1887

Abstract

An aerobic, Gram-stain-positive, rod-shaped, endospore-forming bacterial strain, designated BB3-R1, was isolated from cow faeces sampled in Daejeon, Republic of Korea. Growth was observed at 25–45 °C (optimum, 35–40 °C) and pH 7.0–9.0 (optimum, pH 8.0), with up to 3 % (w/v) NaCl (optimum, 0 % NaCl). analysis of 16S rRNA gene sequences revealed the highest sequence similarity of strain BB3-R1 to NRRL NRS-818 (98.8 %) followed by JCM 15085 (97.5 %). According to 16S rRNA gene and whole-genome based phylogenetic trees, strain BB3-R1 clustered with FJAT-54423 and NRRL NRS-818. OrthoANI and dDDH values of strain BB3-R1 with the closely related strains were lower than 77.5 and 26.8 %, respectively. The major menaquinones and polar lipids of the strain were MK-7 and phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, respectively. The major fatty acids (>10 %) were C iso, C iso, C anteiso and C7 alcohol. The cell-wall peptidoglycan contained cross-linked -diaminopimelic acid (type A1 gamma). The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strain represents a novel species of the genus , for which the name sp. nov. (type strain BB3-R1=KACC 22663=NBRC 115962) is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006204
2023-12-14
2024-12-08
Loading full text...

Full text loading...

References

  1. Shida O, Takagi H, Kadowaki K, Komagata K. Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 1996; 46:939–946 [View Article] [PubMed]
    [Google Scholar]
  2. Hatayama K, Shoun H, Ueda Y, Nakamura A. Brevibacillus fulvus sp. nov., isolated from a compost pile. Int J Syst Evol Microbiol 2014; 64:506–512 [View Article] [PubMed]
    [Google Scholar]
  3. Logan NA, Forsyth G, Lebbe L, Goris J, Heyndrickx M et al. Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov. Int J Syst Evol Microbiol 2002; 52:953–966 [View Article] [PubMed]
    [Google Scholar]
  4. Wang K-X, Li C, He Y-Q, Cui L-Q, Chen R-W et al. Brevibacillus marinus sp. nov., a thermophilic bacterium isolated from deep sea sediment in the South China Sea. Int J Syst Evol Microbiol 2021; 71:ijsem [View Article] [PubMed]
    [Google Scholar]
  5. Inan K, Canakci S, Belduz AO, Sahin F. Brevibacillus aydinogluensis sp. nov., a moderately thermophilic bacterium isolated from Karakoc hot spring. Int J Syst Evol Microbiol 2012; 62:849–855 [View Article] [PubMed]
    [Google Scholar]
  6. Choi MJ, Bae JY, Kim KY, Kang H, Cha CJ. Brevibacillus fluminis sp. nov., isolated from sediment of estuarine wetland. Int J Syst Evol Microbiol 2010; 60:1595–1599 [View Article] [PubMed]
    [Google Scholar]
  7. Shida O, Takagi H, Kadowaki K, Udaka S, Nakamura LK et al. Proposal of Bacillus reuszeri sp. nov., Bacillus formosus sp. nov., nom. rev., and Bacillus borstelensis sp. nov., nom. rev. Int J Syst Bacteriol 1995; 45:93–100 [View Article]
    [Google Scholar]
  8. Bhatt K, Maheshwari DK. Decoding multifarious role of cow dung bacteria in mobilization of zinc fractions along with growth promotion of C. annuum L. Sci Rep 2019; 9:14232 [View Article] [PubMed]
    [Google Scholar]
  9. Adebusoye SA, Ilori MO, Amund OO, Teniola OD, Olatope SO. Microbial degradation of petroleum hydrocarbons in a polluted tropical stream. World J Microbiol Biotechnol 2007; 23:1149–1159 [View Article]
    [Google Scholar]
  10. Akinde SB, Obire O. Aerobic heterotrophic bacteria and petroleum-utilizing bacteria from cow dung and poultry manure. World J Microbiol Biotechnol 2008; 24:1999–2002 [View Article]
    [Google Scholar]
  11. Umanu G, Nwachukwu SCU, Olasode OK. Effects of cow dung on microbial degradation of motor oil in lagoon water. GJBB 2013; 2:542548
    [Google Scholar]
  12. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics vol 1991 Wiley; pp 125–175
    [Google Scholar]
  13. 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]
  14. 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]
  15. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [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. 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]
  19. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  20. Hufnagel DE, Hufford MB, Seetharam AS. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics 2020; 21:429 [View Article] [PubMed]
    [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  24. Lee I, Ouk Kim Y, Park SC, 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]
  25. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  28. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:1–12 [View Article] [PubMed]
    [Google Scholar]
  29. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article] [PubMed]
    [Google Scholar]
  30. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
    [Google Scholar]
  31. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States Department of Energy systems biology knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article] [PubMed]
    [Google Scholar]
  32. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
    [Google Scholar]
  33. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010; 11:431 [View Article]
    [Google Scholar]
  34. Duca D, Lorv J, Patten CL, Rose D, Glick BR. Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 2014; 106:85–125 [View Article] [PubMed]
    [Google Scholar]
  35. Behera SS, Ray RC. Bioprospecting of cowdung microflora for sustainable agricultural, biotechnological and environmental applications. Curr Res Microb Sci 2021; 2:100018 [View Article] [PubMed]
    [Google Scholar]
  36. Lee JH, Shin YM, Ra JS, Kim SB. Brevibacillus humidisoli sp. nov., a moderately thermoalkaliphilic and halotolerant species isolated from riverside soil. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
    [Google Scholar]
  37. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res 2023; 51:D690–D699 [View Article] [PubMed]
    [Google Scholar]
  38. Atlas RM, Atlas RM. Handbook of Microbiological Media CRC press; 2004 [View Article]
    [Google Scholar]
  39. Smibert RM. Phenotypic characteization. In Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  40. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
    [Google Scholar]
  41. 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]
  42. Tang R, Zhang Q, Ye Y, Yang S, Fu T et al. Brevibacillus composti sp. nov., isolated from hyperthermophilic compost. Int J Syst Evol Microbiol 2021; 71:ijsem [View Article] [PubMed]
    [Google Scholar]
  43. Kim MK, Sathiyaraj S, Pulla RK, Yang DC. Brevibacillus panacihumi sp. nov., a beta-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2009; 59:1227–1231 [View Article] [PubMed]
    [Google Scholar]
  44. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006204
Loading
/content/journal/ijsem/10.1099/ijsem.0.006204
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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