바로가기메뉴

본문 바로가기 주메뉴 바로가기

logo

A report of 26 unrecorded bacterial species in Korea, belonging to the Bacteroidetes and Firmicutes

Journal of Species Research / Journal of Species Research, (E)2713-8615
2016, v.5 no.1, pp.166-178
KISEONG JOH (Hankuk University of Foreign Studies)
Haneul Kim (Hankuk University of Foreign Studies)
Jung-Hoon Yoon (Sungkyunkwan University)
CHANG-JUN CHA (Chung-Ang University)
Chi-Nam Seong
Im Wan-Taek
Kwang-Yeop Jahng (Chonbuk National University)
Che Ok Jeon (Chung-Ang University)
Seung Bum Kim
  • Downloaded
  • Viewed

Abstract

An outcome of the study to discover indigenous prokaryotic species in Korea, a total of 26 bacterial species assigned to the classes Bacteroidetes and Firmicutes were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, wetland, plant roots, and fermented foods. From the high 16S rRNA gene sequence similarity (>99.0%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 26 species have been described in Korea; therefore 14 strains for the order Flavobacteriales and two strains for the order Cytophagales were assigned to the class Bacteroidetes, and 8 strains for the order Bacillales and 4 strains for the order Lactobacillales were assigned to the class Firmicutes are reported for new bacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

keywords
16S rRNA, bacterial diversity, Bacteroidetes, Firmicutes, unrecorded species

Reference

1.

Abo-Elnaga, I. G. and O. Kandler. 1965. Zur Taxonomie der Gattung Lactobacillus Beijerinck. I. Das Subgenus Streptobacterium Orla-Jensen. Zentbl Bakteriol Parasitenkd Infektionskr Hyg 119:1-36 (in German).

2.

Allen, T.D., P.A. Lawson, M.D. Collins, E. Falsen and R.S. Tanner. 2006. Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater. International Journal of Systematic and Evolutionary Microbiology 56(6):1311-1316.

3.

Berliner, E. 1915. Über die Schlaffsucht der Mehlmotten raupe (Ephestia kühniella Zell.) und ihren Erreger Bacillus thuringiensis n. sp. Zeitschrift für angewandte Entomologie 2(1):29-56.

4.

Chen, Y.G., D.F. Hao, Q.H. Chen, Y.Q. Zhang, J.B. Liu, J.W. He, S.K. Tang and W.J. Li. 2011. Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Antonie van Leeuwenhoek 99(3):481-488.

5.

Cho, S.H., K.S. Lee, D.S. Shin, J.H. Han, K.S. Park, C.H. Lee, K.H. Park and S.B. Kim. 2010. Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov. Systematic and applied microbiology 33(3):122-127.

6.

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.

7.

Dworkin, M., S. Falkow, E. Rosenberg, K.-H. Schleifer and E. Stackebrandt (editors). 2006. The Prokaryotes, 3rd edn, vol. 3. New York: Springer.

8.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6):368-376.

9.

Felsenstein, J. 1985. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 39(4):783.

10.

Glaeser, S.P., W. Dott, H.J. Busse and P. Kampfer. 2013. Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus. International Journal of Systematic and Evolutionary Microbiology 63(8):2934-2944.

11.

Ivanova, E.P., Y.A. Alexeeva, N.V. Zhukova, N.M. Gorsh kova, V. Buljan, D.V. Nicolau, V.V. Mikhailov and R. Christen. 2004a. Bacillus algicola sp. nov., a novel filamentous organism isolated from brown alga Fucus evanescens. Systematic and applied microbiology 27(3):301-307.

12.

Ivanova, E.P., N.M. Gorshkova, T. Sawabe, N.V. Zhukova, K. Hayashi, V.V. Kurilenko, Y. Alexeeva, V. Buljan, D.V. Nicolau, V.V. Mikhailov and R. Christen. 2004b. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). International Journal of Systematic and Evolutionary Microbiology 54(2):475-480.

13.

Johansen, J.E., P. Nielsen and C. Sjoholm. 1999. Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. International Journal of Systematic Bacteriology 49(3):1231-1240.

14.

Keijser, B.J., E. Zaura, S.M. Huse, J.M. van der Vossen, F.H. Schuren, R.C. Montijn, J.M. ten Cate and W. Crielaard. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. Journal of Dental Research 87:1016-1020.

15.

Kim, J.J., E. Kanaya, H.Y. Weon, Y. Koga, K. Takano, P.F. Dunfield, S.W. Kwon and S. Kanaya. 2012a. Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae. International Journal of Systematic and Evolutionary Microbiology 62(8):2018-2024.

16.

Kim, K.K., M.K. Kim, J.H. Lim, H.Y. Park and S.T. Lee. 2005. Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. International Journal of Systematic and Evolutionary Microbiology 55(3):1287-1293.

17.

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. 2012b. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology 62(3):716-721.

18.

Kloos, W.E., C.G. George, J.S. Olgiate, L. Van Pelt, M.L. McKinnon, B.L. Zimmer, E. Muller, M.P. Weinstein and S. Mirrett. 1998. Staphylococcus hominis subsp. novobiosepticus subsp. nov., a novel trehalose- and N-acetyl-D-glucosamine-negative, novobiocin- and multiple-antibiotic-resistant subspecies isolated from human blood cultures. International Journal of Systematic Bacteriology 48(3):799-812.

19.

Kong, B.H., Q.F. Liu, M. Liu, Y. Liu, L. Liu, C.L. Li, R. Yu and Y.H. Li. 2013. Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L. International Journal of Systematic and Evolutionary Microbiology 63(3):1037-1044.

20.

Krishnamurthi, S., A. Bhattacharya, S. Mayilraj, P. Saha, P. Schumann and T. Chakrabarti. 2009. Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov. International Journal of Systematic and Evolutionary Microbiology 59(6):1364-1370.

21.

Liu, H., R. Liu, S.Y. Yang, W.K. Gao, C.X. Zhang, K.Y. Zhang and R. Lai. 2008. Flavobacterium anhuiense sp. nov., isolated from field soil. International Journal of Systematic and Evolutionary Microbiology 58(4):756-760.

22.

Madhaiyan, M., S. Poonguzhali, J.S. Lee, K.C. Lee and S. Sundaram. 2010. Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean. International Journal of Systematic and Evolutionary Microbiology 60(9):2187-2192.

23.

Moore, W. E. and L. V. Holderman. 1974. Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies. The American Journal of Clinical Nutrition 27:1450-1455.

24.

Nasidze, L., J. Li, D. Quinque, K. Tang and M. Stoneking. 2009a. Global diversity in the human salivary microbiome. Genome Research 19:636-643.

25.

Nasidze, L., D. Quinque, J. Li, M. Li, K. Tang and M. Stone king. 2009b. Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Analytical Biochemistry 391:64-68.

26.

Nedashkovskaya, O.I., S.B. Kim, S.K. Han, A.M. Lysenko, M. Rohde, M.S. Rhee, G.M. Frolova, E. Falsen, V.V. Mikhailov and K.S. Bae. 2004. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. International Journal of Systematic and Evolutionary Microbiology 54(4):1017-1023.

27.

Nedashkovskaya, O.I., S.B. Kim, A.M. Lysenko, K.H. Lee, K.S. Bae and V.V. Mikhailov. 2007. Arenibacter echinorum sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. International Journal of Systematic and Evolutionary Microbiology 57(11):2655-2659.

28.

Nielsen, P., D. Fritze and F.G. Priest. 1995. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141(7):1745-1761.

29.

Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics (Oxford, England) 28(14):1823-1829.

30.

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.

31.

Sghir, A., G. Grament, A. Suau, V. Rochet, P. Pochart and J. Dore. 2000. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Applied and Environmental Microbiology 66:2263-2266.

32.

Shahina, M., A. Hameed, S.Y. Lin, W.A. Lai, Y.H. Hsu and C.C. Young. 2014. Description of Algoriphagus taiwanensis sp. nov., a xylanolytic bacterium isolated from surface seawater, and emended descriptions of Algoriphagus mannitolivorans, Algoriphagus olei, Algoriphagus aquatilis and Algoriphagus ratkowskyi. Antonie van Leeuwenhoek 106(5):1031-1040.

33.

Sheu, S.Y., Y.S. Chen, Y.W. Shiau and W.M. Chen. 2013. Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river. International Journal of Systematic and Evolutionary Microbiology 63(10):3861-3867.

34.

Srinivas, T.N., S. Prasad, P. Manasa, B. Sailaja, Z. Begum and S. Shivaji. 2013. Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix. International Journal of Systematic and Evolutionary Microbiology 63(2):729-734.

35.

Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30(12):2725-2729.

36.

Tannock, G. (editor) 2005. Probiotics and Prebiotics: Scientific Aspects (1st ed.). Caister Academic Press.

37.

Thomas, F., J. Hehemann, E. Rebuffet, M. Czjzek and G. Michel. 2011. Environmental and gut Bacteroidetes: the food connection. Frontiers in Microbiology 2:1-16.

38.

Woose, C.R. 1987. Bacterial evolution. Microbiological Reviews 51:221-271.

39.

Woose, C.R., D. Yang, L. Mandelco and K. O. Stetter. 1990. The flexibacter-flavobacter connection. Systematic and Applied Microbiology 13:161-165.

40.

Zanoni, P., J.A. Farrow, B.A. Phillips and M.D. Collins. 1987. Lactobacillus pentosus (Fred, Peterson, and Anderson) sp. nov., nom. rev. International Journal of Systematic Bacteriology 37(4):339-341.

41.

Zhang, D.C., H.X. Wang, H.C. Liu, X.Z. Dong and P.J. Zhou. 2006. Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. International Journal of Systematic and Evolutionary Microbiology 56(12):2921-2925.

42.

Zhu, F., S. Wang and P. Zhou. 2003. Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier. International Journal of Systematic and Evolutionary Microbiology 53(3):853-857.

Journal of Species Research