1887

Abstract

A strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4–2.1×0.5–0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31 formed a distinct phylogenetic lineage that reflects a new genus within cluster XIVa in the family , with highest similarity to DSM 3982 (94.6 %). The DNA G+C content was calculated to be 47.0 mol% from whole genome sequencing. Predicted genes associated with synthesis of teichuronic acid, polyamines, polar lipids and diaminopimelic acid were detected. The peptidoglycan contained -diaminopimelic acid and the main polar lipid detected was phosphatidylglycerol. The major metabolic end product of glucose was acetic acid, which was in agreement with those of most members of the family. However, the profile of major cellular fatty acids (C, C, summed feature 4 and C) and overall enzyme activity demonstrated phenotypic differentiation of strain BR31 from other closely related genera. Thus, based on distinct phenotypic, phylogenetic, genotypic and chemotaxonomic characteristics, strain BR31 is considered to represent a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is BR31 (=KCTC 15482=JCM 30748).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001977
2017-07-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/7/2430.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001977&mimeType=html&fmt=ahah

References

  1. Hooper LV, Macpherson AJ. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol 2010; 10:159–169 [View Article][PubMed]
    [Google Scholar]
  2. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915–1920 [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. 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]
  5. Brestoff JR, Artis D. Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol 2013; 14:676–684 [View Article][PubMed]
    [Google Scholar]
  6. Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013; 504:451–455 [View Article][PubMed]
    [Google Scholar]
  7. Duncan SH, Hold GL, Harmsen HJ, 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]
  8. 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]
  9. Kim OS, Cho YJ, Lee K, Yoon SH, 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]
  10. Jeon YS, Lee K, Park SC, Kim BS, Cho YJ 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]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  13. Sohpal VK, Dey A, Singh A. MEGA biocentric software for sequence and phylogenetic analysis: a review. Int J Bioinform Res Appl 2010; 6:230–240 [View Article][PubMed]
    [Google Scholar]
  14. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism vol. 3 New York: Academic Press; 1969 pp. 21–132 [CrossRef]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  16. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19:1572–1574 [View Article][PubMed]
    [Google Scholar]
  17. Holdeman LV, Cato EP, Moore W. Eubacterium contortum (Prévot) comb. nov.: emendation of description and designation of the type strain. Int J Syst Evol Microbiol 1971; 21:304–306
    [Google Scholar]
  18. Kitahara M, Takamine F, Imamura T, Benno Y. Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7α-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2000; 50:971–978 [View Article][PubMed]
    [Google Scholar]
  19. Holdeman LV, Moore WEC. New genus, Coprococcus, twelve new species, and emended descriptions of four previously described species of bacteria from human feces. Int J Syst Bacteriol 1974; 24:260–277 [View Article]
    [Google Scholar]
  20. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  21. Kim M, Oh HS, Park SC, 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]
  22. Wayne LG, Brenner D, Colwell R, Grimont P, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [CrossRef]
    [Google Scholar]
  26. Holdeman L, Cato E, Moore W. Anaerobic Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  27. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505:559–563 [View Article][PubMed]
    [Google Scholar]
  28. Tindall BJ, Rosselló-Móra R, Busse HJ, 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]
  29. 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]
  30. Morris GN, Winter J, Cato EP, Ritchie AE, Bokkenheuser VD. Clostridium scindens sp. nov., a human intestinal bacterium with desmolytic activity on corticoids. Int J Syst Bacteriol 1985; 35:478–481 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001977
Loading
/content/journal/ijsem/10.1099/ijsem.0.001977
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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