- KOREAN
- E-ISSN2713-8615
- KCI
E-ISSN : 2713-8615
A report of 14 unrecorded bacterial species in Korea isolated in 2017
Myung Kyum Kim
Soohyun Maeng
Myung-Suk Kang
Jun Hwee Jang
Abstract
Fourteen bacterial strains, low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 assigned to the phylum Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes were isolated from soil samples. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 were most closely related to Marmoricola aurantiacus (98.9%), Calidifontibacter indicus (99.8%), Gordonia soli (98.8%), Rhodococcus globerulus (99.5%), Pseudarthrobacter siccitolerans (99.1%), Hymenobacter qilianensis (98.7%), Hymenobacter terrae (99.0%), Deinococcus yunweiensis (99.2%), Deinococcus proteolyticus (99.7%), Domibacillus indicus (99.2%), Exiguobacterium mexicanum (100.0%), Kurthia senegalensis (99.1%), Lysinibacillus composti (99.6%), and Bacillus loiseleuriae (99.3%). These fourteen species have never been reported in Korea, therefore we report them here for the first time.
- keywords
- 16S rRNA, Actinobacteria, bacterial diversity, Bacteroidetes, Deinococcus-Thermus, Firmicutes, unreported species
Reference
Battista, J.R. 2016. Deinococcus-Thermus Group. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0021151
Barka, E.A., P. Vatsa, L. Sanchez, N. Gaveau-Vaillant, C. Jacquard, H.-P. Klenk, C. Clement, Y. Ouhdouch and G. P. van Wezel. 2016. Microbiol Mol Biol Rev 80:1-43.
Doetsch, R.N. 1981. Determinative methods of light microscopy. Manual of Methods for General Bacteriology, pp. 21-33. In: P. Gerhardt, R.G.E. Murray, R.N. Costilow, E.W. Nester, W.A. Wood, N.R. Krieg and G.H. Phillips (eds.), American Society for Microbiology. Washington, DC, USA.
Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
Edwards, C. 1993. Isolation properties and potential applications of thermophilic Actinomycetes. Appl Biochem Biotechnol 42:161-179.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
Griffths, E. and R.S. Gupta. 2007. Identifcation of signature proteins that are distinctive of the Deinococcus-Thermus phylum. Int Microbiol 10:201-208.
Hall, T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, 1999. vol 41. [London]: Information Retrieval Ltd., c1979-c2000. pp. 95-98.
Hayashi, H., K. Shibata, M.A. Bakir, M. Sakamoto, S. Tomita and Y. Benno. 2007. Bacteroides coprophilus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 57:1323-1326.
Ho, J., M. Adeolu, B. Khadka and R.S. Gupta. 2016. Identifcation of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups. Syst Appl Microbiol 39:453-463.
Johnson, E.L., S.L. Heaver, W.A. Walters and R.E. Ley. 2016. Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. J Mol Med. DOI 10.1007/s00109-016-1492-2
Kim, O.-S. et al. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-721.
Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press.
Lake, J.A., R.G. Skophammer, C.W. Herbold and J.A. Servin. 2009. Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci 364:2177-2185.
Lanza, F.V., A.P. Tedim, J.L. Martinez, F. Baquero and T.M. Coque. 2015. The plasmidome of Firmicutes: impact on the emergence and the spread of resistance to antimicrobials. Microbiol Spectr 3(2):PLAS-0039-2014.
Madigan, M. and J. Martinko, eds. (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall.
Mira, A., R. Pushker, B.A. Legault, D. Moreira and F. Rodriguez-Valera. 2004. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol. 4:50.
Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
Sakamoto, M. and M. Ohkuma. 2011. Identification and classifcation of the genus Bacteroides by multilocus sequence analysis. Microbiol 157:3388-3397.
Scarpellini, E., G. Ianiro, F. Attili, C. Bassanelli, A. De Santis d and A. Gasbarrini. 2015. The human gut microbiota and virome: Potential therapeutic implications. Dig Liver Dis 47:1007-1012.
Shah, H.N., I. Olsen, K. Bernard, S.M. Finegold, S. Gharbia and R.S. Gupta. 2009. Approaches to the study of the systematics of anaerobic, Gram-negative, non-sporeforming rods: current status and perspectives. Anaerobe 15:179-194.
Srinivasan, S., M.K. Kim, S. Lim, M. Joe and M. Lee. 2012a. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int J Syst Evol Microbiol 62:1265-1270.
Srinivasan, S., J.J. Lee, S. Lim, M. Joe and M.K. Kim. 2012b. Deinococcus humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 62:2844-2850.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Mol Biol Evol 28:2731-2739.
Weisburg, W.G., S.M. Barns, D.A. Pelletier, D.J. Lane. 1991. 16S ribosomal DNA amplifcation for phylogenetic study. J Bacteriol 173:697-703.
Wragg, P., L. Randall and A. Whatmore. 2014. Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest. J Microbiol Methods 105:16-21.
- Downloaded
- Viewed
- 0KCI Citations
- 0WOS Citations