1887

Abstract

Strain 2CBEGH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3 represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084 (93.6 % sequence similarity), Olsenella umbonata strain lac31 (93.0 %), Olsenella profusa JCM 14553 (92.7 %) and Olsenella scatoligenes strain SK9K4 (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1–84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94–98 : 2–6. The isolate formed characteristic crater-like colonies on Eggerth–Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3 represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3 (=JCM 31932=DSM 105194).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002645
2018-02-15
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/4/1165.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002645&mimeType=html&fmt=ahah

References

  1. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. Diversity of the human intestinal microbial flora. Science 2005; 308: 1635– 1638 [CrossRef] [PubMed]
    [Google Scholar]
  2. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59– 65 [CrossRef] [PubMed]
    [Google Scholar]
  3. Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas. Int J Syst Evol Microbiol 2014; 64: 2992– 2997 [CrossRef] [PubMed]
    [Google Scholar]
  4. Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Parabacteroides faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2015; 65: 1342– 1346 [CrossRef] [PubMed]
    [Google Scholar]
  5. 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]
  6. Gupta RS, Chen WJ, Adeolu M, Chai Y. Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int J Syst Evol Microbiol 2013; 63: 3379– 3397 [CrossRef] [PubMed]
    [Google Scholar]
  7. 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 [CrossRef] [PubMed]
    [Google Scholar]
  8. McClung LS, Lindberg RB. The study of obligately anaerobic bacteria. In Pelczar MJ. (editor) Mannual of Microbiological Methods New York: McGraw-Hill; 1957; pp. 120– 139
    [Google Scholar]
  9. Shah HN. The genus Bacteroides and related taxa. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed. New York: Springer; 1992; pp. 3593– 3607 [Crossref]
    [Google Scholar]
  10. 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 [CrossRef] [PubMed]
    [Google Scholar]
  11. 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 [CrossRef] [PubMed]
    [Google Scholar]
  12. 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 [CrossRef] [PubMed]
    [Google Scholar]
  13. 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]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  15. Sakamoto M, Ohkuma M. Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 2010; 59: 1293– 1302 [CrossRef] [PubMed]
    [Google Scholar]
  16. Sakamoto M, Suzuki N, Benno Y. hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes. Int J Syst Evol Microbiol 2010; 60: 2984– 2990 [CrossRef] [PubMed]
    [Google Scholar]
  17. Bilen M, Cadoret F, Fournier PE, Daoud Z, Raoult D. "Libanicoccus massiliensis" gen. nov., sp. nov., a new bacterium isolated from a stool sample from a pygmy woman. New Microbes New Infect 2017; 15: 40– 41 [CrossRef] [PubMed]
    [Google Scholar]
  18. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  19. 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 [CrossRef] [PubMed]
    [Google Scholar]
  20. Li X, Jensen RL, Højberg O, Canibe N, Jensen BB. Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces. Int J Syst Evol Microbiol 2015; 65: 1227– 1233 [CrossRef] [PubMed]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. 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]
  23. Dewhirst FE, Paster BJ, Tzellas N, Coleman B, Downes J et al. Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int J Syst Evol Microbiol 2001; 51: 1797– 1804 [CrossRef] [PubMed]
    [Google Scholar]
  24. Clavel T, Lepage P, Charrier C. The family Coriobacteriaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes – Actinobacteria, 4th ed. Berlin Heidelberg: Springer-Verlag; 2014; pp. 201– 238
    [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. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1975; 47: 87– 95 [CrossRef]
    [Google Scholar]
  27. Dittmer JC, Lester RL. A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1964; 5: 126– 127 [PubMed]
    [Google Scholar]
  28. Akasaka H, Ueki A, Hanada S, Kamagata Y, Ueki K. Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil. Int J Syst Evol Microbiol 2003; 53: 1991– 1998 [CrossRef] [PubMed]
    [Google Scholar]
  29. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25: 125– 128 [CrossRef]
    [Google Scholar]
  30. Collins MD, Wallbanks S. Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium. FEMS Microbiol Lett 1992; 74: 235– 240 [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002645
Loading
/content/journal/ijsem/10.1099/ijsem.0.002645
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