Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
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A report of 10 unrecorded bacterial species of Korea, belonging to the phylum Firmicutes

  • Kim, Eunji (Department of Public Health Sciences, Graduate School, Korea University) ;
  • Choi, Sungmi (Department of Public Health Sciences, Graduate School, Korea University) ;
  • Bae, Jin-Woo (Department of Biology, Kyung Hee University) ;
  • Cha, Chang-Jun (Department of Biotechnology, Chung-Ang University) ;
  • Im, Wan-Taek (Department of Biotechnology, Hankyong National University) ;
  • Jahng, Kwang-Yeop (Department of Life Sciences, Chonbuk National University) ;
  • Joh, Ki-seong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Yi, Hana (Department of Public Health Sciences, Graduate School, Korea University)
  • Received : 2016.02.26
  • Accepted : 2016.06.15
  • Published : 2016.06.30
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Abstract

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.

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References

  1. Backhed, F., H. Ding, T. Wang, L.V. Hooper, G.Y. Koh, A. Nagy, C.F. Semenkovich and J.I. Gordon. 2004. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101(44):15718-15723. https://doi.org/10.1073/pnas.0407076101
  2. De Vos, P., G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.H. Schleifer and W.B. Whitman. 2009. Bergey's manual of systematic bacteriology, New York: Springer.
  3. Felsenstein, J. 1985. Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39(4):783-791. https://doi.org/10.2307/2408678
  4. Felsenstein, J. 1993. PHYLIP(phylogenetic inference package) version 3.5.1. Department of Genetics, University of Washington, Seattle, WA, USA.
  5. Gibbons, N.E. and R.G.E. Murray. 1978. Proposals concerning higher taxa of bacteria. Int J Syst Bacteriol 28(1):1-6. https://doi.org/10.1099/00207713-28-1-1
  6. Jeon, Y.S., K. Lee, S.C. Park, B.S. Kim, Y.J. Cho, S.M. Ha and J. Chun. 2014. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 64(2):689-691. https://doi.org/10.1099/ijs.0.059360-0
  7. Kim, O.S., Y.J. Cho, K. Lee, S.H. Yoon, M. Kim, H. Na, S.C. Park, Y.S. Jeon, J.H. Lee, H. Yi, S. Won and J. Chun. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62(3):716-721. https://doi.org/10.1099/ijs.0.038075-0
  8. Kimura, M. 1983. Rare variant alleles in the light of the neutral theory. Mol Biol Evol 1(1):84-93.
  9. Le Chatelier, E., T. Nielsen, J. Qin, E. Prifti, F. Hildebrand, G. Falony, M. Almeida, M. Arumugam, J.M. Batto, S. Kennedy, P. Leonard, J. Li, K. Burgdorf, N. Grarup, T. Jorgensen, I. Brandslund, H.B. Nielsen, A.S. Juncker, M. Bertalan, F. Levenez, N. Pons, S. Rasmussen, S. Sunagawa, J. Tap, S. Tims, E.G. Zoetendal, S. Brunak, K. Clement, J. Dore, M. Kleerebezem, K. Kristiansen, P. Renault, T. Sicheritz-Ponten, W.M. de Vos, J.D. Zucker, J. Raes, T. Hansen, H.I.T.c. Meta, P. Bork, J. Wang, S.D. Ehrlich and O. Pedersen. 2013. Richness of human gut microbiome correlates with metabolic markers. Nature 500(7464):541-546. https://doi.org/10.1038/nature12506
  10. Ley, R.E., D.A. Peterson and J.I. Gordon. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124(4):837-848. https://doi.org/10.1016/j.cell.2006.02.017
  11. Ley, R.E., P.J. Turnbaugh, S. Klein and J.I. Gordon. 2006. Microbial ecology - Human gut microbes associated with obesity. Nature 444(7122):1022-1023. https://doi.org/10.1038/4441022a
  12. Marchandin, H., C. Teyssier, J. Campos, H. Jean-Pierre, F. Roger, B. Gay, J.P. Carlier and E. Jumas-Bilak. 2010. Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes. Int J Syst Evol Microbiol 60(6):1271-1279. https://doi.org/10.1099/ijs.0.013102-0
  13. Rosenberg, E., E.F. DeLong, S. Lory, E. Stackebrandt and F. Thompson. 2014. The Prokaryotes, Springer.
  14. Saitou, N. and M. Nei. 1987. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406-425.
  15. Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30(12):2725-2729. https://doi.org/10.1093/molbev/mst197
  16. Turnbaugh, P.J., F. Backhed, L. Fulton and J.I. Gordon. 2008. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3(4):213-223. https://doi.org/10.1016/j.chom.2008.02.015
  17. Wood, B. 1998. Microbiology of Fermented Foods, Blackie, London.