1
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Tisza MJ, Smith DDN, Clark AE, Youn JH, Khil PP, Dekker JP. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group. Nat Commun 2023; 14:4082. [PMID: 37429841 DOI: 10.1038/s41467-023-39892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.
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Affiliation(s)
- Michael J Tisza
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiol, Baylor College of Medicine, Houston, TX, USA
| | - Derek D N Smith
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- Environment and Climate Change Canada, Ecotoxicology and Wildlife Health Division, Wildlife Toxicology Research Section, Ottawa, ON, Canada
| | - Andrew E Clark
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jung-Ho Youn
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA.
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA.
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2
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Nielsen FD, Skov MN, Sydenham TV, Justesen US. Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data. Microbiol Spectr 2023:e0511122. [PMID: 36943061 PMCID: PMC10101032 DOI: 10.1128/spectrum.05111-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.
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Affiliation(s)
- Flemming D Nielsen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne N Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas V Sydenham
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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3
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Letourneau J, Holmes ZC, Dallow EP, Durand HK, Jiang S, Carrion VM, Gupta SK, Mincey AC, Muehlbauer MJ, Bain JR, David LA. Ecological memory of prior nutrient exposure in the human gut microbiome. THE ISME JOURNAL 2022; 16:2479-2490. [PMID: 35871250 PMCID: PMC9563064 DOI: 10.1038/s41396-022-01292-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 04/20/2023]
Abstract
Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an "ecological memory" of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual's habitual exposure to dietary fiber was associated with their gut microbiome's efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
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Affiliation(s)
- Jeffrey Letourneau
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Eric P Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Verónica M Carrion
- Duke Office of Clinical Research, Duke University School of Medicine, Durham, NC, USA
| | - Savita K Gupta
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Adam C Mincey
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Michael J Muehlbauer
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - James R Bain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine (Endocrinology), Duke University School of Medicine, Durham, NC, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
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4
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Bacteroides pyogenes isolated from appendiceal abscess in a patient without animal contact. New Microbes New Infect 2021; 44:100933. [PMID: 34631109 PMCID: PMC8488308 DOI: 10.1016/j.nmni.2021.100933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteroides pyogenes is a member of the oral flora of cats and dogs. We report a case of B. pyogenes isolated from an appendiceal abscess in a patient without a history of animal contact. This species was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and sequencing of 16S rRNA, rpoB, gyrB and hsp60 genes.
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5
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A Soluble Fiber Diet Increases Bacteroides fragilis Group Abundance and Immunoglobulin A Production in the Gut. Appl Environ Microbiol 2020; 86:AEM.00405-20. [PMID: 32332136 DOI: 10.1128/aem.00405-20] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Immunoglobulin A (IgA) is essential for defense of the intestinal mucosa against harmful pathogens. Previous studies have shown that Bacteroidetes, the major phylum of gut microbiota together with Firmicutes, impact IgA production. However, the relative abundances of species of Bacteroidetes responsible for IgA production were not well understood. In the present study, we identified some specific Bacteroidetes species that were associated with gut IgA induction by hsp60-based profiling of species distribution among Bacteroidetes The levels of IgA and the expression of the gene encoding activation-induced cytidine deaminase (AID) in the large intestine lamina propria, which is crucial for class switch recombination from IgM to IgA, were increased in soluble high-fiber diet (sHFD)-fed mice. We found that Bacteroides acidifaciens was the most abundant Bacteroidetes species in both sHFD- and normal diet-fed mice. In addition, the gut IgA levels were associated with the relative abundance of Bacteroides fragilis group species such as Bacteroides faecis, Bacteroides caccae, and Bacteroides acidifaciens Conversely, the ratio of B. acidifaciens to other Bacteroidetes species was reduced in insoluble high-fiber diet fed- and no-fiber diet-fed mice. To investigate whether B. acidifaciens increases IgA production, we generated B. acidifaciens monoassociated mice and found increased gut IgA production and AID expression. Collectively, soluble dietary fiber increases the ratio of gut Bacteroides fragilis group, such as B. acidifaciens, and IgA production. This might improve gut immune function, thereby protecting against bowel pathogens and reducing the incidence of inflammatory bowel diseases.IMPORTANCE Immunoglobulin A (IgA) is essential for defense of the intestinal mucosa against harmful pathogens. Gut microbiota impact IgA production, but the specific species responsible for IgA production remain largely elusive. Previous studies have shown that IgA and Bacteroidetes, the major phyla of gut microbiota, were increased in soluble high-fiber diet-fed mice. We show here that the levels of IgA in the gut and the expression of activation-induced cytidine deaminase (AID) in the large intestine lamina propria, which is crucial for class switch recombination from IgM to IgA, were correlated with the abundance of Bacteroides fragilis group species such as Bacteroides faecis, Bacteroides caccae, and Bacteroides acidifaciens B. acidifaciens monoassociated mice increased gut IgA production and AID expression. Soluble dietary fiber may improve gut immune function, thereby protecting against bowel pathogens and reducing inflammatory bowel diseases.
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6
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Nakata H, Kanda H, Nakakita Y, Kaneko T, Tsuchiya Y. Prevotella cerevisiae sp. nov., beer-spoilage obligate anaerobic bacteria isolated from brewery wastewater. Int J Syst Evol Microbiol 2019; 69:1789-1793. [DOI: 10.1099/ijsem.0.003393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hajime Nakata
- 1Frontier Laboratories for Value Creation, Sapporo Holdings Ltd, 10 Okatome, Yaizu, Shizuoka, Japan
| | - Hajime Kanda
- 2Second Beverage Development Group, second Product Development Department, Pokka Sapporo Food & Beverage Ltd, 45-2 Juniso, Kumanosho, Kitanagoya, Aichi, Japan
| | - Yasukazu Nakakita
- 1Frontier Laboratories for Value Creation, Sapporo Holdings Ltd, 10 Okatome, Yaizu, Shizuoka, Japan
| | - Takeshi Kaneko
- 1Frontier Laboratories for Value Creation, Sapporo Holdings Ltd, 10 Okatome, Yaizu, Shizuoka, Japan
| | - Youichi Tsuchiya
- 1Frontier Laboratories for Value Creation, Sapporo Holdings Ltd, 10 Okatome, Yaizu, Shizuoka, Japan
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7
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Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ. The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. eLife 2019; 8:39982. [PMID: 30666959 PMCID: PMC6342529 DOI: 10.7554/elife.39982] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel disease (IBD) is driven by dysfunction between host genetics, the microbiota, and immune system. Knowledge gaps remain regarding how IBD genetic risk loci drive gut microbiota changes. The Crohn's disease risk allele ATG16L1 T300A results in abnormal Paneth cells due to decreased selective autophagy, increased cytokine release, and decreased intracellular bacterial clearance. To unravel the effects of ATG16L1 T300A on the microbiota and immune system, we employed a gnotobiotic model using human fecal transfers into ATG16L1 T300A knock-in mice. We observed increases in Bacteroides ovatus and Th1 and Th17 cells in ATG16L1 T300A mice. Association of altered Schaedler flora mice with B. ovatus specifically increased Th17 cells selectively in ATG16L1 T300A knock-in mice. Changes occur before disease onset, suggesting that ATG16L1 T300A contributes to dysbiosis and immune infiltration prior to disease symptoms. Our work provides insight for future studies on IBD subtypes, IBD patient treatment and diagnostics.
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Affiliation(s)
- Sydney Lavoie
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Kara L Conway
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Kara G Lassen
- Broad Institute of Harvard and MIT, Cambridge, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Humberto B Jijon
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Hui Pan
- Joslin Diabetes Center, Boston, United States
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Monia Michaud
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Jessica K Lang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Carey Ann Gallini Comeau
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | | | - Jonathan N Glickman
- Department of Pathology, Harvard Medical School, Boston, United States.,Beth Israel Deaconess Medical Center, Boston, United States
| | - Hera Vlamakis
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ashwin Ananthakrishnan
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Aleksander Kostic
- Joslin Diabetes Center, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Department and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Ramnik J Xavier
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
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8
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Buya Y, Shigoka T, Tahara H, Uehara Y, Motomura R, Sakurai S, Tanimoto K, Matsumoto T. First case report of bacteremia caused by Dysgonomonas mossii. Anaerobe 2018; 54:111-114. [PMID: 30165110 DOI: 10.1016/j.anaerobe.2018.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/26/2018] [Indexed: 02/07/2023]
Abstract
We here report a case of Dysgonomonas mossii bacteremia with cholangitis. An 85-year-old male patient with recurrent hepatitis B surface antigen-negative/anti-hepatitis C virus-negative hepatocellular carcinoma came to our hospital in poor physical condition. Two sets of blood cultures revealed a positive result for D. mossii. As matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify D. mossii, analysis of 16S rRNA gene sequencing was performed; however, this gene is not specific enough to distinguish between D. mossii and D. oryzarvi. Finally, D. mossii infection was confirmed by gyrB and recA sequencing. To our knowledge, this is the first report of D. mossii causing human infection, which was identified in culture and confirmed using a combination of 16S rRNA, gyrB, and recA sequencing.
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Affiliation(s)
- Yoko Buya
- Department of Clinical Laboratory, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Toshiyuki Shigoka
- Department of Clinical Laboratory, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Hiroki Tahara
- Department of Gastroenterology, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Yuka Uehara
- Department of Clinical Laboratory, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Reina Motomura
- Department of Clinical Laboratory, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Shinji Sakurai
- Department of Clinical Laboratory, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan; Department of Diagnostic Pathology, Japan Community Healthcare Organization Gunma Chuo Hospital, Maebashi, Gunma, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan.
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9
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Ismaeil M, Yoshida N, Katayama A. Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment. J Microbiol 2018; 56:619-627. [DOI: 10.1007/s12275-018-8187-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
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10
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Sárvári KP, Sóki J, Iván M, Miszti C, Latkóczy K, Melegh SZ, Urbán E. MALDI-TOF MS versus 16S rRNA sequencing: Minor discrepancy between tools in identification of Bacteroides isolates. Acta Microbiol Immunol Hung 2018; 65:173-181. [PMID: 28889758 DOI: 10.1556/030.64.2017.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Members of the genus Bacteroides are important components of the normal microbiota of gastrointestinal tract; however, as opportunistic pathogens are also associated with severe or even life-threatening infections with significant mortality. Various species within Bacteroides fragilis group are phenotypically very similar; thus, their identifications with traditional-automated biochemical methods are frequently inaccurate. The identification of the newly discovered or reclassified bacteria can be doubtful because of the lack of biochemical profile in the database of these tests. The aim of this study was to determine the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method by testing of 400 Hungarian Bacteroides clinical isolates. Inaccurate identification results with MALDI-TOF MS were confirmed by 16S rRNA gene sequencing and findings were compared with traditional-automated biochemical test rapid ID 32A method as well.
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Affiliation(s)
| | - József Sóki
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Miklós Iván
- 2 Institute of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Cecilia Miszti
- 3 Institute of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | | | - Szilvia Zsóka Melegh
- 5 Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Edit Urbán
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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11
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Schwab S, Terra LA, Baldani JI. Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems. Mol Genet Genomics 2018; 293:997-1016. [PMID: 29696375 DOI: 10.1007/s00438-018-1439-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 04/18/2018] [Indexed: 02/07/2023]
Abstract
Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.
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Affiliation(s)
- Stefan Schwab
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil.
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil.
| | - Leonardo Araujo Terra
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, km 7, Seropédica, RJ, 23890-000, Brazil
| | - José Ivo Baldani
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil
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12
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Abstract
This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species as ecological species because the genomovar G3 genomic cluster, which initially includes clinical strains, now also includes plant-associated and cave isolates.
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Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
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13
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Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219-1227. [PMID: 28556772 DOI: 10.1099/ijsem.0.001790] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two bacterial strains, designated EGH7T and TSAH33, were isolated from human faeces and characterized by using a polyphasic taxonomic approach that included analysis of morphology, phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA and hsp60 gene sequence analyses. The results of 16S rRNA gene sequence analysis indicated that these strains represented members of the family Lachnospiraceae and formed a monophyletic cluster near Eubacterium contortum JCM 6483T (95 % sequence similarity), Ruminococcus gnavus JCM 6515T (95 %), Clostridium oroticum JCM 1429T (95 %), Eubacterium fissicatena JCM 31501T (95 %) and Clostridium nexile JCM 31500T (94 %). The results of a hsp60 gene sequence analysis supported the phylogenetic tree based on the 16S rRNA gene sequence, with a sequence similarity value of between 77.9 and 84.8 % to the five strains listed above. The novel strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive cocco-bacilli. The strains formed characteristic umbilicated colonies on EG agar plates. The major cellular fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 1ω9c dimethyl acetal (DMA). EGH7T and TSAH33 have DNA G+C contents of 46.9 and 45.5 mol%, respectively. On the basis of these data, strains EGH7T and TSAH33 represent a novel species of a novel genus, for which the name Faecalimonas umbilicata gen. nov., sp. nov. is proposed. The type strain of F. umbilicata is EGH7T (=JCM 30896T=DSM 103426T).
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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14
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Sóki J, Hedberg M, Patrick S, Bálint B, Herczeg R, Nagy I, Hecht DW, Nagy E, Urbán E. Emergence and evolution of an international cluster of MDRBacteroides fragilisisolates. J Antimicrob Chemother 2016; 71:2441-8. [DOI: 10.1093/jac/dkw175] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/17/2016] [Indexed: 12/29/2022] Open
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15
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Irisawa T, Saputra S, Kitahara M, Sakamoto M, Sulistiani, Yulineri T, Dinoto A, Ohkuma M. Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken. Int J Syst Evol Microbiol 2016; 66:1431-1437. [DOI: 10.1099/ijsem.0.000899] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tomohiro Irisawa
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Sugiyono Saputra
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Sulistiani
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Titin Yulineri
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Achmad Dinoto
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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16
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Tan MF, Siow CC, Dutta A, Mutha NV, Wee WY, Heydari H, Tan SY, Ang MY, Wong GJ, Choo SW. Development of ListeriaBase and comparative analysis of Listeria monocytogenes. BMC Genomics 2015; 16:755. [PMID: 26444974 PMCID: PMC4595109 DOI: 10.1186/s12864-015-1959-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. Description With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. Conclusions ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1959-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mui Fern Tan
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Avirup Dutta
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Naresh Vr Mutha
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Hamed Heydari
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Computer Science and Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, 1468588-0115, USA.
| | - Shi Yang Tan
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Mia Yang Ang
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, Kuala Lumpur, 50603, Malaysia.
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17
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Nograšek B, Accetto T, Fanedl L, Avguštin G. Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits. J Microbiol 2015. [PMID: 26224452 DOI: 10.1007/s12275-015-5142-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Five strictly anaerobic Gram-negative bacterial strains, P4-65, P4-76(T), P5-60, P5-119, and P5-125, presumably belonging to the genus Prevotella were isolated from pig fecal samples. Strains were tested for various phenotypic traits and nearcomplete genome sequences were obtained and analyzed. Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis based on five conserved genes confirmed that the strains belong to the genus Prevotella, revealing that they represent a novel and discrete lineage distinct from other known species of this genus. The size of the genome of the isolated strains is 3-3.3 Mbp, and the DNA G+C content is 47.5-48.1 mol%. The isolates are strictly anaerobic, rod-shaped with rounded ends, non-motile and non-spore-forming. The main fermentation products are succinate and acetate, with minor concentrations of isovalerate, propionate and isobutyrate. Hydrogen is also produced. Major cellular fatty acids consist of anteiso-C(15:0) and iso-C(15:0), and a number of additional acids are present in lower concentrations. A substantial portion of genes involved in carbohydrate utilization is devoted to pectin degradation and utilization, while those supporting growth on xylan in ruminal Prevotella could not have been revealed. On the basis of the presented results, a novel species, Prevotella pectinovora sp. nov. is proposed. The type strain is P4-76(T) (=DSM 29996(T) =ZIM B1020(T)).
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Affiliation(s)
- Brigita Nograšek
- Biotechnical Faculty, Animal Science Department, Division of Microbiology and Microbial Biotechnology, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia
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18
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Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses. PLoS One 2015; 10:e0130265. [PMID: 26103050 PMCID: PMC4477887 DOI: 10.1371/journal.pone.0130265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/18/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. METHODS The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. RESULTS Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. CONCLUSION Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were relatively low, ranging from 68.7-97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.
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19
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Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y, Ohkuma M. Porphyromonas pasteri sp. nov., isolated from human saliva. Int J Syst Evol Microbiol 2015; 65:2511-2515. [PMID: 25933621 DOI: 10.1099/ijs.0.000294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated KUFDS01T, isolated from human saliva was characterized using a polyphasic taxonomic approach that included analysis of physiological and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. Cells of the strain were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strain was inhibited on medium containing 20% bile. The 16S rRNA gene sequence analysis showed that the strain was a member of the genus Porphyromonas. Strain KUFDS01T was closely related to Porphyromonas catoniae JCM 13863T (96.6% sequence similarity). An hsp60 gene sequence analysis indicated that strain KUFDS01T was different from P. catoniae JCM 13863T, with a sequence similarity value of 87.8%. The major cellular fatty acids of strain KUFDS01T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 2ω6, 9c and C18 : 1ω9c. The DNA G+C content of strain KUFDS01T was 57.7 ± 0.66 mol%. On the basis of these data, strain KUFDS01T represents a novel species of the genus Porphyromonas, for which the name Porphyromonas pasteri sp. nov. is proposed. The type strain of P. pasteri is KUFDS01T ( = JCM 30531T = CCUG 66735T).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Dan Li
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Yukie Shibata
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Toru Takeshita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Yoshihisa Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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20
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Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Parabacteroides faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2015; 65:1342-1346. [PMID: 25667391 DOI: 10.1099/ijs.0.000109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A bacterial strain, designated 157(T), isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20% (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157(T) was closely related to Parabacteroides gordonii JCM 15724(T) (96% sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157(T) was different from P. gordonii JCM 15724(T), with a hsp60 gene sequence similarity of 96.1%. The major cellular fatty acids of strain 157(T) were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH, C(18 : 1)ω9c and anteiso-C(17 : 0) 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157(T) was 41.8 mol%. On the basis of these data, strain 157(T) represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157(T) ( = JCM 18682(T) = CCUG 66681(T)).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshiki Tanaka
- Biofermin Kobe Research Institute, Nishi-ku, Kobe 651-2242, Japan.,Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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21
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Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV. Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature 2014; 514:638-41. [PMID: 25274297 PMCID: PMC4214913 DOI: 10.1038/nature13823] [Citation(s) in RCA: 384] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/03/2014] [Indexed: 02/06/2023]
Abstract
Systemic infection induces conserved physiological responses that include both resistance and 'tolerance of infection' mechanisms. Temporary anorexia associated with an infection is often beneficial, reallocating energy from food foraging towards resistance to infection or depriving pathogens of nutrients. However, it imposes a stress on intestinal commensals, as they also experience reduced substrate availability; this affects host fitness owing to the loss of caloric intake and colonization resistance (protection from additional infections). We hypothesized that the host might utilize internal resources to support the gut microbiota during the acute phase of the disease. Here we show that systemic exposure to Toll-like receptor (TLR) ligands causes rapid α(1,2)-fucosylation of small intestine epithelial cells (IECs) in mice, which requires the sensing of TLR agonists, as well as the production of interleukin (IL)-23 by dendritic cells, activation of innate lymphoid cells and expression of fucosyltransferase 2 (Fut2) by IL-22-stimulated IECs. Fucosylated proteins are shed into the lumen and fucose is liberated and metabolized by the gut microbiota, as shown by reporter bacteria and community-wide analysis of microbial gene expression. Fucose affects the expression of microbial metabolic pathways and reduces the expression of bacterial virulence genes. It also improves host tolerance of the mild pathogen Citrobacter rodentium. Thus, rapid IEC fucosylation appears to be a protective mechanism that utilizes the host's resources to maintain host-microbial interactions during pathogen-induced stress.
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Affiliation(s)
- Joseph M Pickard
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | - Michael C Abt
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | | | - Tatyana V Golovkina
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Said R Bogatyrev
- California Institute of Technology, Pasadena, California 91125, USA
| | | | - Eric G Pamer
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexander V Chervonsky
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, Illinois 60637, USA
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Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas. Int J Syst Evol Microbiol 2014; 64:2992-2997. [DOI: 10.1099/ijs.0.065318-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated 180-3T and 214-4T, isolated from human faeces were characterized by using a polyphasic taxonomic approach that included analysis of their phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these strains represented members of the genus
Butyricimonas
. These strains shared 97.9 % 16S rRNA gene sequence similarity with each other and were related to
Butyricimonas virosa
JCM 15149T (97 % sequence similarity) and
Butyricimonas synergistica
JCM 15148T (94–95 %). Although strain 180-3T was related to (but distinct from)
B. virosa
JCM 15149T and
B. synergistica
JCM 15148T, with hsp60 gene sequence similarities of 89.4 and 84.6 %, respectively, strain 214-4T exhibited high hsp60 gene sequence similarity (100 %) with
B. virosa
JCM 15149T and was different from
B. synergistica
JCM 15148T (83.5 %). DNA–DNA hybridization experiments demonstrated a genomic distinction of strains 180-3T and 214-4T from
B. virosa
JCM 15149T and
B. synergistica
JCM 15148T. The strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The two strains produced butyric and isobutyric acids as the end products from glucose, as has been observed in the other two species of the genus
Butyricimonas
. The major cellular fatty acid of strains 180-3T and 214-4T was iso-C15 : 0. The major menaquinone of the isolates was MK-10 (>50 %). Strains 180-3T and 214-4T have DNA G+C contents of 45 mol%. On the basis of these data, strains 180-3T and 214-4T represent two novel species of the genus
Butyricimonas
, for which the names Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., respectively, are proposed. The type strains of B. faecihominis and B. paravirosa are 180-3T ( = JCM 18676T = CCUG 65562T) and 214-4T ( = JCM 18677T = CCUG 65563T), respectively.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshiki Tanaka
- Biofermin Kobe Research Institute, Nishi-ku, Kobe 651-2242, Japan
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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Hatamoto M, Kaneshige M, Nakamura A, Yamaguchi T. Bacteroides luti sp. nov., an anaerobic, cellulolytic and xylanolytic bacterium isolated from methanogenic sludge. Int J Syst Evol Microbiol 2014; 64:1770-1774. [DOI: 10.1099/ijs.0.056630-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, anaerobic, cellulolytic and xylanolytic strain, UasXn-3T, was isolated from anaerobic granular sludge in a mesophilic upflow anaerobic sludge blanket reactor, which was used to treat municipal sewage. The cells were Gram-stain-negative, non-motile, and non-spore-forming rods. The optimal temperature for growth was 37–40 °C and the optimal pH for growth was pH 6.5–7.0. Strain UasXn-3T could grow on several polysaccharides and sugars, including cellulose, cellobiose, xylan, xylose, glucose, fructose, arabinose, mannose, raffinose, trehalose and starch. The DNA G+C content was 44.4 mol%. On the basis of comparative 16S rRNA gene sequence analysis, strain UasXn-3T was identified as a member of the genus
Bacteroides
and most closely related to
Bacteroides oleiciplenus
,
B. intestinalis
,
B. cellulosilyticus
and
B. graminisolvens
(sequence similarities of 91.3–91.6 %). Since the genetic and phenotypic properties suggest that strain UasXn-3T represents a novel species, we propose the name Bacteroides luti sp. nov. The type strain is UasXn-3T ( = JCM 19020T = DSM 26991T).
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Affiliation(s)
- Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masami Kaneshige
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Akinobu Nakamura
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Gao RY, Zhu QC, Wu W, Qin HL. Compositional differences in fecal microbiota between rats with colorectal cancer and normal rats. Shijie Huaren Xiaohua Zazhi 2014; 22:661-667. [DOI: 10.11569/wcjd.v22.i5.661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the compositional differences in fecal flora between rats with colorectal cancer and normal rats.
METHODS: A rat model of colorectal cancer was developed by intraperitoneal injection of 1, 2-dimethyl hydrazine (DMH). Fecal samples were collected from rats with colorectal cancer and normal controls, and the microbiota was isolated by PCR-DGGE technique to perform flora similarity analysis (cluster analysis) and polymorphism analysis (richness, uniformity, Shannon-Wiener index, Simpson index) and to compare with the GenBank to identify the genus so as to study the variation.
RESULTS: Compared with normal rats, the abundance of Lachnospiraceae, Ruminococcaceae, Lactobacillus intestinalis, Paraprevotella, Lactobacillus murinus, Lactobacillus, Prevotella, Lactobacillus crispatus and Lachnospiracea incertae sedis was significantly reduced and that of Coprobacillus was significantly increased in rats with colorectal cancer. Although the flora diversity between the two groups showed no statistical difference, there was a significant difference in flora composition.
CONCLUSION: The composition of fecal microflora changes in rats with colorectal cancer compared with normal rats, with the number of beneficial bacteria reduced and that of potential pathogens increased.
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Mun S, Lee J, Lee S, Han K, Ahn TY. Phylogeny of flavobacteria group isolated from freshwater using multilocus sequencing analysis. Genomics Inform 2013; 11:272-6. [PMID: 24465240 PMCID: PMC3897856 DOI: 10.5808/gi.2013.11.4.272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/15/2013] [Accepted: 11/16/2013] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species.
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Affiliation(s)
- Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea
| | - Jungnam Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea
| | - Siwon Lee
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon 443-440, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea
| | - Tae-Young Ahn
- Department of Microbiology, Dankook University, Cheonan 330-714, Korea
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Antiabong JF, Boardman W, Moore RB, Brown MH, Ball AS. The oral microbial community of gingivitis and lumpy jaw in captive macropods. Res Vet Sci 2013; 95:996-1005. [PMID: 24012349 DOI: 10.1016/j.rvsc.2013.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 06/26/2013] [Accepted: 08/12/2013] [Indexed: 11/20/2022]
Abstract
Gingivitis and lumpy jaw are diseases of polymicrobial aetiology. Although Fusobacterium necrophorum has been associated with these diseases in macropods, little is known about other organisms associated with these diseases in this animal species. PCR-DGGE analysis revealed the potential pathogens associated with gingivitis and lumpy jaw in macropods. PCR-DGGE profile comparison between the healthy and disease groups indicated a shift in the oral bacterial community structures with similarity coefficients of 48% and 35% for gingivitis and lumpy jaw respectively. Moreover, gingivitis was associated with increase in bacterial diversity (Shannon index = 2.87; PL curve = 45%) while lumpy jaw resulted in a decline in bacterial diversity (Shannon index = 2.47; PL curve = 74%). This study suggest that the establishment of gingivitis and lumpy jaw diseases follows the ecological plaque hypothesis. This forms the basis for an expanded investigation in an epidemiological scale and suggests the need for the appropriate choice of antimicrobial agent(s) and for the effective management and control of polymicrobial diseases.
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Affiliation(s)
- John F Antiabong
- School of Biological Sciences, Flinders University, Bedford Park, South Australia 5042, Australia; School of Applied Sciences, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia.
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Sóki J. Extended role for insertion sequence elements in the antibiotic resistance of Bacteroides. World J Clin Infect Dis 2013; 3:1-12. [DOI: 10.5495/wjcid.v3.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 12/04/2012] [Accepted: 12/17/2012] [Indexed: 02/06/2023] Open
Abstract
The Bacteroides species are important micro-organisms, both in the normal physiology of the intestines and as frequent opportunistic anaerobic pathogens, with a deeply-rooted phylogenetic origin endowing them with some interesting biological features. Their prevalence in anaerobic clinical specimens is around 60%-80%, and they display the most numerous and highest rates of antibiotic resistance among all pathogenic anaerobes. In these antibiotic resistance mechanisms there is a noteworthy role for the insertion sequence (IS) elements, which are usually regarded as representatives of ‘selfish’ genes; the IS elements of Bacteroides are usually capable of up-regulating the antibiotic resistance genes. These include the cepA (penicillin and cephalosporin), cfxA (cephamycin), cfiA (carbapenem), nim (metronidazole) and ermF (clindamycin) resistance genes. This is achieved by outward-oriented promoter sequences on the ISs. Although some representatives are well characterized, e.g., the resistance gene-IS element pairs in certain resistant strains, open questions remain in this field concerning a better understanding of the molecular biology of the antibiotic resistance mechanisms of Bacteroides, which will have clinical implications.
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Sakamoto M, Ohkuma M. Porphyromonas crevioricanis
is an earlier heterotypic synonym of
Porphyromonas cansulci
and has priority. Int J Syst Evol Microbiol 2013; 63:454-457. [DOI: 10.1099/ijs.0.042531-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A DNA–DNA hybridization experiment was carried out to clarify the relationship between
Porphyromonas crevioricanis
and
Porphyromonas cansulci
. The taxonomic standing of these two species was unclear so far because of the high 16S rRNA gene sequence similarity value (99.9 %). The DNA–DNA relatedness values between
P. crevioricanis
JCM 15906T and
P. cansulci
JCM 13913T were above 91 % (91–99 %). In addition,
P. crevioricanis
JCM 15906T exhibited high hsp60 gene sequence similarity with
P. cansulci
JCM 13913T (100 %). The hsp60 gene sequence analysis and the DNA–DNA relatedness values demonstrated that
P. crevioricanis
JCM 15906T and
P. cansulci
JCM 13913T are a single species. Based on these data, we propose
Porphyromonas cansulci
as a later heterotypic synonym of
Porphyromonas crevioricanis
.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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