Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
권호 표지
DOI QR코드

DOI QR Code

A report of 43 unrecorded bacterial species within the phyla Bacteroidetes and Firmicutes isolated from various sources from Korea in 2019

  • Kang, Heeyoung (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Kim, Haneul (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Yi, Hana (School of Biosystem and Biomedical Science, Korea University) ;
  • Kim, Wonyong (Department of Microbiology, Chung-Ang University College of Medicine) ;
  • Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University) ;
  • Im, Wan-Taek (Department of Biotechnology, Hankyong National University) ;
  • Kim, Myung Kyum (Department of Bio & Environmental Technology, Seoul Women's University) ;
  • Seong, Chi Nam (Department of Biology, Sunchon National University) ;
  • Kim, Seung Bum (Department of Microbiology, Chungnam National University) ;
  • Cha, Chang-Jun (Department of Systems Biotechnology, Chung-Ang University) ;
  • Jeon, Che Ok (Department of Life Science, Chung-Ang University) ;
  • Joh, Kiseong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies)
  • Received : 2020.11.23
  • Accepted : 2021.01.20
  • Published : 2021.05.31
Download PDF
⟨ Previous Next ⟩

Abstract

In 2019, 43 bacterial strains were isolated from food, soil, marine environments, human, and animals related sources from the Republic of Korea. Based on the analysis of 16S rRNA gene sequence, these isolates were allocated to the phyla Bacteroidetes and Firmicutes as unrecorded species in Korea. The 10 Bacteroidetes strains were classified into the families Bacteroidaceae, Chitinophagaceae, Cytophagaceae, Flavobacteriaceae, and Prolixibacteraceae (of the orders Bacteroidales, Chitinophagales, Cytophagales, Flavobacteriales, and Marinilabiliales, respectively). The 33 Firmicutes strains belonged to the families Bacillaceae, Paenibacillaceae, Planococcaceae, Staphylococcaceae, Clostridiaceae, Lachnospiraceae, Peptostreptococcaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae (of the orders Bacillales, Clostridiales, and Lactobacillales). These unrecorded bacteria were determined based on taxonomic criterion (>98.7%; 16S rRNA gene sequence similarity). In addition, their phylogenetic affiliation, as well as cell and colony morphologies, staining reactions, and physiological and biochemical properties were investigated. Therefore, we report 43 isolates as unrecorded species, and described basic features, isolation source, and locations of these strains.

Keywords

Acknowledgement

This work was supported by a grant from the National Institute of Biological Resources(NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201902203).

References

  1. Alexander, S.K. and D. Strete. 2001. Microbiology: a photographic atlas for the laboratory. San Francisco, CA: Benjamin Cummings.
  2. Brown, A.E. 2007. Benson's microbiological application laboratory manual in general microbiology, 10th edn. New York: McGraw-Hill.
  3. De Vos, P., G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.-H. Schleifer and W.B. Whitman (editors). 2009. Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 3, The Firmicutes. New York: Springer.
  4. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6):368-376. https://doi.org/10.1007/BF01734359
  5. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783. https://doi.org/10.2307/2408678
  6. Fitch, W.M. 1971. Toward defining course of evolution minimum change for a specific tree topology. Systematic Zoology 20(4):406-416. https://doi.org/10.2307/2412116
  7. Garcia-Lopez, M., J.P. Meier-Kolthoff, B.J. Tindall, S. Gronow, T. Woyke, N.C. Kyrpides, R.L. Hahnke and M. Goker. 2019. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Frontiers in Microbiology 10:1-74. https://doi.org/10.3389/fmicb.2019.00001
  8. Gupta, R.S. and S. Patel. 2019. Robust demarcation of the Family Caryophanaceae (Planococcaceae) and its different genera including three novel genera based on phylogenomics and highly specific molecular signatures. Frontiers in Microbiology 10:1-28. https://doi.org/10.3389/fmicb.2019.00001
  9. Haakensen, M., C.M. Dobson, H. Deneer and B. Ziola. 2008. Real-time PCR detection of bacteria belonging to the Firmicutes Phylum. International Journal of Food Microbiology 125(3):236-241. https://doi.org/10.1016/j.ijfoodmicro.2008.04.002
  10. Haas, K.N. and J.L. Blanchard. 2020. Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. International Journal of Systematic and Evolutionary Microbiology 70(1):23-34. https://doi.org/10.1099/ijsem.0.003698
  11. Hahnke, R.L., J.P. Meier-Kolthoff, M. Garcia-Lopez, S. Mukherjee, M. Huntemann, N.N. Ivanova, T. Woyke, N.C. Kyrpides, H.-P. Klenk and M. Goker. 2016. Genome-based taxonomic classification of Bacteroidetes. Frontiers in Microbiology 7:1-37.
  12. Janda, J.M. and S.L. Abbott. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology 45(9):2761-2764. https://doi.org/10.1128/JCM.01228-07
  13. Kim, H., J.H. Yoon, C.J. Cha, C.N. Seong, W.T. Im, K.Y. Jahng, C.O. Jeon, S.B. Kim and K. Joh. 2016. A report of 26 unrecorded bacterial species in Korea, belonging to the Bacteroidetes and Firmicutes. Journal of Species Research 5(1):166-178. https://doi.org/10.12651/JSR.2016.5.1.166
  14. Koliada, A., G. Syzenko, V. Moseiko, L. Budovska, K. Puchkov, V. Perederiy, Y. Gavalko, A. Dorofeyev, M. Romanenko, S. Tkach, L. Sineok, O. Lushchak and L. Sineok. 2017. Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiology 17(1):1-6. https://doi.org/10.1186/s12866-016-0921-2
  15. Krieg, N.R., W. Ludwig, J. Euzeby and W.B. Whitman. 2010. Phylum XIV. Bacteroidetes phyl. nov. Bergey's Manual of Systematic Bacteriology, 2nd edn. Edited by N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund et al. New York, Springer 4:25.
  16. Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870-1874. https://doi.org/10.1093/molbev/msw054
  17. Lane, D.J. 1991. 16S/23S rRNA sequencing. In: E. Stackebrandt and M. Goodfellow (eds.), Nucleic acid techniques in bacterial systematics, John Wiley & Sons, New York. pp. 115-175.
  18. Ley, R.E., P.J. Turnbaugh, S. Klein and J.I. Gordon. 2006. Human gut microbes associated with obesity. Nature 444(7122):1022-1023. https://doi.org/10.1038/4441022a
  19. Magee, C.M., G. Rodenheaver, M.T. Edgerton and R.F. Edlich. 1975. A more reliable Gram staining technique for diagnosis of surgical infections. American Journal of Surgery 130(3):341-346. https://doi.org/10.1016/0002-9610(75)90398-0
  20. Nahar, S., D.H. Lee, J.W. Bae, W.T. Im, K.Y. Jahng, K. Joh, W. Kim, S.D. Lee, H. Yi and C.J. Cha. 2018. Report on 30 unrecorded bacterial species of the phylum Firmicutes isolated from Korea in 2016. Journal of Species Research 7(1):50-59. https://doi.org/10.12651/JSR.2018.7.1.050
  21. Patel, S. and R.S. Gupta. 2020. 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. International Journal of Systematic and Evolutionary Microbiology 70(1):406-438. https://doi.org/10.1099/ijsem.0.003775
  22. Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28(14):1823-1829. https://doi.org/10.1093/bioinformatics/bts252
  23. Russell, A.B., A.G. Wexler, B.N. Harding, J.C. Whitney, A.J. Bohn, Y.A. Goo, B.Q. Tran, N.A. Barry, H. Zheng, S.B. Peterson, S. Chou, T. Gonen, D.R. Goodlett, A.L. Goodman and J.D. Mougous. 2014. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host & Microbe 16(2):227-236. https://doi.org/10.1016/j.chom.2014.07.007
  24. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
  25. Sharmin, F., S. Wakelin, F. Huygens and M. Hargreaves. 2013. Firmicutes dominate the bacterial taxa within sugar-cane processing plants. Scientific reports 3:1-7.
  26. Yoon, S.H., S.M. Ha, S. Kwon, J. Lim, Y. Kim, H. Seo and J. Chun. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology 67(5):1613-1617. https://doi.org/10.1099/ijsem.0.001755
  27. Zheng, J., S. Wittouck, E. Salvetti, C.M.B. Franz, H.M.B. Harris, P. Mattarelli, P.W. O'Toole, B. Pot, P. Vandamme, J. Walter, K. Watanabe, S. Wuyts, G.E. Felis, M.G. Ganzle and S. Lebeer. 2020. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. International Journal of Systematic and Evolutionary Microbiology 70(4):2782-2858. https://doi.org/10.1099/ijsem.0.004107