Alistipes Timonensis Sp. Nov
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Acetobacteroides Hydrogenigenes Gen. Nov., Sp. Nov., an Anaerobic Hydrogen-Producing Bacterium in the Family Rikenellaceae Isolated from a Reed Swamp
%paper no. ije063917 charlesworth ref: ije063917& New Taxa - Bacteroidetes International Journal of Systematic and Evolutionary Microbiology (2014), 64, 000–000 DOI 10.1099/ijs.0.063917-0 Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp Xiao-Li Su,1,2 Qi Tian,1,3 Jie Zhang,1,2 Xian-Zheng Yuan,1 Xiao-Shuang Shi,1 Rong-Bo Guo1 and Yan-Ling Qiu1 Correspondence 1Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Yan-Ling Qiu Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China [email protected] 2University of Chinese Academy of Sciences, Beijing 100049, PR China 3Ocean University of China, Qingdao, 266101, PR China A strictly anaerobic, mesophilic, carbohydrate-fermenting, hydrogen-producing bacterium, designated strain RL-CT, was isolated from a reed swamp in China. Cells were Gram-stain- negative, catalase-negative, non-spore-forming, non-motile rods measuring 0.7–1.0 mm in width and 3.0–8.0 mm in length. The optimum temperature for growth of strain RL-CT was 37 6C (range 25–40 6C) and pH 7.0–7.5 (range pH 5.7–8.0). The strain could grow fermentatively on yeast extract, tryptone, arabinose, glucose, galactose, mannose, maltose, lactose, glycogen, pectin and starch. The main end products of glucose fermentation were acetate, H2 and CO2. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth; however, it stimulated growth slightly. Nitrate, sulfate, sulfite, thiosulfate, elemental sulfur and Fe(III) nitrilotriacetate were not reduced as terminal electron acceptors. -
Complete Thesis
University of Groningen The interplay between genetics, the microbiome, DNA‐methylation & gene‐expression Bonder, Marc Jan IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2017 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Bonder, M. J. (2017). The interplay between genetics, the microbiome, DNA‐methylation & gene‐ expression. University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 10-10-2021 The interplay between genetics, the microbiome, DNA-methylation & gene-expression Marc Jan Bonder Marc Jan Bonder The interplay between genetics, the microbiome, DNA-methylation & gene-expression Second edition. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
Alistipes Obesi Sp. Nov
Standards in Genomic Sciences (2013) 7:427-439 DOI:10.4056/sigs.3336746 Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov Perrine Hugon1*, Dhamodharan Ramasamy1*, Jean-Christophe Lagier1, Romain Rivet1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1¶ 1Aix-Marseille Université, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Alistipes obesi, genome, culturomics, taxono-genomics Alistipes obesi sp. nov. strain ph8T is the type strain of A. obesi, a new species within the ge- nus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. obesi is an obligately anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,162,233 bp long genome (1 chromosome but no plasmid) contains 2,623 protein-coding and 49 RNA genes, including three rRNA genes. Introduction Alistipes obesi strain ph8T (CSUR= P186, DSMZ= bacteremia, appendicitis, perirectal and brain ab- 25724) is the type strain of A. obesi sp. nov. This scess [18-20]. A 16S rRNA phylogenetic analysis bacterium is a Gram-negative, anaerobic, indole- revealed that A. obesi was closely related to A. negative bacillus and was isolated from the stool shahii, A. senegalensis and A. timonensis. To the best of a French patient suffering from morbid obesity of our knowledge, A. obesi sp. nov. is the first as part of a culturomics study aiming at cultivating Alistipes species isolated from the digestive flora of individually all species within human feces [1]. -
Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis
Journal of Clinical Medicine Article Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis Kei Nomura 1 , Dai Ishikawa 1,2,* , Koki Okahara 1, Shoko Ito 1, Keiichi Haga 1, Masahito Takahashi 1, Atsushi Arakawa 3, Tomoyoshi Shibuya 1 , Taro Osada 1, Kyoko Kuwahara-Arai 4, Teruo Kirikae 4 and Akihito Nagahara 1,2 1 Department of Gastroenterology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] (K.N.); [email protected] (K.O.); [email protected] (S.I.); [email protected] (K.H.); [email protected] (M.T.); [email protected] (T.S.); [email protected] (T.O.); [email protected] (A.N.) 2 Department of Intestinal Microbiota Therapy, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan 3 Department of Human Pathology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] 4 Department of Microbiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] (K.K.-A.); [email protected] (T.K.) * Correspondence: [email protected]; Tel.: +81-(0)3-5802-1060 Abstract: Fecal microbiota transplantation following triple-antibiotic therapy (amoxicillin/fosfomycin/ metronidazole) improves dysbiosis caused by reduced Bacteroidetes diversity in patients with ulcer- ative colitis (UC). We investigated the correlation between Bacteroidetes species abundance and UC activity. Fecal samples from 34 healthy controls and 52 patients with active UC (Lichtiger’s clinical activity index ≥5 or Mayo endoscopic subscore ≥1) were subjected to next-generation sequencing Citation: Nomura, K.; Ishikawa, D.; Okahara, K.; Ito, S.; Haga, K.; with HSP60 as a target in bacterial metagenome analysis. -
Measuring the Human Gut Microbiome: New Tools and Non Alcoholic Fatty Liver Disease
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 6-13-2016 12:00 AM Measuring the human gut microbiome: new tools and non alcoholic fatty liver disease Ruth G. Wong The University of Western Ontario Supervisor Dr. Gregory B. Gloor The University of Western Ontario Graduate Program in Biochemistry A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Ruth G. Wong 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Bioinformatics Commons Recommended Citation Wong, Ruth G., "Measuring the human gut microbiome: new tools and non alcoholic fatty liver disease" (2016). Electronic Thesis and Dissertation Repository. 3839. https://ir.lib.uwo.ca/etd/3839 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract With the advent of next generation DNA and RNA sequencing, scientists can obtain a more comprehensive snapshot of the bacterial communities on the human body (known as the ‘human microbiome’), leading to information about the bacterial composition, what genes are present, and what proteins are produced. The scientific community is in a phase of developing the experiments and accompanying statistical techniques to investigate the mechanisms by which the human microbiome affects health and disease. In this thesis, I explore alternatives to the standard weighted and unweighted UniFrac distance metric that measure the difference between microbiome samples. These alternative weightings allow for the extraction of subtle differences between samples and identification of outliers not visible with traditional methods. -
This Electronic Thesis Or Dissertation Has Been Downloaded from the King’S Research Portal At
This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Microbial Community Ecology of the Cystic Fibrosis Lung Cuthbertson, Leah Forbes Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 06. Oct. 2021 The Microbial Community Ecology of the Cystic Fibrosis Lung A thesis submitted for the degree of Doctor of Philosophy in the Institute of Pharmaceutical Science, Molecular Microbiology Research Laboratory, King's College London By Leah Cuthbertson Pharmaceutical Sciences Research Division Kings College London October 2014 PhD – Kings College London – 2014 Declaration “I declare that I have personally prepared this report and that it has not in whole or in part been submitted for any degree or qualification. -
Understanding Horizontal Gene Transfer Network in Human Gut Microbiota Chen Li†, Jiaxing Chen† and Shuai Cheng Li*
Li et al. Gut Pathog (2020) 12:33 https://doi.org/10.1186/s13099-020-00370-9 Gut Pathogens RESEARCH Open Access Understanding Horizontal Gene Transfer network in human gut microbiota Chen Li†, Jiaxing Chen† and Shuai Cheng Li* Abstract Background: Horizontal Gene Transfer (HGT) is the process of transferring genetic materials between species. Through sharing genetic materials, microorganisms in the human microbiota form a network. The network can provide insights into understanding the microbiota. Here, we constructed the HGT networks from the gut microbiota sequencing data and performed network analysis to characterize the HGT networks of gut microbiota. Results: We constructed the HGT network and perform the network analysis to two typical gut microbiota datasets, a 283-sample dataset of Mother-to-Child and a 148-sample dataset of longitudinal infammatory bowel disease (IBD) metagenome. The results indicated that (1) the HGT networks are scale-free. (2) The networks expand their complexi- ties, sizes, and edge numbers, accompanying the early stage of lives; and microbiota established in children shared high similarity as their mother (p-value 0.0138), supporting the transmission of microbiota from mother to child. (3) Groups harbor group-specifc network= edges, and network communities, which can potentially serve as biomark- ers. For instances, IBD patient group harbors highly abundant communities of Proteobacteria (p-value 0.0194) and Actinobacteria (p-value 0.0316); children host highly abundant communities of Proteobacteria (p-value= 2.8785e−5 ) and Actinobacteria (p-value= 0.0015), and the mothers host highly abundant communities of Firmicutes = (p-value 8.0091e−7 ). IBD patient= networks contain more HGT edges in pathogenic genus, including Mycobacterium, Sutterella=, and Pseudomonas. -
Bacteroidales Recruit IL-6-Producing Intraepithelial Lymphocytes in the Colon to Promote Barrier Integrity
ARTICLES Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity KA Kuhn1,2, HM Schulz1,2, EH Regner3, EL Severs1,2, JD Hendrickson1,2, G Mehta1,2, AK Whitney2,3, DIr4, N Ohri1,2, CE Robertson4, DN Frank4, EL Campbell2,3 and SP Colgan2,3 Interactions between the microbiota and distal gut are important for the maintenance of a healthy intestinal barrier; dysbiosis of intestinal microbial communities has emerged as a likely contributor to diseases that arise at the level of the mucosa. Intraepithelial lymphocytes (IELs) are positioned within the epithelial barrier, and in the small intestine they function to maintain epithelial homeostasis. We hypothesized that colon IELs promote epithelial barrier function through the expression of cytokines in response to interactions with commensal bacteria. Profiling of bacterial 16S ribosomal RNA revealed that candidate bacteria in the order Bacteroidales are sufficient to promote IEL presence in the colon that in turn produce interleukin-6 (IL-6) in a MyD88 (myeloid differentiation primary response 88)-dependent manner. IEL-derived IL-6 is functionally important in the maintenance of the epithelial barrier as IL-6 À / À mice were noted to have increased paracellular permeability, decreased claudin-1 expression, and a thinner mucus gel layer, all of which were reversed by transfer of IL-6 þ / þ IELs, leading to protection of mice in response to Citrobacter rodentium infection. Therefore, we conclude that microbiota provide a homeostatic role for epithelial barrier function through regulation of IEL-derived IL-6. INTRODUCTION One hallmark of SI IELs is the expression of CD103 The mammalian gastrointestinal tract supports the existence of (aE integrin) that allows them to home to the SI. -
Reconstruction of Bacterial Strain Genomes from Shotgun Metagenomic Reads
University of Central Florida STARS Electronic Theses and Dissertations, 2020- 2020 Reconstruction of Bacterial Strain Genomes from Shotgun Metagenomic Reads Xin Li University of Central Florida Part of the Computer Sciences Commons Find similar works at: https://stars.library.ucf.edu/etd2020 University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2020- by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Li, Xin, "Reconstruction of Bacterial Strain Genomes from Shotgun Metagenomic Reads" (2020). Electronic Theses and Dissertations, 2020-. 377. https://stars.library.ucf.edu/etd2020/377 RECONSTRUCTION OF BACTERIAL STRAIN GENOMES FROM SHOTGUN METAGENOMIC READS by XIN LI B.E. Yanshan University, 2010 M.S. Florida International University, 2013 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Computer Science in the Department of Computer Science in the College of Engineering and Computer Science at the University of Central Florida Orlando, Florida Fall Term 2020 Major Professor: Haiyan Hu ABSTRACT It is necessary to study bacterial strains in environmental samples. The environmental samples are mixed DNA samples collected from the ocean, soil, lake, human body sites, etc. In a natural environment, they provide us new insights into the diversity of our earth. As for bacterial strains on or inside human bodies, to select the proper treatment for diseases caused by bacterial strains, it is critical to identify the corresponding strains and reconstruct their genomes. -
The Genus Alistipes: Gut Bacteria with Emerging Implications to Inflammation, Cancer, and Mental Health
University of Groningen The GenusAlistipes Parker, Bianca J.; Wearsch, Pamela A.; Veloo, Alida C. M.; Rodriguez-Palacios, Alex Published in: Frontiers in Immunology DOI: 10.3389/fimmu.2020.00906 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Parker, B. J., Wearsch, P. A., Veloo, A. C. M., & Rodriguez-Palacios, A. (2020). The GenusAlistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health. Frontiers in Immunology, 11, [906]. https://doi.org/10.3389/fimmu.2020.00906 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 28-09-2021 REVIEW published: 09 June 2020 doi: 10.3389/fimmu.2020.00906 The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health Bianca J.