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Volume 71, Issue 3

sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow Free

Abstract

A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131, which grew at 20–40 °C (optimum 30 °C), pH 3.0–11.0 (optimum pH 4.0) and in the presence of 0–18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131 formed a group within the genus , and showed the highest sequence similarity with DSM 28131 (96.9 %), following by DSM 18926 (96.6 %). The genome of AGMB 02131 comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA–DNA hybridization revealed that AGMB 02131 displayed 21.4 % genomic DNA relatedness with the most closely related strain, DSM 18926. AGMB 02131 contains all of the conserved signature indels that are specific for members of the genus . The major cellular fatty acids (>10 %) of AGMB 02131 were Cω9, C and C. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is AGMB 02131 (=KCTC 43221=CCTCC AB 2020077).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): novel species , Peribacillus faecalis sp. nov , phylogeny and polyphasic taxonomy
Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology (Award KGM5282021)
    • Principle Award Recipient: JiyoungLee
  • National Research Foundation of Korea (Award NRF-2019M3A9F3065226)
    • Principle Award Recipient: JuHuck Lee
© 2021 The Authors
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2021-03-02
2024-04-24
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References

  1. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article][PubMed]
     [Google Scholar]
  2. Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article][PubMed]
     [Google Scholar]
  3. Feng L, Liu D, Sun X, Wang G, Li M. Bacillus cavernae sp. nov. isolated from cave soil. Int J Syst Evol Microbiol 2016; 66:801–806 [View Article][PubMed]
     [Google Scholar]
  4. Zhang L, Wu G-L, Wang Y, Dai J, Fang C-X. Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. Antonie Van Leeuwenhoek 2011; 99:221–229 [View Article][PubMed]
     [Google Scholar]
  5. Yumoto I, Hirota K, Yamaga S, Nodasaka Y, Kawasaki T et al. Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids. Int J Syst Evol Microbiol 2004; 54:1997–2001 [View Article][PubMed]
     [Google Scholar]
  6. Lim J-M, Jeon CO, Lee JR, Park D-J, Kim C-J. Bacillus kribbensis sp. nov., isolated from a soil sample in Jeju, Korea. Int J Syst Evol Microbiol 2007; 57:2912–2916 [View Article][PubMed]
     [Google Scholar]
  7. Kuisiene N, Raugalas J, Spröer C, Kroppenstedt RM, Chitavichius D. Bacillus butanolivorans sp. nov., a species with industrial application for the remediation of n-butanol. Int J Syst Evol Microbiol 2008; 58:505–509 [View Article][PubMed]
     [Google Scholar]
  8. Li J, Yang G, Wu M, Zhao Y, Zhou S. Bacillus huizhouensis sp. nov., isolated from a paddy field soil. Antonie van Leeuwenhoek 2014; 106:357–363 [View Article][PubMed]
     [Google Scholar]
  9. Liu B, Liu G-H, Zhu Y-J, Wang J-P, Che J-M et al. Bacillus loiseleuriae sp. nov., isolated from rhizosphere soil from a loiseleuria plant. Int J Syst Evol Microbiol 2016; 66:2678–2683 [View Article][PubMed]
     [Google Scholar]
  10. Ma K, Yin Q, Chen L, Lai Q, Xu Y. Bacillus acanthi sp. nov., isolated from the rhizosphere soil of a mangrove plant Acanthus ilicifolius . Int J Syst Evol Microbiol 2018; 68:3047–3051 [View Article][PubMed]
     [Google Scholar]
  11. Zhang YZ, Chen WF, Li M, Sui XH, Liu H-C et al. Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root. Int J Syst Evol Microbiol 2012; 62:359–363 [View Article][PubMed]
     [Google Scholar]
  12. Kämpfer P, Busse H-J, McInroy JA, Glaeser SP. Bacillus gossypii sp. nov., isolated from the stem of Gossypium hirsutum . Int J Syst Evol Microbiol 2015; 65:4163–4168 [View Article][PubMed]
     [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic acid techniques in bacterial systematics New York: John Wiley and Sons; 1991.4.19 pp 115–175
     [Google Scholar]
  14. 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]
  15. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for window 95/98/NT. In nucleic acids symposium series; 1999; 4195–98
  16. 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]
  17. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  18. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990; 28:1942–1946 [View Article][PubMed]
     [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Hwang SH, Hwang WM, Kang K, Ahn T-Y. Gramella fulva sp. nov., isolated from a dry surface of tidal flat. J Microbiol 2019; 57:23–29 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980; 48:277–282 [View Article][PubMed]
     [Google Scholar]
  27. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME 19713, MIDI Technical Note #101. MIDI Inc: 125 Sandy Drive Newark, DE; 2006
     [Google Scholar]
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Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow
Int J Syst Evol Microbiol 71, 004721 (2021); https://doi.org/10.1099/ijsem.0.004721
/content/journal/ijsem/10.1099/ijsem.0.004721
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