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Volume 71, Issue 1

sp. nov., isolated from human faeces Free

Abstract

An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386 was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0–2.5×0.6–0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386 was within the family . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386 was (95.6 %), followed by (94.8 %), (94.8 %) and (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386 had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C and C. Compared to those of the closely related species, strain SNUG30386 showed distinct biochemical activities such as being unable to utilize most of carbon sources except -glucose and -arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain of the novel species is SNUG30386 (=KCTC 15633= JCM 32258).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Clostridium cluster XIVa , gut microbiome and Lachnospiraceae
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2012H1A2A1049234)
    • Principle Award Recipient: BoramSeo
  • National Research Foundation of Korea (Award 2018R1A2A1A05078258)
    • Principle Award Recipient: GwangPyoKo
© 2021 The Authors
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2020-11-30
2024-04-25
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References

  1. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV et al. Current understanding of the human microbiome. Nat Med 2018; 24:392–400 [View Article][PubMed]
     [Google Scholar]
  2. Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 2016; 14:20–32 [View Article][PubMed]
     [Google Scholar]
  3. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA et al. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533:543–546 [View Article][PubMed]
     [Google Scholar]
  4. Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013; 504:446–450 [View Article][PubMed]
     [Google Scholar]
  5. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 2009; 294:1–8 [View Article][PubMed]
     [Google Scholar]
  6. Lagier J-C, Dubourg G, Million M, Cadoret F, Bilen M et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol 2018; 16:540–550 [View Article]
     [Google Scholar]
  7. Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 2016; 1:1–8 [View Article][PubMed]
     [Google Scholar]
  8. Yutin N, Galperin MY. A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 2013; 15:n/a–2641 [View Article][PubMed]
     [Google Scholar]
  9. Haas KN, Blanchard JL. Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. Int J Syst Evol Microbiol 2020; 70:23–34 [View Article][PubMed]
     [Google Scholar]
  10. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826 [View Article][PubMed]
     [Google Scholar]
  11. Finegold SM, Song Y, Liu C. Taxonomy--General comments and update on taxonomy of clostridia and anaerobic cocci. Anaerobe 2002; 8:283–285 [View Article][PubMed]
     [Google Scholar]
  12. Rainey FA, Family V. Lachnospiraceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology 3 New York: Springer; 2009 pp 921–968
     [Google Scholar]
  13. Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:2141–2146 [View Article][PubMed]
     [Google Scholar]
  14. Wrzosek L, Miquel S, Noordine M-L, Bouet S, Joncquel Chevalier-Curt M et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol 2013; 11:61 [View Article][PubMed]
     [Google Scholar]
  15. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article][PubMed]
     [Google Scholar]
  16. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  17. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article][PubMed]
     [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  22. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19:1572–1574 [View Article][PubMed]
     [Google Scholar]
  23. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article][PubMed]
     [Google Scholar]
  24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
     [Google Scholar]
  25. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  26. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  27. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  28. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  29. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
     [Google Scholar]
  30. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using diamond. Nat Methods 2015; 12:59–60 [View Article][PubMed]
     [Google Scholar]
  31. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  32. Adams JL, Battjes CJ, Buthala DA. Biological specimen preparation for SEM by a method other than critical point drying. In Bailey GW. editor Proceedings of the 45th Annual Meeting of the Electron Microscopy Society of America 45 San Francisco: San Francisco Press; 1987956–957 [View Article]
     [Google Scholar]
  33. Seo B, Jeon K, Baek I, Lee YM, Baek K et al. Faecalibacillus intestinalis gen. nov., sp. nov. and Faecalibacillus faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:2120–2128 [View Article][PubMed]
     [Google Scholar]
  34. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  35. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  36. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  37. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  38. Kobayashi H, Nakasato T, Sakamoto M, Ohtani Y, Terada F et al. Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage. Int J Syst Evol Microbiol 2017; 67:4974–4978 [View Article][PubMed]
     [Google Scholar]
  39. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
     [Google Scholar]
  40. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
     [Google Scholar]
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Clostridium fessum sp. nov., isolated from human faeces
Int J Syst Evol Microbiol 71, 004579 (2020); https://doi.org/10.1099/ijsem.0.004579
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