Identifying Clostridioides Difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly
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Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. -
Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility. -
W O 2017/079450 Al 11 May 2017 (11.05.2017) W IPOI PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date W O 2017/079450 Al 11 May 2017 (11.05.2017) W IPOI PCT (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61K35/741 (2015.01) A61K 35/744 (2015.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, A61K 35/745 (2015.01) A61K35/74 (2015.01) DO, DZ, EC, EE, EG, ES, Fl, GB, GD, GE, GH, GM, GT, C12N1/20 (2006.01) A61K 9/48 (2006.01) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, A61K 45/06 (2006.01) KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (21) International Application Number: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, PCT/US2016/060353 SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (22) International Filing Date: TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 3 November 2016 (03.11.2016) ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated,for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (30) Priority Data: TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 62/250,277 3 November 2015 (03.11.2015) US TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, Fl, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, (71) Applicants: THE BRIGHAM AND WOMEN'S HOS- LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, PITAL [US/US]; 75 Francis Street, Boston, Massachusetts SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, 02115 (US). -
Downloaded from the VFDB Data- Base (Virulence Factors Database) Containing Nucleotide Sample Collection and Metagenomic Sequencing Sequences of 2585 Genes [53]
Dubinkina et al. Microbiome (2017) 5:141 DOI 10.1186/s40168-017-0359-2 RESEARCH Open Access Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease Veronika B. Dubinkina1,2,3,4, Alexander V. Tyakht2,5*, Vera Y. Odintsova2, Konstantin S. Yarygin1,2, Boris A. Kovarsky2, Alexander V. Pavlenko1,2, Dmitry S. Ischenko1,2, Anna S. Popenko2, Dmitry G. Alexeev1,2, Anastasiya Y. Taraskina6, Regina F. Nasyrova6, Evgeny M. Krupitsky6, Nino V. Shalikiani7, Igor G. Bakulin7, Petr L. Shcherbakov7, Lyubov O. Skorodumova2, Andrei K. Larin2, Elena S. Kostryukova1,2, Rustam A. Abdulkhakov8, Sayar R. Abdulkhakov8,9, Sergey Y. Malanin9, Ruzilya K. Ismagilova9, Tatiana V. Grigoryeva9, Elena N. Ilina2 and Vadim M. Govorun1,2 Abstract Background: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative “shotgun” metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts—with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. Results: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. -
Parabacteroides Distasonis
University of Groningen Parabacteroides distasonis Ezeji, Jessica C.; Sarikonda, Daven K.; Hopperton, Austin; Erkkila, Hailey L.; Cohen, Daniel E.; Martinez, Sandra P.; Cominelli, Fabio; Kuwahara, Tomomi; Dichosa, Armand E. K.; Good, Caryn E. Published in: Gut Microbes DOI: 10.1080/19490976.2021.1922241 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: 2021 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Ezeji, J. C., Sarikonda, D. K., Hopperton, A., Erkkila, H. L., Cohen, D. E., Martinez, S. P., Cominelli, F., Kuwahara, T., Dichosa, A. E. K., Good, C. E., Jacobs, M. R., Khoretonenko, M., Veloo, A., & Rodriguez- Palacios, A. (2021). Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes, 13(1), [1922241]. https://doi.org/10.1080/19490976.2021.1922241 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. -
The Clinical Link Between Human Intestinal Microbiota and Systemic Cancer Therapy
International Journal of Molecular Sciences Review The Clinical Link between Human Intestinal Microbiota and Systemic Cancer Therapy 1,2, , 1,2, 3,4 2,4 Romy Aarnoutse * y, Janine Ziemons y, John Penders , Sander S. Rensen , Judith de Vos-Geelen 1,5 and Marjolein L. Smidt 1,2 1 GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands 2 Department of Surgery, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands 3 Department of Medical Microbiology, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands 4 NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands 5 Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands * Correspondence: [email protected] or [email protected]; Tel.: +31-(0)6-82019105 These authors contributed equally to this work. y Received: 31 July 2019; Accepted: 22 August 2019; Published: 25 August 2019 Abstract: Clinical interest in the human intestinal microbiota has increased considerably. However, an overview of clinical studies investigating the link between the human intestinal microbiota and systemic cancer therapy is lacking. This systematic review summarizes all clinical studies describing the association between baseline intestinal microbiota and systemic cancer therapy outcome as well as therapy-related changes in intestinal microbiota composition. A systematic literature search was performed and provided 23 articles. There were strong indications for a close association between the intestinal microbiota and outcome of immunotherapy. Furthermore, the development of chemotherapy-induced infectious complications seemed to be associated with the baseline microbiota profile. -
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. -
1,520 Reference Genomes from Cultivated Human Gut Bacteria Enable Functional Microbiome Analyses
RESOURCE https://doi.org/10.1038/s41587-018-0008-8 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses Yuanqiang Zou 1,2,3,13, Wenbin Xue1,2,13, Guangwen Luo1,2,4,13, Ziqing Deng 1,2,13, Panpan Qin 1,2,5,13, Ruijin Guo1,2, Haipeng Sun1,2, Yan Xia1,2,5, Suisha Liang1,2,6, Ying Dai1,2, Daiwei Wan1,2, Rongrong Jiang1,2, Lili Su1,2, Qiang Feng1,2, Zhuye Jie1,2, Tongkun Guo1,2, Zhongkui Xia1,2, Chuan Liu1,2,6, Jinghong Yu1,2, Yuxiang Lin1,2, Shanmei Tang1,2, Guicheng Huo4, Xun Xu1,2, Yong Hou 1,2, Xin Liu 1,2,7, Jian Wang1,8, Huanming Yang1,8, Karsten Kristiansen 1,2,3,9, Junhua Li 1,2,10*, Huijue Jia 1,2,11* and Liang Xiao 1,2,6,9,12* Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. -
Supplementary Table 8 Spearman's Correlations Between Targeted Urinary Urolithins and Microbiota
Supplementary material Gut Supplementary Table 8 Spearman's correlations between targeted urinary urolithins and microbiota. Urolithin- Urolithin- Urolithin- Total A- B- C- Urolithins Family level Taxonomy glucuronid glucuronid glucuronid (A+B+C) e e e Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium adolescentis_msp_0263 -0.18 -0.09 -0.16 -0.18 Bifidobacteriaceae Bifidobacterium; Bifidobacterium adolescentis Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium bifidum_msp_0419 -0.12 -0.2 -0.08 -0.13 Bifidobacteriaceae Bifidobacterium; Bifidobacterium bifidum Actinobacteria; Coriobacteriia; Coriobacteriales; Coriobacteriaceae; Collinsella; Collinsella aerofaciens_msp_1244 -0.15 -0.06 -0.04 -0.18 Coriobacteriaceae Collinsella aerofaciens Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Adlercreutzia; unclassified Adlercreutzia_msp_0396 0.09 0.01 0.16 0.12 Eggerthellaceae unclassified Adlercreutzia Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Eggerthella; Eggerthella lenta_msp_0573 0.03 -0.15 0.08 0.03 Eggerthellaceae Eggerthella lenta Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Gordonibacter; Gordonibacter urolithinfaciens_msp_1339 0.19 -0.05 0.18 0.19 Eggerthellaceae Gordonibacter urolithinfaciens Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; Bacteroides cellulosilyticus_msp_0003 0.12 0.11 0.15 0.15 Bacteroidaceae Bacteroides cellulosilyticus Bacteroidetes; Bacteroidia; Bacteroidales; -
Commensal Obligate Anaerobic Bacteria and Health: Production, Storage, and Delivery Strategies
REVIEW published: 05 June 2020 doi: 10.3389/fbioe.2020.00550 Commensal Obligate Anaerobic Bacteria and Health: Production, Storage, and Delivery Strategies José Carlos Andrade 1†, Diana Almeida 2†, Melany Domingos 2, Catarina Leal Seabra 2‡, Daniela Machado 2, Ana Cristina Freitas 2* and Ana Maria Gomes 2 1 CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, Portugal, 2 CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal Edited by: Eduardo Jacob-Lopes, Federal University of Santa In the last years several human commensals have emerged from the gut microbiota Maria, Brazil studies as potential probiotics or therapeutic agents. Strains of human gut inhabitants Reviewed by: Julio Plaza-Diaz, such as Akkermansia, Bacteroides, or Faecalibacterium have shown several interesting University of Granada, Spain bioactivities and are thus currently being considered as food supplements or as John MacSharry, live biotherapeutics, as is already the case with other human commensals such as University College Cork, Ireland bifidobacteria. The large-scale use of these bacteria will pose many challenges and *Correspondence: Ana Cristina Freitas drawbacks mainly because they are quite sensitive to oxygen and/or very difficult [email protected] to cultivate. This review highlights the properties of some of the most promising †These authors have contributed human commensals bacteria and summarizes the most up-to-date knowledge on their equally to this work and share first potential health effects. A comprehensive outlook on the potential strategies currently authorship employed and/or available to produce, stabilize, and deliver these microorganisms is ‡Present address: Catarina Leal Seabra, also presented. -
Parabacteroides Massiliensis Sp. Nov., a New Bacterium Isolated from a Fresh Human Stool Specimen
NEW SPECIES Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen S. Bellali1,2,C.I.Lo2,3, S. Naud1,2, M. D. M. Fonkou1,2, N. Armstrong1,2, D. Raoult1,2, P.-E. Fournier2,3 and F. Fenollar2,3 1) Aix Marseille Université, IRD, AP-HM, MEVI, 2) IHU-Méditerranée Infection and 3) Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France Abstract Parabacteroides massiliensis sp. nov., strain Marseille-P2231T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides. © 2019 The Authors. Published by Elsevier Ltd. Keywords: Bacteria, culturomics, human gut, Parabacteroides massiliensis, taxono-genomics Original Submission: 29 July 2019; Accepted: 30 August 2019 Article published online: 7 September 2019 description and genome sequencing, to describe this strain Corresponding author: F. Fenollar, Institut Hospitalo-Universitaire [10,11]. Here we describe a new Parabacteroides massiliensis Méditerranée-Infection, 19–21 Boulevard Jean Moulin, 13385, Mar- T seille cedex 05, France. sp. nov., strain Marseille-P2231 (= CSURP2231 = DSM E-mail: fl[email protected] 101860) according the concept of taxono-genomics. Isolation and growth conditions Introduction In 2017, we isolated from a fresh stool sample of a 25- year-old healthy woman an unidentified bacterial strain. -
Type VI Secretion Systems of Human Gut Bacteroidales Segregate Into Three Genetic Architectures, Two of Which Are Contained on Mobile Genetic Elements Michael J
Coyne et al. BMC Genomics (2016) 17:58 DOI 10.1186/s12864-016-2377-z RESEARCH ARTICLE Open Access Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements Michael J. Coyne, Kevin G. Roelofs and Laurie E. Comstock* Abstract Background: Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by Gram negative bacteria to intoxicate other bacteria or eukaryotic cells. T6SSs were recently discovered in a few Bacteroidetes strains, thereby extending the presence of these systems beyond Proteobacteria. The present study was designed to analyze in a global nature the diversity, abundance, and properties of T6SSs in the Bacteroidales, the most predominant Gram negative bacterial order of the human gut. Results: By performing extensive bioinformatics analyses and creating hidden Markov models for Bacteroidales Tss proteins, we identified 130 T6SS loci in 205 human gut Bacteroidales genomes. Of the 13 core T6SS proteins of Proteobacteria, human gut Bacteroidales T6SS loci encode orthologs of nine, and an additional five other core proteins not present in Proteobacterial T6SSs. The Bacteroidales T6SS loci segregate into three distinct genetic architectures with extensive DNA identity between loci of a given genetic architecture. We found that divergent DNA regions of a genetic architecture encode numerous types of effector and immunity proteins and likely include new classes of these proteins. TheT6SS loci of genetic architecture 1 are contained on highly similar integrative conjugative elements (ICEs), as are the T6SS loci of genetic architecture 2, whereas the T6SS loci of genetic architecture 3 are not and are confined to Bacteroides fragilis.