- KOREAN
- E-ISSN2713-8615
- KCI
E-ISSN : 2713-8615
A report of 43 unrecorded bacterial species within the phyla Bacteroidetes and Firmicutes isolated from various sources from Korea in 2019
Haneul Kim (Hankuk University of Foreign Studies)
Hana Yi (School of Biosystem and Biomedical Science, Korea University)
Kim Wonyong
Jung-Hoon Yoon (Sungkyunkwan University)
Im Wan-Taek
Myung Kyum Kim
Chi-Nam Seong
Seung Bum Kim
Cha Chang Jun
Che Ok Jeon
KISEONG JOH (Hankuk University of Foreign Studies)
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
- 16S rRNA gene, Bacteroidetes, Firmicutes, unrecorded species
Reference
Alexander, S.K. and D. Strete. 2001. Microbiology: a pho-tographic atlas for the laboratory. San Francisco, CA: Benjamin Cummings.
Brown, A.E. 2007. Benson’s microbiological application laboratory manual in general microbiology, 10th edn. New York: McGraw-Hill.
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.
Felsenstein, J. 1981. Evolutionary trees from DNA sequenc-es: a maximum likelihood approach. Journal of Molecu-lar Evolution 17(6):368-376.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783.
Fitch, W.M. 1971. Toward defining course of evolution min-imum change for a specific tree topology. Systematic Zoology 20(4):406-416.
García-López, M., J.P. Meier-Kolthoff, B.J. Tindall, S. Gronow, T. Woyke, N.C. Kyrpides, R.L. Hahnke and M. Göker. 2019. Analysis of 1,000 type-strain genomes im-proves taxonomic classification of Bacteroidetes. Fron-tiers in Microbiology 10:1-74.
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.
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.
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.
Hahnke, R.L., J.P. Meier-Kolthoff, M. García-López, S. Mukherjee, M. Huntemann, N.N. Ivanova, T. Woyke, N.C. Kyrpides, H.-P. Klenk and M. Göker. 2016. Ge-nome-based taxonomic classification of Bacteroidetes. Frontiers in Microbiology 7:1-37.
Janda, J.M. and S.L. Abbott. 2007. 16S rRNA gene sequenc-ing for bacterial identification in the diagnostic laborato-ry: pluses, perils, and pitfalls. Journal of Clinical Micro-biology 45(9):2761-2764.
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.
Koliada, A., G. Syzenko, V. Moseiko, L. Budovska, K. Puc-hkov, V. Perederiy, Y. Gavalko, A. Dorofeyev, M. Roma-nenko, S. Tkach, L. Sineok, O. Lushchak and L. Sineok. 2017. Association between body mass index and Firmic-utes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiology 17(1):1-6.
Krieg, N.R., W. Ludwig, J. Euzéby 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.
Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: Molec-ular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870- 1874.
Lane, D.J. 1991. 16S/23S rRNA sequencing. In: E. Stacke-brandt and M. Goodfellow (eds.), Nucleic acid tech-niques in bacterial systematics, John Wiley & Sons, New York. pp. 115-175.
Ley, R.E., P.J. Turnbaugh, S. Klein and J.I. Gordon. 2006. Human gut microbes associated with obesity. Nature 444(7122):1022-1023.
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.
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 Firmic-utes isolated from Korea in 2016. Journal of Species Research 7(1):50-59.
Patel, S. and R.S. Gupta. 2020. A phylogenomic and compar-ative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacil-lus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacil-lus gen. nov. and Alkalihalobacillus gen. nov. Internation-al Journal of Systematic and Evolutionary Microbiology 70(1):406-438.
Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accu-rate high-throughput multiple sequence alignment of ri-bosomal RNA genes. Bioinformatics 28(14):1823-1829.
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. Good-man and J.D. Mougous. 2014. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antago-nism. Cell Host & Microbe 16(2):227-236.
Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mo-lecular Biology and Evolution 4(4):406-425.
Sharmin, F., S. Wakelin, F. Huygens and M. Hargreaves. 2013. Firmicutes dominate the bacterial taxa within sug-ar-cane processing plants. Scientific reports 3:1-7.
Yoon, S.H., S.M. Ha, S. Kwon, J. Lim, Y. Kim, H. Seo and J. Chun. 2017. Introducing EzBioCloud: a taxonomi-cally united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Sys-tematic and Evolutionary Microbiology 67(5):1613-1617.
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. Gän-zle 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 Mi-crobiology 70(4):2782-2858.
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