1887

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).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003230
2019-01-17
2019-10-18
Loading full text...

Full text loading...

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 [CrossRef][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 [CrossRef][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 [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. 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 [CrossRef][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 [CrossRef][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 [CrossRef][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 [CrossRef]
    [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 [CrossRef][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 [CrossRef][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 [CrossRef][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 [CrossRef][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 [CrossRef]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  18. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef][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 [CrossRef][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 [CrossRef][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 [CrossRef]
    [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 [CrossRef][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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003230
Loading
/content/journal/ijsem/10.1099/ijsem.0.003230
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