1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Zenner . 2021 as comb. nov. No Access

Abstract

Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14 showed the highest 16S rRNA gene sequence similarity to Cla-CZ-80 (97.5 %) and ‘’ Marseille-P3177 (97.2 %). Strain 12BBH14 was also closely related to sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with sp. c-25. Near this monophyletic cluster, Cla-CZ-80 and ‘ Marseille-P3177 formed a cluster and did not form a cluster with other species. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14, 9CFEGH4, 10CPCBH12 and 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 . Based on the collected data, strains 12BBH14, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is 12BBH14 (=JCM 35899=DSM 115701). sp. c-25 belongs to . In addition, is transferred to the genus as comb. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bile acid 7α-dehydroxylating bacteria , Claveliimonas , deoxycholic acid , human faeces and secondary bile acid
Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award 19H05689)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Agency for Medical Research and Development (Award JP22ae0121035)
    • Principle Award Recipient: MitsuoSakamoto
  • Japan Agency for Medical Research and Development (Award JP19gm6010007)
    • Principle Award Recipient: MitsuoSakamoto
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006030
2023-09-21
2024-04-29
Loading full text...

Full text loading...

References

  1. Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S et al. Comparative genomic and physiological analysis against Clostridium scindens reveals Eubacterium sp. c-25 as an atypical deoxycholic acid producer of the human gut microbiota. Microorganisms 2021; 9:2254 [View Article] [PubMed]
     [Google Scholar]
  2. McGarr SE, Ridlon JM, Hylemon PB. Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. J Clin Gastroenterol 2005; 39:98–109 [PubMed]
     [Google Scholar]
  3. Cao H, Xu M, Dong W, Deng B, Wang S et al. Secondary bile acid-induced dysbiosis promotes intestinal carcinogenesis. Int J Cancer 2017; 140:2545–2556 [View Article] [PubMed]
     [Google Scholar]
  4. Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S et al. Early-life immune system maturation in chickens using a synthetic community of cultured gut bacteria. mSystems 2021; 6:e01300-20 [View Article] [PubMed]
     [Google Scholar]
  5. Brahimi S, Cadoret F, Fournier PE, Moal V, Raoult D. ‘Lachnoclostridium urinimassiliense’ sp. nov. and ‘Lachnoclostridium phocaeense’ sp. nov., two new bacterial species isolated from human urine after kidney transplantation. New Microbes New Infect 2017; 16:73–75
     [Google Scholar]
  6. Hisatomi A, Ohkuma M, Sakamoto M. Sellimonas catena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73:005853 [View Article] [PubMed]
     [Google Scholar]
  7. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. 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]
  10. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  11. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon S-H, Ha S-M, Lim JM, 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]
  16. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  17. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  20. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
     [Google Scholar]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  22. Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 2020; 21:180 [View Article] [PubMed]
     [Google Scholar]
  23. de Luca G, de Philip P, Rousset M, Belaich JP, Dermoun Z. The NADP-reducing hydrogenase of Desulfovibrio fructosovorans: evidence for a native complex with hydrogen-dependent methyl-viologen-reducing activity. Biochem Biophys Res Commun 1998; 248:591–596 [View Article] [PubMed]
     [Google Scholar]
  24. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012; 28:464–469 [View Article] [PubMed]
     [Google Scholar]
  25. Solovyev V, Salamov A. Automatic annotation of microbial genomes and metagenomic sequences. In Li RW. ed Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies New York: Nova Science Publishers; 2011 pp 61–78
     [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] [PubMed]
     [Google Scholar]
  27. 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]
  28. McClung LS, Lindberg RB. The study of obligately anaerobic bacteria. In Pelczar MJ. ed Manual of Microbiological Methods New York: McGraw-Hill; 1957 pp 120–139
     [Google Scholar]
  29. Tawthep S, Fukiya S, Lee J-Y, Hagio M, Ogura Y et al. Isolation of six novel 7-oxo- or urso-type secondary bile acid-producing bacteria from rat cecal contents. J Biosci Bioeng 2017; 124:514–522 [View Article] [PubMed]
     [Google Scholar]
  30. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
     [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006030
Loading
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 73, 006030 (2023); https://doi.org/10.1099/ijsem.0.006030
/content/journal/ijsem/10.1099/ijsem.0.006030
/content/journal/ijsem/10.1099/ijsem.0.006030
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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