1887

Abstract

Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus belonging to the family in the phylum , were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24 and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to ‘’ ph8 (99.73 %). Group II (strain 5CPEGH6) was related to WAL 8301 (96.82 %). Ten strains of group III (3BBH6, 5CPYCFAH4, 5NYCFAH2 and others) were related to DSM 19147 (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6 could be differentiated from JCM 16773 by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of JCM 16771. Strains 5CBH24, 6CPBBH3 and ‘’ ph8 shared 98.8–98.9 % average nucleotide identity (ANI) with each other. In addition, the DNA–DNA hybridization (DDH) values among three strains were 86.7–89.4 %. Strain 5CPEGH6 showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6, 5CPYCFAH4 and 5NYCFAH2) shared 97.9–99.9% ANI with each other. These three strains showed 96.9–97.3 % ANI with DSM 19147. The DDH values of strains 3BBH6, 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5–99.8 %, while those compared to DSM 19147 were 71.0–73.4 %. On the basis of the collected data, three novel species, sp. nov. (5CBH24=JCM 32850=DSM 108979), sp. nov. (5CPEGH6=JCM 32848=DSM 108978) and subsp. subsp. nov. (3BBH6=JCM 32839=DSM 108977), are proposed.

Keyword(s): Alistipes , quinone , hsp60 and human faeces
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003778
2019-10-21
2019-11-22
Loading full text...

Full text loading...

References

  1. Kitahara M, Sakamoto M, Ike M, Sakata S, Benno Y. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2005;55: 2143– 2147 [CrossRef]
    [Google Scholar]
  2. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides intestinalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006;56: 151– 154 [CrossRef]
    [Google Scholar]
  3. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides finegoldii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006;56: 931– 935 [CrossRef]
    [Google Scholar]
  4. Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno Y et al. Bacteroides dorei sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006;56: 1639– 1643 [CrossRef]
    [Google Scholar]
  5. Hayashi H, Shibata K, Bakir MA, Sakamoto M, Tomita S et al. Bacteroides coprophilus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007;57: 1323– 1326 [CrossRef]
    [Google Scholar]
  6. Hugon P, Ramasamy D, Lagier J-C, Rivet R, Couderc C et al. Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci 2013;7: 427– 439 [CrossRef]
    [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
    [Google Scholar]
  8. Yoon SH, SM H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017;67: 1613– 1617
    [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 [CrossRef]
    [Google Scholar]
  10. 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]
    [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
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [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]
    [Google Scholar]
  16. Sakamoto M, Suzuki N, Benno Y. hsp 60 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]
    [Google Scholar]
  17. Ogata Y, Suda W, Ikeyama N, Hattori M, Ohkuma M et al. Complete Genome Sequence of Phascolarctobacterium faecium JCM 30894, a Succinate-Utilizing Bacterium Isolated from Human Feces. Microbiol Resour Announc 2019;8: e01487– 18 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. 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 [CrossRef]
    [Google Scholar]
  20. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57: 81– 91 [CrossRef]
    [Google Scholar]
  21. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014;9: 2 [CrossRef]
    [Google Scholar]
  22. 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
    [Google Scholar]
  23. 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]
    [Google Scholar]
  24. 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]
  25. Shah HN. The genus Bacteroides and related taxa In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. eds The Prokaryotes, 2nd ed. New York: Springer; 1992; pp 3593– 3607
    [Google Scholar]
  26. Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R. Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces. Int J Syst Evol Microbiol 2010;60: 1296– 1302 [CrossRef]
    [Google Scholar]
  27. Rautio M, Eerola E, Väisänen-Tunkelrott M-L, Molitoris D, Lawson P et al. Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Syst Appl Microbiol 2003;26: 182– 188 [CrossRef]
    [Google Scholar]
  28. Shkoporov AN, Chaplin AV, Khokhlova EV, Shcherbakova VA, Motuzova OV et al. Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2015;65: 4580– 4588 [CrossRef]
    [Google Scholar]
  29. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  30. Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma M et al. Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Int J Syst Evol Microbiol 2015;65: 681– 685 [CrossRef]
    [Google Scholar]
  31. Song Y, Könönen E, Rautio M, Liu C, Bryk A et al. Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin. Int J Syst Evol Microbiol 2006;56: 1985– 1990 [CrossRef]
    [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 [CrossRef]
    [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
    [Google Scholar]
  34. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37: 911– 917 [CrossRef]
    [Google Scholar]
  35. 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.0.003778
Loading
/content/journal/ijsem/10.1099/ijsem.0.003778
Loading

Data & Media loading...

Supplements

Supplementary material 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