sp. nov., isolated from human faeces Free

Abstract

A strictly anaerobic predominant bacterium, designated as strain gm001, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001 was identified as a member of the genus , and a comparison of 16S rRNA and gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of . Phylogenomic tree analysis indicated that the gm001 cluster is an independent lineage of DSM 18205. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001 and DSM 18205 were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C, C and iso-C. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is gm001 (=BCRC 81118=JCM 33280).

Funding
This study was supported by the:
  • Japan Agency for Medical Research and Development (Award JP19gm6010007)
    • Principle Award Recipient: Mitsuo Sakamoto
  • Ministry of Economic Affairs (Award Project No. 109-EC-17-A-22–0525)
    • Principle Award Recipient: Jong-Shian Liou
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004342
2020-07-22
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4767.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004342&mimeType=html&fmt=ahah

References

  1. Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides . Int J Syst Bacteriol 1990; 40:205–208 [View Article][PubMed]
    [Google Scholar]
  2. Alauzet C, Marchandin H, Lozniewski A. New insights into Prevotella diversity and medical microbiology. Future Microbiol 2010; 5:1695–1718 [View Article][PubMed]
    [Google Scholar]
  3. Ueki A, Akasaka H, Satoh A, Suzuki D, Ueki K. Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil. Int J Syst Evol Microbiol 2007; 57:1803–1809 [View Article][PubMed]
    [Google Scholar]
  4. Nakata H, Kanda H, Nakakita Y, Kaneko T, Tsuchiya Y. Prevotella cerevisiae sp. nov., beer-spoilage obligate anaerobic bacteria isolated from brewery wastewater. Int J Syst Evol Microbiol 2019; 69:1789–1793 [View Article][PubMed]
    [Google Scholar]
  5. Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 2017; 151:363–374 [View Article][PubMed]
    [Google Scholar]
  6. Fernández-Veledo S, Vendrell J. Gut microbiota-derived succinate: friend or foe in human metabolic diseases?. Rev Endocr Metab Disord 2019; 20:439–447 [View Article][PubMed]
    [Google Scholar]
  7. Precup G, Vodnar D-C. Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: a comprehensive literature review. Br J Nutr 2019; 122:131–140 [View Article][PubMed]
    [Google Scholar]
  8. De Vadder F, Kovatcheva-Datchary P, Zitoun C, Duchampt A, Bäckhed F et al. Microbiota-produced succinate improves glucose homeostasis via intestinal gluconeogenesis. Cell Metab 2016; 24:151–157 [View Article][PubMed]
    [Google Scholar]
  9. Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BAH et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016; 535:376–381 [View Article][PubMed]
    [Google Scholar]
  10. Alpizar-Rodriguez D, Lesker TR, Gronow A, Gilbert B, Raemy E et al. Prevotella copri in individuals at risk for rheumatoid arthritis. Ann Rheum Dis 2019; 78:590–593 [View Article][PubMed]
    [Google Scholar]
  11. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R et al. The human microbiome project. Nature 2007; 449:804–810 [View Article][PubMed]
    [Google Scholar]
  12. Bilen M, Dufour J-C, Lagier J-C, Cadoret F, Daoud Z et al. The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species. Microbiome 2018; 6:94 [View Article][PubMed]
    [Google Scholar]
  13. Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ et al. 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]
  14. Huang C-H, Liou J-S, Lee A-Y, Tseng M, Miyashita M et al. Polyphasic characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: Description of L. chiayiensis sp. nov. Syst Appl Microbiol 2018; 41:270–278 [View Article][PubMed]
    [Google Scholar]
  15. Goh SH, Potter S, Wood JO, Hemmingsen SM, Reynolds RP et al. HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. J Clin Microbiol 1996; 34:818–823 [View Article][PubMed]
    [Google Scholar]
  16. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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]
  17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  20. Chor B, Hendy MD, Snir S. Maximum likelihood Jukes-Cantor triplets: analytic solutions. Mol Biol Evol 2006; 23:626–632 [View Article][PubMed]
    [Google Scholar]
  21. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. 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 [View Article][PubMed]
    [Google Scholar]
  24. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  25. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article][PubMed]
    [Google Scholar]
  26. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F-J et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154 [View Article][PubMed]
    [Google Scholar]
  27. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  32. Lin S-T, Wang L-T, Wu Y-C, Guu J-RJ, Tamura T et al. Weissella muntiaci sp. nov., isolated from faeces of Formosan barking deer (Muntiacus reevesi). Int J Syst Evol Microbiol 2020; 70:1578–1584 [View Article][PubMed]
    [Google Scholar]
  33. Barrow GI, Feltham RK. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. London: Cambridge University Press; 1993
    [Google Scholar]
  34. Chern L-L, Stackebrandt E, Lee S-F, Lee F-L, Chen J-K et al. Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan. Int J Syst Evol Microbiol 2004; 54:1387–1391 [View Article][PubMed]
    [Google Scholar]
  35. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  36. 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]
  37. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  38. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  39. Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007; 57:941–946 [View Article][PubMed]
    [Google Scholar]
  40. Sakamoto M, Suzuki M, Huang Y, Umeda M, Ishikawa I et al. Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2004; 54:877–883 [View Article][PubMed]
    [Google Scholar]
  41. Shah HN, Collins MD, Watabe J, Mitsuoka T. Bacteroides oulorum sp. nov., a nonpigmented saccharolytic species from the oral cavity. Int J Syst Bacteriol 1985; 35:193–197 [View Article]
    [Google Scholar]
  42. Downes J, Hooper SJ, Wilson MJ, Wade WG. Prevotella histicola sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2008; 58:1788–1791 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004342
Loading
/content/journal/ijsem/10.1099/ijsem.0.004342
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed