Browse > Article
http://dx.doi.org/10.12651/JSR.2020.9.1.035

A report of 12 unrecorded prokaryotic species isolated from gastrointestinal tracts and feces of various endangered animals in Korea  

Kim, Pil Soo (Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University)
Lee, Ki-Eun (Microorganism Resources Division, National Institute of Biological Resources)
Tak, Euon Jung (Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University)
Kang, Myung-Suk (Biological Resources Utilization Department, National Institute of Biological Resources)
Bae, Jin-Woo (Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University)
Publication Information
Journal of Species Research / v.9, no.1, 2020 , pp. 35-45 More about this Journal
Abstract
In 2016 and 2017, as part of a comprehensive investigation to identify the prokaryotic species in Korea, a total of 12 bacterial strains were isolated from the gastrointestinal tract and/or fecal samples of four endangered species, including reptile, bird, and marine and terrestrial mammals. Phylogenetic analysis with the 16S rRNA gene sequence was used to assign these strains to the phyla, Firmicutes, Actinobacteria or Proteobacteria. Furthermore, most of the strains Firmicutes belonged to the order Lactobacillales. Interestingly, 12 of the isolated strains have not been previously reported from the Korean Peninsula. Also, based on their high 16S rRNA gene sequence similarities(>98.7%) and formation of strong monophyletic clades with the closest type species, each isolated strain of isolates was assigned to an independent, predefined bacterial species. Gram-stain reaction, colony and cell morphology, biochemical characteristics, isolation source, and NIBR IDs are described in the species description section.
Keywords
16S rRNA sequence; endangered animals; gut microbiota; Korean Peninsula; unrecorded species;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Stecher, B., R. Robbiani, A.W. Walker, A.M. Westendorf, M. Barthel, M. Kremer, S. Chaffron, A.J. Macpherson, J. Buer and J. Parkhill. 2007. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biology 5:e244.   DOI
2 Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673-4680.   DOI
3 Turnbaugh, P.J., R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis and J.I. Gordon. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1131.   DOI
4 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 67:1613-1617.   DOI
5 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. Proceedings of the National Academy of Sciences of the United States of America 101:15718-15723.
6 Backhed, F., R.E. Ley, J.L. Sonnenburg, D.A. Peterson and J.I. Gordon. 2005. Host-bacterial mutualism in the human intestine. 307:1915-1920.   DOI
7 Hall, T.A. 1999. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series 41:95-98.
8 Baillie, J., C. Hilton-Taylor and S.N. Stuart. 2004. 2004 IUCN red list of threatened species: a global species assessment. (Iucn).
9 Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376.   DOI
10 Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.   DOI
11 Hoffmann, C., D.A. Hill, N. Minkah, T. Kirn, A. Troy, D. Artis and F. Bushman. 2009. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infection and Immunity 77:4668-4678.   DOI
12 Kluge, A.G. and F.S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Systemic Zoology 18:1-32.   DOI
13 Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870-1874.   DOI
14 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.
15 Round, J.L. and S.K. Mazmanian. 2009. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology 9:313-323.   DOI
16 Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.