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Liu FL, Abdugheni R, Ran CG, Zhou N, Liu SJ. Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739685 DOI: 10.1099/ijsem.0.006380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.
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Affiliation(s)
- Feng-Lan Liu
- College of Life Sciences, Hebei University, Baoding, 071000, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Cong-Guo Ran
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
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Bläckberg A, Holm K, Liderot K, Nilson B, Sunnerhagen T. Eubacterium bacteremia - a retrospective observational study of a seldom found anaerobic pathogen. Diagn Microbiol Infect Dis 2024; 108:116185. [PMID: 38232640 DOI: 10.1016/j.diagmicrobio.2024.116185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024]
Abstract
BACKGROUND Human infections due to Eubacterium are rare and knowledge of the condition is limited. This study aimed to describe clinical characteristics and outcome in patients with Eubacterium bacteremia. METHODS Episodes of Eubacterium bacteremia were identified through the clinical microbiology laboratory in Lund, Sweden. Medical records were retrospectively reviewed. Blood isolates of Eubacterium were collected and antibiotic susceptibility testing was performed with agar dilution. RESULTS Seventeen patients with Eubacterium bacteremia were identified of whom six had monomicrobial bacteremia. The incidence was 1.7 cases of Eubacterium bacteremia per million inhabitants and year. The median age was 67 years (interquartile range 63-79 years), and six patients had some form of malignancy. Most of the patients an abdominal focus of infection and the 30-day mortality was low (n = 1). CONCLUSIONS Invasive infections with Eubacterium have a low incidence. The condition has a low mortality and an abdominal focus of infection, and malignancy, is common.
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Affiliation(s)
- Anna Bläckberg
- Department of Infectious Diseases, Skåne University Hospital Lund, Sweden; Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden
| | - Karin Holm
- Department of Infectious Diseases, Skåne University Hospital Lund, Sweden; Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden
| | - Karin Liderot
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Bo Nilson
- Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Lund, Sweden; Division of Medical Microbiology, Department of Laboratory Medicine Lund, Lund University, Lund, Sweden
| | - Torgny Sunnerhagen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden; Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Lund, Sweden.
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Kaur A, Pickles IB, Sharma M, Madeido Soler N, Scott NE, Pidot SJ, Goddard-Borger ED, Davies GJ, Williams SJ. Widespread Family of NAD +-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. J Am Chem Soc 2023; 145:28216-28223. [PMID: 38100472 PMCID: PMC10755693 DOI: 10.1021/jacs.3c11126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+ as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+ provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.
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Affiliation(s)
- Arashdeep Kaur
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Isabelle B. Pickles
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Niccolay Madeido Soler
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nichollas E. Scott
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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Lemons JMS, Narrowe AB, Liu L, Firrman J, Mahalak KK, Van den Abbeele P, Baudot A, Deyaert S, Li Y, Yu L(L. Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome. Front Cell Infect Microbiol 2023; 13:1298392. [PMID: 38145049 PMCID: PMC10740150 DOI: 10.3389/fcimb.2023.1298392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction In traditional Chinese medicine, the rhizome of Atractylodes macrocephala (Baizhu), the leaves of Isatis indigotica (Daqingye), and the flowers of Albizia julibrissin (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, and mental health issues. Modern researchers are now exploring the underlying mechanisms responsible for their efficacy. Previous studies often focused on the impact of purified chemicals or mixed extracts from these plants on cells in tissue culture or in rodent models. Methods As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR®) technology (n=6). Results and discussion Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related Bifidobacterium spp. and short chain fatty acids which may contribute to Baizhu's efficacy against gastrointestinal ailments. The changes upon Hehuanhua treatment were larger and included increases in multiple bacterial species, including Agathobaculum butyriciproducens, Adlercreutzia equolifaciens, and Gordonibacter pamelaeae, known to produce secondary metabolites beneficial to mental health. In addition, many of the changes induced by Hehuanhua correlated with a rise in Enterobacteriaceae spp., which may make the tested dose of this herb contraindicated for some individuals. Overall, there is some evidence to suggest that the palliative effect of these herbs may be mediated, in part, by their impact on the gut microbiome, but more research is needed to elucidate the exact mechanisms.
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Affiliation(s)
- Johanna M. S. Lemons
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Adrienne B. Narrowe
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - LinShu Liu
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Jenni Firrman
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Karley K. Mahalak
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | | | | | | | - Yanfang Li
- Department of Nutrition and Food Science, 0112 Skinner Building University of Maryland, College Park, MD, United States
| | - Liangli (Lucy) Yu
- Department of Nutrition and Food Science, 0112 Skinner Building University of Maryland, College Park, MD, United States
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Pereida-Aguilar JC, Barragán-Vargas C, Domínguez-Sánchez C, Álvarez-Martínez RC, Acevedo-Whitehouse K. Bacterial dysbiosis and epithelial status of the California sea lion (Zalophus californianus) in the Gulf of California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105474. [PMID: 37356747 DOI: 10.1016/j.meegid.2023.105474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Despite the high incidence of urogenital carcinoma (UGC) in California sea lions stranded along California, no UGC has been reported in other areas of their distribution; however, cell morphologies typical of premalignant states have been found. Risk factors for UGC include high of organochlorines and infection with a gammaherpesvirus, OtHV-1, but the importance of the bacteriome for epithelial status remains unknown. We characterized the genital bacteriome of adult female California sea lions along their distribution in the Gulf of California and examined whether the diversity and abundance of the bacteriome varied spatially, whether there were detectable differences in the bacteriome between healthy and altered epithelia, and whether the bacteriome was different in California sea lions infected with OtHV-1 or papillomavirus. We detected 2270 ASVs in the genital samples, of which 35 met the criteria for inclusion in the core bacteriome. Fusobacteriia and Clostridia were present in all samples, at high abundances, and Actinobacteria, Alphaproteobacteria, and Campylobacteria were also well-represented. Alpha diversity and abundance of the California sea lion genital bacteriome varied geographically. The abundance of bacterial ASVs varied depending on the genital epithelial status and inflammation, with differences driven by classes Fusobacteriia, Clostridia, Campylobacteria and Alphaproteobacteria. Alpha diversity and abundance were lowest in samples in which OtHV-1 was detected, and highest those with papillomavirus. Our study is the first investigation of how the bacteriome is related to epithelial status in a wild marine species prone to developing cancer.
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Affiliation(s)
- Juan Carlos Pereida-Aguilar
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Cecilia Barragán-Vargas
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Carlos Domínguez-Sánchez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Roberto Carlos Álvarez-Martínez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico.
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Hisatomi A, Kastawa NWEPG, Song I, Ohkuma M, Fukiya S, Sakamoto M. Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737068 DOI: 10.1099/ijsem.0.006030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14T, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14T showed the highest 16S rRNA gene sequence similarity to Sellimonas monacensis Cla-CZ-80T (97.5 %) and 'Lachnoclostridium phocaeense' Marseille-P3177T (97.2 %). Strain 12BBH14T was also closely related to Eubacterium sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14T, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with Eubacterium sp. c-25. Near this monophyletic cluster, S. monacensis Cla-CZ-80T and 'L. phocaeense' Marseille-P3177T formed a cluster and did not form a cluster with other Sellimonas species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14T, 9CFEGH4, 10CPCBH12 and Eubacterium sp. c-25 were higher than the cut-off values of species demarcation (>88 % dDDH and >98 % ANI), indicating that these four strains are the same species. On the other hand, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<29 % dDDH and <76 % ANI). Moreover, the average amino acid identity values among these strains were higher than the genus boundary. These results indicate that the isolates should be considered to belong to a new genus of the family Lachnospiraceae. Based on the collected data, strains 12BBH14T, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name Claveliimonas bilis gen. nov., sp. nov. is proposed. The type strain of C. bilis is 12BBH14T (=JCM 35899T=DSM 115701T). Eubacterium sp. c-25 belongs to C. bilis. In addition, S. monacensis is transferred to the genus Claveliimonas as Claveliimonas monacensis comb. nov.
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Kim JY, Kang B, Oh S, Gil Y, Choi IG, Chang IS. Genome-Based Reclassification of Strain KIST612, Previously Classified as Eubacterium limosum, into a New Strain of Eubacterium callanderi. J Microbiol Biotechnol 2023; 33:1084-1090. [PMID: 37218441 PMCID: PMC10468676 DOI: 10.4014/jmb.2304.04011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023]
Abstract
The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486T (99.2%) and E. callanderi DSM 3662T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662T than to E. limosum ATCC 8486T. The ANI between KIST612 and E. callanderi DSM 3662T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486T, it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.
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Affiliation(s)
- Ji-Yeon Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Byeongchan Kang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Soyoung Oh
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Yeji Gil
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
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Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Faecalibacterium hominis Liu et al. 2023 is a later heterotypic synonym of Faecalibacterium duncaniae Sakamoto et al. 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37566461 DOI: 10.1099/ijsem.0.005995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
A strain of the recently validated species Faecalibacterium hominis shares 99.0 % 16S rRNA gene sequence similarity with the type strain of Faecalibacterium duncaniae. The aim of this study was to evaluate the taxonomic relationship between F. hominis and F. duncaniae. F. duncaniae JCM 31915T showed 73.0 % digital DNA-DNA hybridization (dDDH) value with F. hominis JCM 39347T. The average nucleotide identity (ANI) value between these two strains was 96.7 %. These results indicate that F. duncaniae JCM 31915T and F. hominis JCM 39347T represent members of the same species. Based on these data, we propose Faecalibacterium hominis as a later heterotypic synonym of Faecalibacterium duncaniae. An emended description is provided.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naomi Sakurai
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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9
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Hisatomi A, Ohkuma M, Sakamoto M. Sellimonas catena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185104 DOI: 10.1099/ijsem.0.005853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, small-chain coccobacilli, strains 12EGH17T and 18CBH55, were isolated from faecal samples of healthy Japanese humans. Strain 12EGH17T showed the highest 16S rRNA gene sequence similarity to Sellimonas intestinalis BR72T (95.5 %), Coprococcus comes ATCC 27758T (94.4 %) and Clostridium nexile DSM 1787T (93.7 %). The percentage of conserved proteins values between the genome of strain 12EGH17T and that of the members of the genus Sellimonas were >54 %, suggesting that strain 12EGH17T belongs to the genus Sellimonas. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12EGH17T and 18CBH55 were higher than the cut-off values of species demarcation (90 % dDDH and 99 % ANI), indicating these two strains are the same species. However, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<30 % dDDH and <79 % ANI). These results indicate that the isolates should be considered to represent a new species of the genus Sellimonas. The isolates were differentiated from the type species, S. intestinalis, by the ability of aesculin hydrolysis. Based on the collected data, strains 12EGH17T and 18CBH55 represent a novel species in the genus Sellimonas, for which the name Sellimonas catena sp. nov. is proposed. The type strain of S. catena is 12EGH17T (=JCM 35622T=DSM 114916T).
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Gaffney J, Embree J, Gilmore S, Embree M. Chordicoccus furentiruminis, gen. nov., sp. nov., a novel succinic acid producing bacterium isolated from a steer on a high grain diet. Int J Syst Evol Microbiol 2023; 73. [PMID: 36861667 DOI: 10.1099/ijsem.0.005751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
This study presents MP1D12T (=NRRL B-67553T=NCTC 14480T), an isolate from the ruminal content of an Angus steer fed a high grain diet. Phenotypic and genotypic traits of the isolate were explored. MP1D12T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that frequently grows in chains. Analysis of metabolic products as a result of carbohydrate fermentation showed succinic acid as the major organic acid produced with lactic acid and acetic acid as minor products. Phylogenetic analysis of MP1D12T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome presents a divergent lineage from other members in the family Lachnospiraceae. 16S rRNA sequence comparison, whole genome average nucleotide identity digital DNA-DNA hybridization and average amino acid identity results suggest that MP1D12T represents a novel species in a novel genus within the family Lachnospiraceae. We propose the creation of the genus Chordicoccus in which MP1D12T represents the type strain for the novel species Chordicoccus furentiruminis.
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Affiliation(s)
- James Gaffney
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Jordan Embree
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Sean Gilmore
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Mallory Embree
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
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11
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Lee S, Choi A, Park KH, Lee S, Yoon H, Kim P. Single-cell hemoprotein (heme-SCP) exerts the prebiotic potential to establish a healthy gut microbiota in small pet dogs. Food Sci Biotechnol 2023; 32:489-496. [PMID: 36911324 PMCID: PMC9992493 DOI: 10.1007/s10068-022-01195-9] [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] [Received: 08/19/2022] [Revised: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2022] Open
Abstract
To investigate the effect of the single-cell hemoprotein (heme-SCP) source on animals, a dog-treat (100 g for each dog) harboring 0.2% heme-SCP was manufactured and fed to seven pet dogs (< 10 kg) in a randomized manner (irrespective of owner's feeding style, dogs' health conditions, and staple diets), and the feces before and after the dog-treat diet were analyzed to define the structure of the microbiota. The total bacterial species of the seven dogs showed no difference (564-584), although the bacterial compositions varied significantly. The Firmicutes phylum increased (54.7-73.7%), showing differential species composition before and after heme-SCP intake. Proteobacteria, Bacteroidetes, and Fusobacteria decreased (5.4-3.8%, 32.9-16.8%, and 6.3-3.6%, respectively), which agreed with the previous observation of deliberate feeding. Therefore, it is conceivable that heme-SCP as a prebiotic can shape the gut microbiota regardless of the administration method. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-022-01195-9.
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Affiliation(s)
- Seungki Lee
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon, Gyeonggi 14662 South Korea
| | - Ahyoung Choi
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon, Gyeonggi 14662 South Korea
| | | | - Seoyeon Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499 South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499 South Korea
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon, Gyeonggi 14662 South Korea.,HemoLab Ltd. Co., Bucheon, 14622 South Korea
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12
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Zgarbová E, Vrzal R. Skatole: A thin red line between its benefits and toxicity. Biochimie 2022; 208:1-12. [PMID: 36586563 DOI: 10.1016/j.biochi.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022]
Abstract
Skatole (3-methylindole) is a heterocyclic compound naturally found in the feces of vertebrates and is produced by certain flowers. Skatole has been used in specific products of the perfume industry or as a flavor additive in ice cream. Additionally, skatole is formed by tryptophan pyrolysis of tobacco and has been demonstrated to be a mutagen. Skatole-induced pulmonotoxicity was reliably described in ruminants and rodents, but no studies have been conducted in humans. Initially, we provide basic knowledge and a historical overview of skatole. Then, skatole bacterial formation in the intestine is described, and the importance of the microbiome during this process is evaluated. Increased skatole concentrations could serve as a marker for intestinal disease development. Therefore, the human molecular targets of skatole that may have significant effects on various processes in the human body are described. Ultimately, we suggest a link between skatole intestinal formation in humans and skatole-induced pulmonotoxicity, which should be explored further in the future.
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Affiliation(s)
- Eliška Zgarbová
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 783 71, Olomouc, Czech Republic
| | - Radim Vrzal
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 783 71, Olomouc, Czech Republic.
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13
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Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005379] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Faecalibacterium prausnitzii
is one of the most important butyrate-producing bacteria in the human gut. Previous studies have suggested the presence of several phylogenetic groups, with differences at the species level, in the species, and a taxonomic re-evaluation is thus essential for further understanding of ecology of the important human symbiont. Here we examine the phenotypic, physiological, chemotaxonomic and phylogenomic characteristics of six
F. prausnitzii
strains (BCRC 81047T=ATCC 27768T, A2-165T=JCM 31915T, APC918/95b=JCM 39207, APC942/30−2=JCM 39208, APC924/119=JCM 39209 and APC922/41−1T=JCM 39210T) deposited in public culture collections with two reference strains of
Faecalibacterium butyricigenerans
JCM 39212T and
Faecalibacterium longum
JCM 39211T.
Faecalibacterium
sp. JCM 17207T isolated from caecum of broiler chicken was also included. Three strains of
F. prausnitzii
(BCRC 81047T, JCM 39207 and JCM 39209) shared more than 96.6 % average nucleotide identity (ANI) and 69.6 % digital DNA–DNA hybridization (dDDH) values, indicating that the three strains are members of the same species. On the other hand, the remaining three strains of
F. prausnitzii
(JCM 31915T, JCM 39208 and JCM 39210T) were clearly separated from the above three strains based on the ANI and dDDH values. Rather, JCM 39208 showed ANI and dDDH values over the cut-off values of species discrimination (>70 % dDDH and >95–96 % ANI) with
F. longum
JCM 39211T, whereas JCM 31915T, JCM 39210T and JCM 17207T did not share dDDH and ANI values over the currently accepted cut-off values with any of the tested strains, including among them. Furthermore, the cellular fatty acid patterns of these strains were slightly different from other
F. prausnitzii
strains. Based on the collected data,
F. prausnitzii
JCM 31915T,
F. prausnitzii
JCM 39210T and
Faecalibacterium
sp. JCM 17207T represent three novel species of the genus
Faecalibacterium
, for which the names Faecalibacterium duncaniae sp. nov. (type strain JCM 31915T=DSM 17677T=A2-165T), Faecalibacterium hattorii sp. nov. (type strain JCM 39210T=DSM 107841T=APC922/41-1T) and Faecalibacterium gallinarum sp. nov. (type strain JCM 17207T=DSM 23680T=ic1379T) are proposed.
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14
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Shin Y, Paek J, Kim H, Kook JK, Chang YH. Faecalicatena absiana sp. nov., an obligately anaerobic bacterium from a pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, Gram-stain-positive, spore-forming, short-rod-shaped bacterium, designated strain YH-C36aT, was isolated from a pig farm faeces dump. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus
Faecalicatena
and is most closely related to
Faecalicatena contorta
KCTC 5831T,
Faecalicatena fissicatena
KCTC 15010T and
Faecalicatena orotica
KCTC 15331T, with 96.3, 96.2, and 96.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-C36aT and the closest related strains were lower than 72 %. The G+C content of the isolate was 43.0 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1
cis 9, C16 : 0 DMA, C18 : 0 DMA and C18:0. The major end products of glucose fermentation were lactate, formate and acetate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, named Faecalicatena absiana sp. nov., is proposed for strain YH-C36aT (=KCTC 25106T=NBRC 114768T).
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Affiliation(s)
- Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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15
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Chaplin AV, Shcherbakova VA, Pikina AP, Sokolova SR, Korzhanova M, Belova VA, Korostin DO, Rebrikov DV, Kardonsky DA, Urban AS, Zakharzhevskaya NB, Suzina NE, Podoprigora IV, Das MS, Kholopova DO, Efimov BA. Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H2 as the end metabolic products. Strains ASD3451 and ASD5720T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720T=JCM 34353T=VKM B-3497T) and Diplocloster modestus sp. nov. (ASD4241T=JCM 34351T=VKM B-3498T) within the family
Lachnospiraceae
.
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Affiliation(s)
- Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Alla P. Pikina
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofia R. Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Kardonsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Anatoly S. Urban
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia B. Zakharzhevskaya
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Irina V. Podoprigora
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Milana S. Das
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Daria O. Kholopova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A. Efimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
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16
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Neoagarooligosaccharides modulate gut microbiota and alleviate body weight gain and metabolic syndrome in high-fat diet-induced obese rats. J Funct Foods 2022. [DOI: 10.1016/j.jff.2021.104869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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17
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Sakamoto M, Ikeyama N, Yuki M, Murakami T, Mori H, Iino T, Ohkuma M. Adlercreutzia hattorii sp. nov., an equol non-producing bacterium isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870581 DOI: 10.1099/ijsem.0.005121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two obligately anaerobic, Gram-stain-positive, rod-shaped bacteria were isolated from faecal samples of healthy humans in Japan. 16S rRNA gene sequence analysis indicated that these two strains (8CFCBH1T and 9CBH6) belonged to the genus Adlercreutzia, which is known as an equol-producing bacterium. The closest neighbours of strain 8CFCBH1T were Adlercreutzia equolifaciens subsp. equolifaciens DSM 19450T (98.6%), Adlercreutzia equolifaciens subsp. celatus do03T (98.4%), Adlercreutzia muris WCA-131-CoC-2T (96.6%), Parvibacter caecicola NR06T (96.4%), Adlercreutzia caecimuris B7T (95.3%) and Adlercreutzia mucosicola Mt1B8T (95.3%). The closest relatives to strain 9CBH6 were A. equolifaciens subsp. equolifaciens DSM 19450T (99.8%), A. equolifaciens subsp. celatus do03T (99.6%) and A. muris WCA-131-CoC-2T (96.8%). Strain 8CFCBH1T showed 22.3-53.5% digital DNA-DNA hybridization (dDDH) values with its related species. In addition, the average nucleotide identity (ANI) values between strain 8CFCBH1T and its related species ranged from 75.4 to 93.3%. On the other hand, strain 9CBH6 was considered as A. equolifaciens based on the dDDH and ANI values (>70% dDDH and >95-96% ANI). Strain 9CBH6 showed daidzein-converting activity, as expected from the result of genome analysis. The genome of strain 8CFCBH1T lacked four genes involved in equol production. Growing cells of strain 8CFCBH1T were not capable of converting daidzein. Based on the collected data, strain 8CFCBH1T represents a novel species in the genus Adlercreutzia, for which the name Adlercreutzia hattorii sp. nov. is proposed. The type strain of A. hattorii is 8CFCBH1T (=JCM 34083T=DSM 112284T).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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18
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Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces. Antonie van Leeuwenhoek 2021; 114:2091-2099. [PMID: 34623538 DOI: 10.1007/s10482-021-01663-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 10/20/2022]
Abstract
An obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped strain AGMB00832T was isolated from swine faeces. Phylogenetic analysis based on the 16S rRNA gene, together with the housekeeping genes, gyrB and rpoD, revealed that strain AGMB00832T belonged to the genus Faecalicatena and was most closely related to Faecalicatena orotica KCTC 15331T. In biochemical analysis, strain AGMB00832T was shown to be negative for catalase, oxidase and urease. Furthermore, the isolate was positive for β-glucosidase, β-glucuronidase, glutamic acid decarboxylase, proline arylamidase, acid phosphatase and naphthol-AS-BI-phosphohydrolase. The major cellular fatty acids (> 10%) of the isolate were C14:0, C16:0 and C18:1ω11t DMA. Based on the whole genome sequence analysis, the DNA G + C content of strain AGMB00832T was 44.2 mol%, and the genome size and numbers of rRNA and tRNA genes were 5,175,159 bp, 11 and 53, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain AGMB00832T and related strains were ≤ 77.4 and 22.5%, respectively. Furthermore, the genome analysis revealed the presence of genes for alkaline shock protein 23 and cation/proton antiporters, which may facilitate growth of strain AGMB00832T in alkaline culture condition. On the basis of polyphasic taxonomic approach, strain AGMB00832T represents a novel species within the genus Faecalicatena, for which the name Faecalicatena faecalis sp. nov. is proposed. The type strain is AGMB00832T (= KCTC 15946T = NBRC 114613T).
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19
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Konishi T, Tamura T, Tobita T, Sakai S, Matsuda N, Kawasaki H. Effusibacillus dendaii sp. nov. isolated from farm soil. Arch Microbiol 2021; 203:4859-4865. [PMID: 34235583 PMCID: PMC8502169 DOI: 10.1007/s00203-021-02470-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 01/22/2023]
Abstract
A Gram-positive, rod-shaped, spore-forming, thermophilic, and acidophilic bacterium, designated as strain skT53T, was isolated from farm soil in Tokyo, Japan. Under aerobic conditions, the strain grew at 35-55 °C (optimum temperature 44-55 °C) and pH 4.0-6.0 (optimum pH 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was moderately related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.2 mol%, and MK-7 was the predominant respiratory quinone in the strain. The major fatty acids were anteiso-C15:0, iso-C15:0, and iso-C16:0. Based on the phenotypic and chemotaxonomic characteristics, as well as 16S rRNA gene sequence similarity and whole genome analyses, strain skT53T represents a novel species in the genus Effusibacillus, for which the name Effusibacillus dendaii sp. nov. has been proposed. The type strain is skT53T (= NBRC 114101 T = TBRC 11241 T).
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Affiliation(s)
- Tomoyuki Konishi
- Graduate School of Engineering, Tokyo Denki University, 5, Senju asahi-cho, Adachi-ku, Tokyo, 120-8551 Japan
| | - Tomohiko Tamura
- National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusa-kamatari, Kisarazu, Chiba Japan
| | - Toru Tobita
- Graduate School of Engineering, Tokyo Denki University, 5, Senju asahi-cho, Adachi-ku, Tokyo, 120-8551 Japan
| | - Saori Sakai
- Graduate School of Engineering, Tokyo Denki University, 5, Senju asahi-cho, Adachi-ku, Tokyo, 120-8551 Japan
| | - Namio Matsuda
- Graduate School of Engineering, Tokyo Denki University, 5, Senju asahi-cho, Adachi-ku, Tokyo, 120-8551 Japan
| | - Hisashi Kawasaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1Bunkyo-ku, Yayoi, Tokyo113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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20
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Shan J, Qu Y, Wang S, Wei Y, Chang L, Ma L, Hashimoto K. Regulation of neurotoxicity in the striatum and colon of MPTP-induced Parkinson's disease mice by gut microbiome. Brain Res Bull 2021; 177:103-110. [PMID: 34560239 DOI: 10.1016/j.brainresbull.2021.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 12/21/2022]
Abstract
Increasing evidence suggests the role of gut-microbiota-brain axis in the pathogenesis of Parkinson's disease (PD). The objective of this study was to examine whether repeated administration of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) can influence the neurotoxicity in the striatum and colon, and the composition of gut microbiota and short-chain fatty acids (SCFAs) in feces of adult mice. MPTP caused the reduction of dopamine transporter (DAT) and tyrosine hydroxylase (TH) in the striatum, and increases in phosphorylated α-synuclein (p-α-Syn) in the striatum and colon. There was a negative correlation between the expression of TH in the striatum and the expression of p-α-Syn in the colon, suggesting a role of gut-brain communication. MPTP caused abnormalities in the α- and β-diversity of gut microbiota in the mice. Furthermore, the relative abundance of the genus Faecalicatena in the MPTP-treated group was significantly lower than that of control group. Interestingly, there was a positive correlation between the genus Faecalicatena and the expression of TH in the striatum. Moreover, MPTP did not alter the levels of SCFAs in feces samples. However, there was a positive correlation between the relative abundance of the genus Faecalicatena and propionic acid. The data suggest that MPTP-induced increases in colonic p-α-Syn expression might be associated with dopaminergic neurotoxicity in the striatum via gut-microbiota-brain axis.
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Affiliation(s)
- Jiajing Shan
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Youge Qu
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Siming Wang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Yan Wei
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Lijia Chang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Li Ma
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan.
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21
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Segura-Wang M, Grabner N, Koestelbauer A, Klose V, Ghanbari M. Genome-Resolved Metagenomics of the Chicken Gut Microbiome. Front Microbiol 2021; 12:726923. [PMID: 34484168 PMCID: PMC8415551 DOI: 10.3389/fmicb.2021.726923] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/29/2021] [Indexed: 01/30/2023] Open
Abstract
Increasing evidence shows that the chicken gastrointestinal microbiota has a major effect on the modulation of metabolic functions and is correlated with economic parameters, such as feed efficiency and health. Some of these effects derive from the capacity of the chicken to digest carbohydrates and produce energy-rich metabolites such as short-chain fatty acids (SCFA) and from host-microbe interactions. In this study, we utilized information from metagenomic assembled genomes (MAGs) from chicken gastrointestinal tract (GIT) samples, with detailed annotation of carbohydrate-active enzymes (CAZymes) and genes involved in SCFA production, to better understand metabolic potential at different ages. Metagenomic sequencing of 751 chicken GIT samples was performed to reconstruct 155 MAGs, representing species which belong to six phyla, primarily Firmicutes followed by Proteobacteria. MAG diversity significantly (p < 0.001) increased with age, with early domination of Lachnospiraceae, followed by other families including Oscillospiraceae. Age-dependent shifts were observed in the abundance of genes involved in CAZyme and SCFA production, exemplified by a significant increase in glycosyltransferases (GTs) and propionic acid production pathways (p < 0.05), and a lower abundance of glycoside hydrolases (GHs) (p < 0.01). Co-occurrence analysis revealed a large cluster highly interconnected by enzymes from GT2_2 and GH3 families, underscoring their importance in the community. Furthermore, several species were identified as interaction hubs, elucidating associations of key microbes and enzymes that more likely drive temporal changes in the chicken gut microbiota, and providing further insights into the structure of the complex microbial community. This study extends prior efforts on the characterization of the chicken GIT microbiome at the taxonomic and functional levels and lays an important foundation toward better understanding the broiler chicken gut microbiome helping in the identification of modulation opportunities to increase animal health and performance.
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22
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Morohoshi S, Kunihiro T, Iino T, Ohkuma M. Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces. Microbiol Immunol 2021; 65:245-256. [PMID: 33913539 DOI: 10.1111/1348-0421.12886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 01/15/2023]
Abstract
An obligately anaerobic, Gram-stain-negative, rod-shaped bacterium, designated strain 2CBH44T , was isolated from the fecal sample of a healthy Japanese man. This strain was initially assigned as a novel species of the genus Coprobacter based on the 16S rRNA gene sequence similarities compared with other Coprobacter species. The 16S rRNA gene sequence analysis revealed strain 2CBH44T had relatively low 16S rRNA gene sequence similarity (97.5%) to Coprobacter secundus 177T . However, strain 2CBH44T showed 96.9% average nucleotide identity value with C. secundus 177T , indicating that strain 2CBH44T and C. secundus 177T belong to the same species. On the other hand, the digital DNA-DNA hybridization value between strain 2CBH44T and C. secundus 177T was 73.5%, indicating that strain 2CBH44T is a subspecies of C. secundus. Another anaerobic, Gram-stain-variable, rod-shaped bacterium, designated strain 12CBH8T , was also isolated from human feces. Strain 12CBH8T had significantly low 16S rRNA gene sequence similarities (<92.0%) to the validated bacterial species within the family Oscillospiraceae. The percentage of conserved protein values between the genome of strain 12CBH8T and that of the validated related taxa were <50%, suggesting that strain 12CBH8T belongs to a novel genus. On the basis of the collected data, strain 2CBH44T represents a novel subspecies of C. secundus, for which the name Coprobacter secundus subsp. similis subsp. nov. (type strain 2CBH44T = JCM 34079T = DSM 111570T ) is proposed. Strain 12CBH8T represents a novel species of a novel genus, for which the name Solibaculum mannosilyticum gen. nov., sp. nov. (type strain 12CBH8T = JCM 34081T = DSM 111571T ) is proposed.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Sho Morohoshi
- TechnoSuruga Laboratory Co. Ltd, Shizuoka-shi, Shizuoka, Japan
| | - Tadao Kunihiro
- TechnoSuruga Laboratory Co. Ltd, Shizuoka-shi, Shizuoka, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject. Pathogens 2021; 10:pathogens10030367. [PMID: 33808593 PMCID: PMC8003473 DOI: 10.3390/pathogens10030367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Catonella currently counts a unique species, C. morbi, isolated from periodontal pockets and associated with periodontitis and endodontic infections. This study contributed to the taxonomical and clinical knowledge of this genus by describing a novel species isolated from a saliva sample from a man in clinical gingival health following successful treatment of periodontitis. Morphological and chemotaxonomic characteristics were investigated using different growth conditions, pH, and temperature. Cellular fatty acid methyl ester (FAME) analysis was conducted by gas chromatography/mass spectrometry (GC/MS). Phylogenetic analysis based on 16S rRNA, orthologous average nucleotide identity (OrthoANI), and digital DNA-DNA hybridization (dDDH) relatedness were performed. Strain Marseille-Q4567T was found to be an anaerobic and non-spore-forming rod-shaped bacterium that grew at 28–41.5 °C (optimum 37 °C), pH 6.5–8.5 (optimum pH 7.5), and 5–10 g/L of NaCl (optimum 5 g/L). The predominant cellular fatty acid was C16:0 (64.2%), followed by unsaturated structures C18:1n9 (12.5%) and C18:2n6 (7.8%). Based on 16S rRNA sequence comparison, the closest phylogenetic neighbor was C. morbi ATCC 51271T (98.23% similarity). The OrthoANI and dDDH values between strain Q4567T and C. morbi ATCC 51271T were respectively 79.43% and 23.8%. Therefore, we concluded that strain Marseille-Q4567T represents a novel species of the genus Catonella, for which the name Catonella massiliensis sp. nov. is proposed (= CSUR Q4567).
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Naud S, Bellali S, Anani H, Lo C, Yacouba A, Tidjani Alou M, Armstrong N, Bonvalet M, Zitvogel L, Raoult D, Lagier JC. Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2021; 40:100850. [PMID: 33732473 PMCID: PMC7941043 DOI: 10.1016/j.nmni.2021.100850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/22/2022] Open
Abstract
An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.
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Affiliation(s)
- S. Naud
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - S. Bellali
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - H. Anani
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Yacouba
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Bonvalet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - L. Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
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25
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Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FK. Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse. Int J Syst Evol Microbiol 2021; 71. [PMID: 33512312 DOI: 10.1099/ijsem.0.004673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52-74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives (D. longicatena, Ruminococcus gnavus, C. scindens, Dorea formicigenerans, Ruminococcus lactaris, Clostridium hylemonae, Merdimonas faecis, Faecalicatena contorta and Faecalicatena fissicatena). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Theresa Streidl
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Esther Wortmann
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Paulina Deptula
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Michael V W Kofoed
- Microbial Conversion Technologies Research Group, Section for Biological and Chemical Engineering, Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Thomas Riedel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Hansen
- Center for Advanced Bioimaging, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Clavel
- ZIEL Core Facility Microbiome, Technical University of Munich, Freising, Germany.,Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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26
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Ikeyama N, Ohkuma M, Sakamoto M. Stress Response of Mesosutterella multiformis Mediated by Nitrate Reduction. Microorganisms 2020; 8:microorganisms8122003. [PMID: 33333944 PMCID: PMC7765368 DOI: 10.3390/microorganisms8122003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Bacterial stress responses are closely associated with the survival and colonization of anaerobes in the human gut. Mesosutterella multiformis JCM 32464T is a novel member of the family Sutterellaceae, an asaccharolytic bacterium. We previously demonstrated energy generation via heme biosynthesis, which is coupled with nitrate reductase. Here, physiological and morphological changes in M. multiformis induced by exposure to nitrate were investigated. The ability of M. multiformis to reduce nitrate was determined using a colorimetric assay. A unique morphology was observed during nitrate reduction under anaerobic conditions. The association between nitrate concentration and cell size or cellular fatty acid composition was evaluated. Nitrate-induced responses of M. multiformis were compared to those of related species. An increase in cellular filamentation and the ratio of saturated: unsaturated fatty acids was mediated specifically by nitrate. This indicates a decrease in cell fluidity and low leakage. Furthermore, a similar response was not observed in other related species cultured in the presence of nitrate. Hence, the nitrate-induced stress response in new anaerobes such as M. multiformis was demonstrated. The response could also be involved in the conservation of menaquinones and the maximization of nitrate reduction.
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Affiliation(s)
- Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba 305-0074, Ibaraki, Japan
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27
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Complete Genome Sequence of Faecalibacillus intestinalis JCM 34082, Isolated from Feces from a Healthy Japanese Female. Microbiol Resour Announc 2020; 9:9/50/e01160-20. [PMID: 33303667 PMCID: PMC7729415 DOI: 10.1128/mra.01160-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report the complete genome sequence of Faecalibacillus intestinalis JCM 34082, a member of the family Erysipelotrichaceae that was isolated from feces from a healthy Japanese woman. The genome assembly comprised 2,869,982 bp, with a G+C content of 29.8%. Here, we report the complete genome sequence of Faecalibacillus intestinalis JCM 34082, a member of the family Erysipelotrichaceae that was isolated from feces from a healthy Japanese woman. The genome assembly comprised 2,869,982 bp, with a G+C content of 29.8%.
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28
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Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger. Front Microbiol 2020; 11:1665. [PMID: 32793154 PMCID: PMC7393233 DOI: 10.3389/fmicb.2020.01665] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.
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Affiliation(s)
- Yao Ning
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jinzhe Qi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Michael T Dobbins
- Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Xin Liang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jingxuan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shiyu Chen
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangshun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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29
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Ikeyama N, Toyoda A, Morohoshi S, Kunihiro T, Murakami T, Mori H, Iino T, Ohkuma M, Sakamoto M. Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:3656-3664. [PMID: 32416738 DOI: 10.1099/ijsem.0.004215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with 'Absiella argi' strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, 'A. argi' JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7-99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA-DNA hybridization (DDH) values among three strains were 88.4-90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5-24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for 'A. argi' strains identified because the name 'A. argi' has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).
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Affiliation(s)
- Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sho Morohoshi
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Tadao Kunihiro
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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30
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Kim JS, Park JE, Lee KC, Choi SH, Oh BS, Yu SY, Eom MK, Kang SW, Han KI, Suh MK, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JH, Lee JS, Park SH. Blautia faecicola sp. nov., isolated from faeces from a healthy human. Int J Syst Evol Microbiol 2020; 70:2059-2065. [PMID: 32100703 DOI: 10.1099/ijsem.0.004015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111T, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111T was closely related to Ruminococcus gauveauii CCRI-16110T (93.9 %) and Blautia stercoris GAM6-1T (93.7 %), followed by Clostridium nexile DSM 1787T (93.5 %), Blautia producta ATCC 27340T (93.4 %), Blautia hydrogenotrophica DSM 10507T (93.1 %) and Blautia coccoides ATCC 29236T (93.1 %) within the family Lachnospiraceae (Clostridium rRNA cluster XIVa). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that KGMB01111T formed a separate branch with species in the genus Blautia. The major cellular fatty acids (>10.0 %) were C16 : 0 and C18 : 1 cis 9 dimethyl acetal (DMA), and the major polar lipids were aminophospholipids and lipids. KGMB01111T contained meso-diaminopimelic acid in cell-wall peptidoglycan. The predominant end product of fermentation produced by KGMB01111T was acetic acid. Based on the whole-genome sequence, the DNA G+C content of the isolate was 44.7 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, KGMB01111T represents a novel species within the genus Blautia for which the name Blautia faecicola sp. nov. is proposed. The type strain is KGMB01111T (=KCTC 15706T=DSM 107827T).
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung Yeob Yu
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do 13620, Republic of Korea
| | - Byung-Yong Kim
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Seung-Jo Yang
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jung-Sook Lee
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.,Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
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31
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Gut metagenomic and short chain fatty acids signature in hypertension: a cross-sectional study. Sci Rep 2020; 10:6436. [PMID: 32296109 PMCID: PMC7160119 DOI: 10.1038/s41598-020-63475-w] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Hypertension is an independent and preventable risk factor for the development of cardiovascular diseases, however, little is known about the impact of gut microbiota composition in its development. We carried out comprehensive gut microbiota analysis and targeted metabolomics in a cross-sectional study of 29 non-treated hypertensive (HT) and 32 normotensive (NT) subjects. We determined fecal microbiota composition by 16S rRNA gene sequencing and bacterial functions by metagenomic analysis. The microbial metabolites analysed were short chain fatty acids (SCFA) both in plasma and feces, and trimethylamine N-oxide (TMAO) in plasma. The overall bacterial composition and diversity of bacterial community in the two groups were not significantly different. However, Ruminococcaceae NK4A214, Ruminococcaceae_UCG-010, Christensenellaceae_R-7, Faecalibacterium prausnitzii and Roseburia hominis were found to be significantly enriched in NT group, whereas, Bacteroides coprocola, Bacteroides plebeius and genera of Lachnospiraceae were increased in HT patients. We found a positive correlation between the HT-associated species and systolic and diastolic blood pressure after adjusted for measured confounders. SCFA showed antagonistic results in plasma and feces, detecting in HT subjects significant higher levels in feces and lower levels in plasma, which could indicate a less efficient SCFA absorption. Overall, our results present a disease classifier based on microbiota and bacterial metabolites to discriminate HT individuals from NT controls in a first disease grade prior to drug treatment.
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32
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Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M. Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov. Int J Syst Evol Microbiol 2020; 70:473-480. [PMID: 31633480 DOI: 10.1099/ijsem.0.003778] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus Alistipes belonging to the family Rikenellaceae in the phylum Bacteroidetes, were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24T and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to 'Alistipes obesi' ph8T (99.73 %). Group II (strain 5CPEGH6T) was related to Alistipes shahii WAL 8301T (96.82 %). Ten strains of group III (3BBH6T, 5CPYCFAH4, 5NYCFAH2 and others) were related to Alistipes onderdonkii DSM 19147T (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6T could be differentiated from A. shahii JCM 16773T by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of A. onderdonkii JCM 16771T. Strains 5CBH24T, 6CPBBH3 and 'A. obesi' ph8T shared 98.8-98.9 % average nucleotide identity (ANI) with each other. In addition, the in silico DNA-DNA hybridization (DDH) values among three strains were 86.7-89.4 %. Strain 5CPEGH6T showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6T, 5CPYCFAH4 and 5NYCFAH2) shared 97.9-99.9% ANI with each other. These three strains showed 96.9-97.3 % ANI with A. onderdonkii DSM 19147T. The DDH values of strains 3BBH6T, 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5-99.8 %, while those compared to A. onderdonkii DSM 19147T were 71.0-73.4 %. On the basis of the collected data, three novel species, Alistipes communis sp. nov. (5CBH24T=JCM 32850T=DSM 108979T), Alistipes dispar sp. nov. (5CPEGH6T=JCM 32848T=DSM 108978T) and Alistipes onderdonkii subsp. vulgaris subsp. nov. (3BBH6T=JCM 32839T=DSM 108977T), are proposed.
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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 Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yusuke Ogata
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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33
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Iino T, Ohkuma M. Dialister hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:589-595. [DOI: 10.1099/ijsem.0.003797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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34
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Soh M, Miyake S, Lim A, Ding Y, Seedorf H. Schaedlerella arabinosiphila gen. nov., sp. nov., a D-arabinose-utilizing bacterium isolated from faeces of C57BL/6J mice that is a close relative of Clostridium species ASF 502. Int J Syst Evol Microbiol 2019; 69:3616-3622. [PMID: 31502946 DOI: 10.1099/ijsem.0.003671] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The use of gnotobiotics has attracted wide interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotic mouse model, the altered Schaedler flora (ASF) has been used for several decades. ASF comprises eight different bacterial strains, which have been characterized to different extent, but only a few are available through public strain collections. Here, the isolation of a close relative of one of the less-studied ASF strains, Clostridium species ASF 502, from faeces of C57BL/6J mice is reported. Isolate TLL-A1T shares 99.5 % 16S rRNA gene sequence identity with Clostridium species ASF 502 and phylogenetic analyses indicate that both strains belong to the uncultured so-called 'Lachnospiraceae UCG 006' clade. The rare sugar d-arabinose was used as a sole carbon source in the anaerobic isolation medium. Results of growth experiments with TLL-A1T on different carbon sources and analysis of its ~6.5 Gb indicate that TLL-A1T harbours a large gene repertoire that enables it to utilize a variety of carbohydrates for growth. Comparative genome analyses of TLL-A1T and Clostridium species ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate-activating enzymes. Based on genomic, molecular and phenotypic differences, we propose to classify strain TLL-A1T (DSM 106076T=KCTC 15657T) as a representative of a new genus and a new species, for which we propose the name Schaedlerella arabinosiphila gen. nov., sp. nov.
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Affiliation(s)
- Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Sou Miyake
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Austin Lim
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Yichen Ding
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117604, Singapore
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35
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Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD, Wagner J. The Microbiome in Paediatric Crohn's Disease-A Longitudinal, Prospective,
Single-Centre Study. J Crohns Colitis 2019; 13:1044-1054. [PMID: 30927743 DOI: 10.1093/ecco-jcc/jjz016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS The gut mucosa is the principal site where Crohn's disease [CD] inflammation occurs. Limited information is available about the gut mucosal microbiome during CD relapse and remission. The aim of our study was to characterize specific changes in the gut microbiome during relapse and remission in a large single-centre paediatric CD cohort. METHODS We analysed the microbiome of 345 biopsies from 204 patients, including 88 CD first diagnosis [CDFD] patients, 38 relapse [CDRL] patients, 12 remission [CDRM] patients, and 66 controls. Species identification was conducted using oligotyping in combination with ARB/SILVA taxonomic annotation. RESULTS We observed 45 bacteria to differ between CDFD samples and controls with statistical significance, with Fusobacterium being the most implicated species in CDFD patients. We also identified gender-specific differences in CD. Five species showed a strong association with CDRL patients and 10 species with CDRM patients. Three taxa showed a positive co-occurrence across the two groups. Hespellia porcina [closest taxonomic neighbour to Clostridium oroticum] was the most strongly associated with CDRL samples. Interestingly, Fusobacterium was not part of the CDRL-associated taxa group. Faecalibacterium prausnitzii was equally present in CDFD and control samples. CONCLUSION This is the first study that has investigated the gut mucosal microbiome in a paediatric CD cohort with longitudinal sampling. Importantly, the microbiome of patients in CDRM did not return to a healthy control state. Neither did the microbiome of patients with CDRL return to the profile seen at CDFD.
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Affiliation(s)
- Shivani Kansal
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia.,Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Anthony G Catto-Smith
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Gastroenterology, Hepatology and Liver Transplant, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Karen Boniface
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Sarah Thomas
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Donald J Cameron
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Mark Oliver
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - George Alex
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill and Melinda Gates Foundation, Seattle, Washington, USA
| | - Josef Wagner
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Wellcome Sanger Institute, Cambridge, UK
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36
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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37
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Kim W, Yang SH, Park MJ, Oh J, Lee JH, Kwon KK. Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field. Int J Syst Evol Microbiol 2019; 69:1934-1940. [PMID: 31038448 DOI: 10.1099/ijsem.0.003404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative oval-rod-shaped, spore-forming anaerobic bacterium, designated as strain MCWD5T, was isolated from sediment of a salt pond in the Republic of Korea (35° 7' 18″ N 126° 19' 4″ E). The 16S rRNA gene sequence analysis revealed that strain MCWD5T had low similarity values to members in the family Lachnospiraceae, such as Robinsoniella peoriensis PPC31T (94.8 %), Ruminococcusgauvreauii CCRI-16110T (94.2 %) and Lachnotalea glycerini DLD10T (94.0 %), and its phylogenetic position is unstable. The strain could grow at 20-42 °C (optimum, 38-42 °C), pH 5.5-10.0 (pH 7.0) and with 0-6 % (2.0 %) NaCl. Strain MCWD5T could not use nitrate, nitrite, sulfate or sulfite as electron acceptors. The strain could utilize various carbohydrates, such as arabinose, cellobiose, glucose, etc., and polymers such as pectin and starch. The major fatty acids of strain MCWD5T were C14 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c DMA and summed feature 8 (C17 : 1ω8c and/or C17 : 2), which was clearly different from those of related genera. The major polar lipids were diphosphatidyglycerol, phosphatidyglycerol and an unknown phospholipid. Based on the results of phylogenetic, physiologic and chemotaxonomic studies, Anaerosacchariphilus polymeriproducens gen. nov., sp. nov. with the type strain MCWD5T (=KCTC 15595T=DSM 105757T) is proposed in the family Lachnospiraceae.
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Affiliation(s)
- Wonduck Kim
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea.,†Present address: Genome and Company, Innovalley A-801, Pangyo-ro 253, Seongnam, Republic of Korea
| | - Sung-Hyun Yang
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Mi-Jeong Park
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea.,2KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jihye Oh
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jung-Hyun Lee
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- 1Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea.,2KIOST School, University of Science and Technology, Daejeon, Republic of Korea
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38
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Sakamoto M, Ikeyama N, Murakami T, Mori H, Yuki M, Ohkuma M. Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov. Int J Syst Evol Microbiol 2019; 69:1123-1129. [DOI: 10.1099/ijsem.0.003283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Previous analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related
Olsenella
species. To clarify the relationship of these two species, we determined the genome sequence of
P. catena
JCM 31932T and compared it with that already sequenced for
L. massiliensis
Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between
P. catena
JCM 31932T and
L. massiliensis
Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that
P. catena
JCM 31932T and
L. massiliensis
Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between
L. massiliensis
Marseille-P3237T and other closely related species. In addition, the genome of
P. catena
JCM 31932T had a high degree of synteny conservation with that of
L. massiliensis
Marseille-P3237T. On the basis of these findings, we propose that
L. massiliensis
should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Takumi Murakami
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Masahiro Yuki
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
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39
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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40
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Kim JS, Lee KC, Suh MK, Han KI, Eom MK, Lee JH, Park SH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS. Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces. J Microbiol 2018; 57:38-44. [PMID: 30594982 DOI: 10.1007/s12275-019-8550-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
A Gram-stain-positive, obligately anaerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung Yeob Yu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | | | | | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea. .,University of Science and Technology, Daejeon, 34113, Republic of Korea.
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41
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Noda S, Sakamoto M, Aihara C, Yuki M, Katsuhara M, Ohkuma M. Lactococcus termiticola sp. nov., isolated from the gut of the wood-feeding higher termite Nasutitermes takasagoensis. Int J Syst Evol Microbiol 2018; 68:3832-3836. [DOI: 10.1099/ijsem.0.003068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Satoko Noda
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Mitsuo Sakamoto
- 3PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Chihiro Aihara
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Masahiro Yuki
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Megumi Katsuhara
- 1Graduate School of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Moriya Ohkuma
- 2Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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42
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Sakamoto M, Ikeyama N, Kunihiro T, Iino T, Yuki M, Ohkuma M. Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megalosphaeroides sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:3942-3950. [PMID: 30394865 DOI: 10.1099/ijsem.0.003096] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two novel, obligately anaerobic, Gram-stain-negative, rod or coccoid-shaped bacteria, designated strains 4NBBH2T and 6FBBBH3T, were isolated from faecal samples of a healthy Japanese woman and man. The 16S rRNA gene sequence analysis showed that these strains represent a distinct lineage within the family Sutterellaceae. Strain 4NBBH2T formed a monophyletic branch between the genera Parasutterella and Sutterella, with sequence similarity to Sutterella stercoricanis CCUG 47620T (92.6 %), followed by Sutterella wadsworthensis WAL 7877 (92.4 %), Sutterella parvirubra YIT 11816T (92.1 %) and Parasutterella secunda YIT 12071T (91.8 %). Strain 6FBBBH3T was affiliated to the genus Sutterella, with highest similarity to S. stercoricanis CCUG 47620T (97.1 %), followed by S. parvirubra YIT 11816T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). Strains 4NBBH2T and 6FBBBH3T were asaccharolytic. Analysis of fatty acids revealed that strain 4NBBH2T could be differentiated from Sutterella species (including strain 6FBBBH3T) by the presence of a low concentration of C16 : 1ω7c. The major respiratory quinones of strain 4NBBH2T were menaquinone (MK)-6 and methylmenaquinone (MMK)-6, whereas those of strain 6FBBBH3T were MK-5 and MMK-5. The G+C content of the genomic DNA of strains 4NBBH2T and 6FBBBH3T were 56.9 and 62.8 mol%, respectively. On the basis of the collected data, strain 4NBBH2T represents a novel species in a novel genus of the family Sutterellaceae, for which the name Mesosutterella multiformis gen. nov., sp. nov. is proposed. The type strain is 4NBBH2T (=JCM 32464T=DSM 106860T). We also propose a novel Sutterella species, Sutterellamegalosphaeroides sp. nov., for strain 6FBBBH3T (=JCM 32470T=DSM 106861T).
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Affiliation(s)
- Mitsuo Sakamoto
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan.,2PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tadao Kunihiro
- 3TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Takao Iino
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM. Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces. Int J Syst Evol Microbiol 2018; 68:3741-3746. [PMID: 30351260 DOI: 10.1099/ijsem.0.003041] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0-98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA-DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7T was 38.6 mol%. The major fatty acids were C16 : 0, C16 : 1cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7T had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353T. Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353T is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353T=ATCC 27751T) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7T should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7T (=DSM 17630T=KCTC 15707T).
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Affiliation(s)
- Sudarshan A Shetty
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands
| | - Simone Zuffa
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands
| | - Thi Phuong Nam Bui
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands
| | - Steven Aalvink
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands
| | - Hauke Smidt
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands
| | - Willem M De Vos
- 1Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Building 124, 6708 WE Wageningen, The Netherlands.,2Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, Finland.,3RPU Immunobiology, Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nat Commun 2018; 9:4224. [PMID: 30310076 PMCID: PMC6181972 DOI: 10.1038/s41467-018-06627-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 12/30/2022] Open
Abstract
Skatole is a malodorous compound that contributes to the characteristic smell of animal faeces. Although skatole has long been known to originate from bacterial tryptophan fermentation, the enzyme catalysing its formation has so far remained elusive. Here we report the use of comparative genomics for the discovery of indoleacetate decarboxylase, an O2-sensitive glycyl radical enzyme catalysing the decarboxylation of indoleacetate to form skatole as the terminal step of tryptophan fermentation in certain anaerobic bacteria. We describe its biochemical characterization and compare it to other glycyl radical decarboxylases. Indoleacetate decarboxylase may serve as a genetic marker for the identification of skatole-producing environmental and human-associated bacteria, with impacts on human health and the livestock industry. Skatole is a bacterial metabolite responsible for boar taint and the objectionable smell of manure. Here, the authors elucidate the final step of skatole biosynthesis, describing the discovery and biochemical characterization of the enzyme catalysing the conversion of indoleacetate into skatole.
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Draft Genome Sequence of Faecalimonas umbilicata JCM 30896 T, an Acetate-Producing Bacterium Isolated from Human Feces. Microbiol Resour Announc 2018; 7:MRA01091-18. [PMID: 30533935 PMCID: PMC6256527 DOI: 10.1128/mra.01091-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/15/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896T, an acetate-producing bacterium isolated from human feces. The genomic analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate the study of the role of this strain in the human gut. Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896T, an acetate-producing bacterium isolated from human feces. The genomic analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate the study of the role of this strain in the human gut.
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Braune A, Blaut M. Catenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae. Int J Syst Evol Microbiol 2018; 68:3356-3361. [PMID: 30179152 DOI: 10.1099/ijsem.0.003001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An anaerobic Gram-stain-positive, non-spore-forming and non-motile bacterium isolated from the human gut, designated CG19-1T, capable of cleaving aromatic C-glucosides was characterized using a polyphasic taxonomic approach. Major fermentation products of this asaccharolytic organism were acetate and butyrate when grown on a complex medium. Growth of strain CG19-1T was stimulated by glucose or pyruvate. Growth inhibition was observed in the presence of several phenolic acids including ferulic acid, which nevertheless was reduced to dihydroferulic acid. Strain CG19-1T contained peptidoglycan type A4β l-Orn-d-Asp. The major cellular fatty acids were C16 : 0 and C18 : 1ω9c. The genomic DNA G+C content was 47.1 mol%. Based on its 16S rRNA gene sequence, strain CG19-1T is a member of the Lachnospiraceae. However, sequence identity to other Lachnospiraceae species with validly published names is approximately 93.0 % with Frisingicoccus caecimuris being the most closely related species according to phylogenetic analysis. Based on these findings, it is proposed to create a novel genus, Catenibacillus, and a novel species, Catenibacillus scindens, with the type strain CG19-1T (=DSM 106146T=CCUG 71490T).
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Affiliation(s)
- Annett Braune
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, D-14558 Nuthetal, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, D-14558 Nuthetal, Germany
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996-1004. [PMID: 30148503 DOI: 10.1038/nbt.4229] [Citation(s) in RCA: 1767] [Impact Index Per Article: 294.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/27/2018] [Indexed: 02/07/2023]
Abstract
Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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Sakamoto M, Iino T, Yuki M, Ohkuma M. Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:2074-2081. [PMID: 29745868 DOI: 10.1099/ijsem.0.002800] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22T, was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22T formed a monophyletic cluster with species in the genera Pseudoflavonifractor and Flavonifractor within the family Ruminococcaceae and had highest similarity to Pseudoflavonifractor capillosus ATCC 29799T (96.7 % sequence similarity), followed by Flavonifractor plautii ATCC 29863T (96.4 %). Acetate and butyrate were produced by strain 3BBH22T as metabolic end-products. The major cellular fatty acids were C14 : 0, C16 : 0, C18 : 1ω9c, C16 : 0 dimethyl acetal, C18 : 0 and C18 : 2ω6,9c. No respiratory quinones were detected. In contrast to F. plautii JCM 32125T, strain 3BBH22T did not degrade quercetin, one of the flavonoids. P. capillosus JCM 32126T also did not. Strain 3BBH22T was differentiated from P. capillosus JCM 32126T by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22T represents a novel species in a novel genus of the family Ruminococcaceae, for which the name Lawsonibacter asaccharolyticus gen. nov., sp. nov. is proposed. The type strain of L. asaccharolyticus is 3BBH22T (=JCM 32166T=DSM 106493T).
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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 Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Sakamoto M, Iino T, Hamada M, Ohkuma M. Parolsenella catena gen. nov., sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1165-1172. [PMID: 29458507 DOI: 10.1099/ijsem.0.002645] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain 2CBEGH3T, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3T represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084T (93.6 % sequence similarity), Olsenella umbonata strain lac31T (93.0 %), Olsenella profusa JCM 14553T (92.7 %) and Olsenella scatoligenes strain SK9K4T (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1-84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3T. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94-98 : 2-6. The isolate formed characteristic crater-like colonies on Eggerth-Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3T represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3T (=JCM 31932T=DSM 105194T).
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriya Ohkuma
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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50
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Yuki M, Sakamoto M, Nishimura Y, Ohkuma M. Lactococcus reticulitermitis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Int J Syst Evol Microbiol 2018; 68:596-601. [DOI: 10.1099/ijsem.0.002549] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Masahiro Yuki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Yuki Nishimura
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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