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Volume 69, Issue 3

Parabacteroides acidifaciens sp. nov., isolated from human faeces Free

Abstract

A polyphasic taxonomic approach was applied to characterize an anaerobic bacterial strain, 426-9, that was isolated from human faeces. The strain was Gram-stain-negative, non-motile, non-spore-forming, non-pigmented and rod-shaped. Strain 426-9 grew anaerobically at 20–45 °C (optimally at 37–40 °C) and at pH 6.0–10.0 (optimally at pH 6.0–8.0). The major polar lipids were phosphatidylethanolamine, seven amino phospholipids and three phospholipids. The major fatty acids of strain 426-9 were anteiso-C15 : 0 and iso-C17 : 0 3-OH, and the predominant respiratory quinones were menaquinones MK-9 and MK-10. End-products of glucose fermentation were acetate, propionate, iso-butyrate and iso-pentanoate. 16S rRNA gene sequence analysis showed that strain 426-9 was a member of the genus Parabacteroides . The level of 16S rRNA gene sequence similarity of strain 426-9 to the type species of the genus, Parabacteroides distasonis ATCC 8503, was 91.0 %. Within the genus Parabacteroides , strain 426-9 was phylogenetically closely related to Parabacteroides johnsonii M-165 (96.0 % 16S rRNA gene sequence similarity). The draft genome of strain 426-9 comprised 5.15 Mb with a DNA G+C content of 45.9 mol%. A total of 4088 genes were predicted and, of those, 3744 were annotated. On the basis of phenotypic, chemotaxonomic and phylogenetic characterization, strain 426-9 represents a novel species within the genus Parabacteroides , for which the name Parabacteroides acidifaciens sp. nov. is proposed. The type strain is 426-9 (=CGMCC 1.13558=NBRC 113433).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): faeces , human intestinal microbiota , Parabacteroides acidifaciens and strain 426-9T
© 2019 IUMS
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2019-01-17
2024-04-26
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References

  1. Sakamoto M, Benno Y. Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 2006; 56:1599–1605 [View Article][PubMed]
     [Google Scholar]
  2. Momose Y, Park SH, Miyamoto Y, Itoh K. Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota. J Appl Microbiol 2011; 111:176–184 [View Article][PubMed]
     [Google Scholar]
  3. Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M et al. Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill. Int J Syst Evol Microbiol 2012; 62:2613–2617 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  5. Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML et al. "Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin. J Clin Microbiol 2005; 43:4522–4527 [View Article][PubMed]
     [Google Scholar]
  6. Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M et al. Parabacteroides gordonii sp. nov., isolated from human blood cultures. Int J Syst Evol Microbiol 2009; 59:2843–2847 [View Article][PubMed]
     [Google Scholar]
  7. Sakamoto M, Kitahara M, Benno Y. Parabacteroides johnsonii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007; 57:293–296 [View Article][PubMed]
     [Google Scholar]
  8. Johnson JL, Moore WEC, Moore LVH. Bacteroides caccae sp. nov., Bacteroides merdae sp. nov., and Bacteroides stercoris sp. nov. isolated from human feces. Int J Syst Bacteriol 1986; 36:499–501 [View Article]
     [Google Scholar]
  9. Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H et al. Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces. Int J Syst Evol Microbiol 2013; 63:3470–3474 [View Article][PubMed]
     [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 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. 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 [View Article][PubMed]
     [Google Scholar]
  13. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evo 1987; 4:406–425
     [Google Scholar]
  14. Felsenstein J. Package phylip―phylogeny Inference. Version 3.2. Cladistics 1989; 5:163–166
     [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  17. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
     [Google Scholar]
  18. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  19. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  21. Yoon SH, Min HS, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286
     [Google Scholar]
  22. Hucker GJ. A new modification and application of. J Bacteriol 1920; 6:395–397
     [Google Scholar]
  23. Cerny G. Studies on the aminopeptidase test for the distinction of gram-negative from gram-positive bacteria. Eur J of Applied Microbiol Biotechnol 1978; 5:113–122 [View Article]
     [Google Scholar]
  24. Shah HN. The genus Bacteroides and related taxa. In Edited by Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed. New York: Springer; 1992 pp. 3593–3607
     [Google Scholar]
  25. Wang K, Bao L, Ma K, Zhang J, Chen B et al. A novel class of α-glucosidase and HMG-CoA reductase inhibitors from Ganoderma leucocontextum and the anti-diabetic properties of ganomycin I in KK-Ay mice. Eur J Med Chem 2017; 127:1035–1046 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Tech Note 2001; 101:1–6
     [Google Scholar]
  28. 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]
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Parabacteroides acidifaciens sp. nov., isolated from human faeces
Int J Syst Evol Microbiol 69, 761 (2019); https://doi.org/10.1099/ijsem.0.003230
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