model of Autism Spectrum Disorder on a Ketogenic Diet
    Trinity College Trinity College Digital Repository Senior Theses and Projects Student Scholarship Spring 2017 An exploration of the gut bacteria in a mouse model of autism spectrum disorder on a ketogenic diet Laura M. Nee Trinity College, Hartford Connecticut, [email protected] Follow this and additional works at: https://digitalrepository.trincoll.edu/theses Recommended Citation Nee, Laura M., "An exploration of the gut bacteria in a mouse model of autism spectrum disorder on a ketogenic diet". Senior Theses, Trinity College, Hartford, CT 2017. Trinity College Digital Repository, https://digitalrepository.trincoll.edu/theses/676 TRINITY COLLEGE AN EXPLORATION OF THE GUT BACTERIA IN A MOUSE MODEL OF AUTISM SPECTRUM DISORDER ON A KETOGENIC DIET BY LAURA M. NEE A THESIS SUBMITTED TO THE FACULTY OF THE DEPARTMENT OF BIOLOGY IN CANDIDACY FOR THE BACCALAUREATE DEGREE WITH HONORS IN BIOLOGY DEPARTMENT OF BIOLOGY HARTFORD, CONNECTICUT 5 MAY 2017 GASTROINTESTINAL FLORA IN BTBR-STRAIN MICE ON KETOGENIC DIET 2 AN EXPLORATION OF THE GUT BACTERIA IN A MOUSE MODEL OF AUTISM SPECTRUM DISORDER ON A KETOGENIC DIET BY LAURA M. NEE Honors ThEsis CommittEE ApprovEd: __________________________________________ Lisa-Anne FostEr, Ph.D., Advisor __________________________________________ KathlEEn ArchEr, Ph.D. __________________________________________ Claire Fournier, Ph.D. DatE: _____________________________________ GASTROINTESTINAL FLORA IN BTBR-STRAIN MICE ON KETOGENIC DIET 3 ABSTRACT ........................................................................................................................................
    [Show full text]
  • Alterations of the Gut Ecological and Functional Microenvironment in Different Stages of Multiple Sclerosis
    Alterations of the gut ecological and functional microenvironment in different stages of multiple sclerosis Daiki Takewakia,b,c, Wataru Sudad,1, Wakiro Satoa,b, Lena Takayasud,e, Naveen Kumard, Kimitoshi Kimuraa,b,f, Naoko Kagag, Toshiki Mizunoc, Sachiko Miyakeh, Masahira Hattorid,i, and Takashi Yamamuraa,b,1 aDepartment of Immunology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, 187-8502 Tokyo, Japan; bMultiple Sclerosis Center, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, 187-8551 Tokyo, Japan; cDepartment of Neurology, Kyoto Prefectural University of Medicine, Kamigyo-ku, 602-8566 Kyoto, Japan; dLaboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, 230-0045 Kanagawa, Japan; eSchool of International Health, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan; fDepartment of Neurology, Kyoto University Hospital and Graduate School of Medicine, Shogoin, Sakyo-ku, 606-8507 Kyoto, Japan; gLaboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Bunkyo-ku, 113-8421 Tokyo, Japan; hDepartment of Immunology, Juntendo University School of Medicine, Bunkyo-ku, 113-8421 Tokyo, Japan; and iGraduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, 169-8555 Tokyo, Japan Edited by Lawrence Steinman, Stanford University School of Medicine, Stanford, CA, and approved July 28, 2020 (received for review June 8, 2020) Multiple sclerosis (MS), an autoimmune disease of the central nervous recent work, showing the involvement of cytotoxic T helper cells in system, generally starts as the relapsing remitting form (RRMS), but SPMS, is supportive of this postulate (2, 3).
    [Show full text]
  • A Primer on the Role of the Microbiome in Colorectal Neoplasia
    REVIEW ARTICLE Annals of Gastroenterology (2020) 33, 1-14 Understanding the microbiome: a primer on the role of the microbiome in colorectal neoplasia Katherine M. Watsona, Christopher A. Gaulkeb, Vassiliki Liana Tsikitisa Oregon Health & Science University, Portland, OR; Oregon Health & Science University, USA Abstract Colorectal cancer is a leading cause of cancer-related death internationally, with mounting evidence pointing to the role of the microbiome in adenoma and cancer development. This article aims to provide clinicians with a foundation for understanding the field of research into the microbiome. We also illustrate the various ways in which the microbiota have been linked to colorectal cancer, with a specific focus on microbiota with identified virulence factors, and also on the ways that byproducts of microbiota metabolism may result in oncogenesis. We also review strategies for manipulating the microbiome for therapeutic effects. Keywords Microbiome, colorectal cancer, colorectal adenomas Ann Gastroenterol 2020; 33 (3): 1-14 Introduction consists of myriad bacteria, as well as fungi and viruses. Bacterial species greatly outnumber other constituents of the Colorectal cancer (CRC) is a leading cause of cancer- microbiome. The words “microbiome” and “microbiota” are related death worldwide [1]. Diet and bad habits, such as often used interchangeably. However, the term “microbiome” high consumption of alcohol and cigarette smoking, have encompasses the entire environment (microorganisms, been accepted as associative factors that place individuals at genomes and microenvironment), while the term “microbiota” refers specifically to the microbes themselves. There are over increased risk for the development of disease. However, the 13 precise changes that occur as a result of these factors have not 3.8 × 10 bacterial cells in the human body (compared to 3.0 × 1013 human cells), with the majority residing in the colon been clearly identified.
    [Show full text]