1887

Abstract

A bacterial strain designated L2-7, phylogenetically related to Eubacterium hallii DSM 3353, was previously isolated from infant faeces. The complete genome of strain L2-7 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 3319 (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7 to be a novel species, related to type strain E. hallii DSM 3353. The experimentally observed DNA–DNA hybridization value between strain L2-7 and E. hallii DSM 3353 was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7 was 38.6 mol%. The major fatty acids were C16 : 0, C16 : 1 cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7 had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353 (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353. Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353 is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353=ATCC 27751) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7 should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7 (=DSM 17630=KCTC 15707).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003041
2018-10-23
2019-12-09
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/12/3741.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003041&mimeType=html&fmt=ahah

References

  1. Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS et al. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol 2000;66:1654–1661 [CrossRef][PubMed]
    [Google Scholar]
  2. Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 2004;70:5810–5817 [CrossRef][PubMed]
    [Google Scholar]
  3. Engels C, Ruscheweyh HJ, Beerenwinkel N, Lacroix C, Schwab C. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation. Front Microbiol 2016;7:713 [CrossRef][PubMed]
    [Google Scholar]
  4. Udayappan S, Manneras-Holm L, Chaplin-Scott A, Belzer C, Herrema H et al. Oral treatment with Eubacterium hallii improves insulin sensitivity in db/db mice. NPJ Biofilms Microbiomes 2016;2:16009 [CrossRef][PubMed]
    [Google Scholar]
  5. Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev 2017;41:182–199 [CrossRef][PubMed]
    [Google Scholar]
  6. Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylum Firmicutes. In Bergey’s Manual® of Systematic Bacteriology Springer-Verlag, New York: Springer; 2009; pp.1–13
    [Google Scholar]
  7. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2012;40:D13–D25 [CrossRef][PubMed]
    [Google Scholar]
  8. Shetty SA, Ritari J, Paulin L, Smidt H, de Vos WM. Complete genome sequence of Eubacterium hallii strain L2-7. Genome Announc 2017;5:e01167-17 [CrossRef][PubMed]
    [Google Scholar]
  9. Allen-Vercoe E, Daigneault M, White A, Panaccione R, Duncan SH et al. Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976. Anaerobe 2012;18:523–529 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014;9:111–118
    [Google Scholar]
  12. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005;21:2329–2335 [CrossRef][PubMed]
    [Google Scholar]
  13. Wade WG. The genus Eubacterium and related genera. In The prokaryotes New York, NY: Springer; 2006; pp.823–835
    [Google Scholar]
  14. Jarzembowska M, Sousa DZ, Beyer F, Zwijnenburg A, Plugge CM et al. Lachnotalea glycerini gen. nov., sp. nov., an anaerobe isolated from a nanofiltration unit treating anoxic groundwater. Int J Syst Evol Microbiol 2016;66:774–779 [CrossRef][PubMed]
    [Google Scholar]
  15. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. Bergey's Manual of Systematic Bacteriologyvol. 3, The Firmicutes New York, NY: Springer Science & Business Media; 2011
    [Google Scholar]
  16. Dworkin M. The Prokaryotes: Vol. 4: Bacteria: Firmicutes, Cyanobacteria New York, NY: Springer Science & Business Media; 2006
    [Google Scholar]
  17. Kuykendall L, Roy M, O'Neill J, Devine T. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988;38:358–361
    [Google Scholar]
  18. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42:989–1005 [CrossRef]
    [Google Scholar]
  19. 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[PubMed]
    [Google Scholar]
  20. Schumann P. Peptidoglycan structure. Methods Microbiol 2011;38:101–129
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Moore WE, Holdeman LV. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl Microbiol 1974;27:961–979[PubMed]
    [Google Scholar]
  23. Holdeman LV, Moore W. New genus, Coprococcus, twelve new species, and emended descriptions of four previously described species of bacteria from human feces. Int J Syst Evol Microbiol 1974;24:260–277
    [Google Scholar]
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003041
Loading
/content/journal/ijsem/10.1099/ijsem.0.003041
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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