1887

Abstract

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 strains (BCRC 81047=ATCC 27768, A2-165=JCM 31915, APC918/95b=JCM 39207, APC942/30−2=JCM 39208, APC924/119=JCM 39209 and APC922/41−1=JCM 39210) deposited in public culture collections with two reference strains of JCM 39212 and JCM 39211. sp. JCM 17207 isolated from caecum of broiler chicken was also included. Three strains of (BCRC 81047, 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 (JCM 31915, JCM 39208 and JCM 39210) 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 JCM 39211, whereas JCM 31915, JCM 39210 and JCM 17207 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 strains. Based on the collected data, JCM 31915, JCM 39210 and sp. JCM 17207 represent three novel species of the genus , for which the names sp. nov. (type strain JCM 31915=DSM 17677=A2-165), sp. nov. (type strain JCM 39210=DSM 107841=APC922/41-1) and sp. nov. (type strain JCM 17207=DSM 23680=ic1379) are proposed.

Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award 20K05792)
    • Principle Award Recipient: AkihitoEndo
  • Japan Society for the Promotion of Science (Award 19H05679)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Society for the Promotion of Science (Award JP21J11100)
    • Principle Award Recipient: HirokiTanno
  • Japan Agency for Medical Research and Development (Award JP21ae0121035)
    • Principle Award Recipient: MitsuoSakamoto
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005379
2022-04-13
2024-05-27
Loading full text...

Full text loading...

References

  1. 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]
  2. Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J 2017; 11:841–852 [View Article] [PubMed]
    [Google Scholar]
  3. Zou Y, Lin X, Xue W, Tuo L, Chen M-S et al. Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces. Sci Rep 2021; 11:11340 [View Article]
    [Google Scholar]
  4. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71:004943
    [Google Scholar]
  5. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71:005096
    [Google Scholar]
  6. Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJM, Garcia-Gil LJ et al. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 2012; 78:420–428 [View Article] [PubMed]
    [Google Scholar]
  7. Benevides L, Burman S, Martin R, Robert V, Thomas M et al. New insights into the diversity of the genus Faecalibacterium. Front Microbiol 2017; 8:1790 [View Article]
    [Google Scholar]
  8. Tanno H, Maeno S, Salminen S, Gueimonde M, Endo A. 16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis. FEMS Microbiol Ecol 2022; 98:fiac004 [View Article] [PubMed]
    [Google Scholar]
  9. Fitzgerald CB, Shkoporov AN, Sutton TDS, Chaplin AV, Velayudhan V et al. Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa. BMC Genomics 2018; 19:931 [View Article] [PubMed]
    [Google Scholar]
  10. Oren A, Garrity GM. On neotypes and nomina nova: commentary on “Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa”, by C.B. Fitzgerald et al. (BMC Genomics (2018) 19:931). BMC Genomics 2020; 21:335 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. Stecher G, Tamura K, Kumar S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol Biol Evol 2020; 37:1237–1239 [View Article] [PubMed]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  18. Endo A, Okada S. Lactobacillus satsumensis sp. nov., isolated from mashes of shochu, a traditional Japanese distilled spirit made from fermented rice and other starchy materials. Int J Syst Evol Microbiol 2005; 55:83–85 [View Article] [PubMed]
    [Google Scholar]
  19. Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2020; 27:dsaa014 [View Article] [PubMed]
    [Google Scholar]
  20. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  23. Yoon SH, Ha SM, Lim JM, Kwon SJ, 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]
  24. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219–1227 [View Article]
    [Google Scholar]
  27. McClung LS, Lindberg RB. The study of obligately anaerobic bacteria. In Pelczar MJ. eds Manual of Microbiological Methods New York: McGraw-Hill; 1957 pp 120–139
    [Google Scholar]
  28. Miyazaki K, Martin JC, Marinsek-Logar R, Flint HJ. Degradation and utilization of xylans by the rumen anaerobe Prevotella bryantii (formerly P. ruminicola subsp. brevis) B(1)4. Anaerobe 1997; 3:373–381 [View Article]
    [Google Scholar]
  29. Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma M. Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Int J Syst Evol Microbiol 2015; 65:681–685 [View Article] [PubMed]
    [Google Scholar]
  30. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  31. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005379
Loading
/content/journal/ijsem/10.1099/ijsem.0.005379
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error