1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 4

sp. nov. and sp. nov., isolated from human faeces Free

Abstract

Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141 and HF-106) was most closely related to XB1A (98.0–98.3 % similarity) and ATCC 8483 (97.3–97.5 %), whereas cluster II (strains HF-5287 and HF-5300) exhibited a similarity range of 96.8–97.0 % to JCM 13345, 96.7–96.9 % to MAJ27 and 96.4–96.5 % to XB1A. The DNA G+C contents of type strains HF-5141 and HF-5287 were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus . However, the average nucleotide identity and digital DNA–DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus . Therefore, strains HF-5141 and HF-5287 represent two novel species in the genus , for which the names sp. nov. and sp. nov. are proposed, with HF-5141 (=CGMCC 1.16787=GDMCC 1.1591=JCM 33480) and HF-5287 (=CGMCC 1.16724=GDMCC 1.1590=JCM 33481) as type strains.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroides luhongzhouii , Bacteroides zhangwenhongii , gut microbiota and taxonomy
Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
  • National Key R&D Program of China (Award 2019YFC1200505)
    • Principle Award Recipient: JingYang
  • National Key R&D Program of China (Award 2019YFC1200500)
    • Principle Award Recipient: JingYang
  • National Science and Technology Major Project of China (Award 2017ZX10303405-005-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2017ZX10303405-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: ShanLu
  • National Science and Technology of China (Award 2017FY101202)
    • Principle Award Recipient: DongJin
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004772
2021-04-21
2024-09-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/4/ijsem004772.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004772&mimeType=html&fmt=ahah

References

  1. Kim M-S, Roh SW, Bae J-W. Bacteroides faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2010; 60:2572–2576 [View Article][PubMed]
     [Google Scholar]
  2. Irisawa T, Saputra S, Kitahara M, Sakamoto M, Sulistiani et al. Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken. Int J Syst Evol Microbiol 2016; 66:1431–1437 [View Article][PubMed]
     [Google Scholar]
  3. Shin Y, Park S-J, Paek J, Kim J-S, Rhee M-S et al. Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides . Int J Syst Evol Microbiol 2017; 67:4352–4357 [View Article][PubMed]
     [Google Scholar]
  4. Yu SY, Kim J-S, Oh BS, Park S-H, Kang SW et al. Bacteroides faecalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:3824–3829 [View Article][PubMed]
     [Google Scholar]
  5. Watanabe Y, Nagai F, Morotomi M, Sakon H, Tanaka R. Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2010; 60:1864–1869 [View Article][PubMed]
     [Google Scholar]
  6. Lan PTN, Sakamoto M, Sakata S, Benno Y. Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 2006; 56:2853–2859 [View Article][PubMed]
     [Google Scholar]
  7. Ismaeil M, Yoshida N, Katayama A. Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment. J Microbiol 2018; 56:619–627 [View Article][PubMed]
     [Google Scholar]
  8. Nishiyama T, Ueki A, Kaku N, Watanabe K, Ueki K. Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol 2009; 59:1901–1907 [View Article][PubMed]
     [Google Scholar]
  9. Yang J, Pu J, Lu S, Bai X, Wu Y et al. Species-level analysis of human gut microbiota with metataxonomics. Front Microbiol 2020; 11:11 [View Article][PubMed]
     [Google Scholar]
  10. Ge Y, Yang J, Lai X-H, Zhang G, Jin D et al. Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content. Int J Syst Evol Microbiol 2020; 70:2493–2498 [View Article][PubMed]
     [Google Scholar]
  11. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  12. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  13. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article][PubMed]
     [Google Scholar]
  14. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2020; 70:2960–2966 [View Article][PubMed]
     [Google Scholar]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  18. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  21. Goebel BM, Stackebrandt E. Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 1994; 60:1614–1621 [View Article][PubMed]
     [Google Scholar]
  22. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article][PubMed]
     [Google Scholar]
  23. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
     [Google Scholar]
  24. Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015; 33:623–630 [View Article][PubMed]
     [Google Scholar]
  25. Chen C, Zhang W, Zheng H, Lan R, Wang H et al. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013; 51:2582–2591 [View Article][PubMed]
     [Google Scholar]
  26. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article][PubMed]
     [Google Scholar]
  27. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
     [Google Scholar]
  28. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  30. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  31. Austrian R. The gram stain and the etiology of lobar pneumonia, an historical note. Bacteriol Rev 1960; 24:261–265 [View Article][PubMed]
     [Google Scholar]
  32. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article][PubMed]
     [Google Scholar]
  33. Borsodi AK, Tóth E, Aszalós JM, Bárány Ágnes, Schumann P et al. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil. Int J Syst Evol Microbiol 2017; 67:3490–3495 [View Article][PubMed]
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
     [Google Scholar]
  35. 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]
  36. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:251–256 [View Article][PubMed]
     [Google Scholar]
  37. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  38. Shah HN, Collins MD. Genus Bacteroides. A chemotaxonomical perspective. J Appl Bacteriol 1983; 55:403–416 [View Article][PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004772
Loading
Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces
Int J Syst Evol Microbiol 71, 004772 (2021); https://doi.org/10.1099/ijsem.0.004772
/content/journal/ijsem/10.1099/ijsem.0.004772
/content/journal/ijsem/10.1099/ijsem.0.004772
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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