Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 7, 2014, Pages 2312-2318

  Hyun, Dong Wook ^a   Shin, Na Ri ^a   Kim, Min Soo ^a   Oh, Sei Joon ^a   Kim, Pil Soo ^a   Whon, Tae Woong ^a   Bae, Jin Woo ^a  

^a Kyung Hee University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOPHOSPHOLIPID; CARDIOLIPIN; FATTY ACID; GENOMIC DNA; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHOLIPID; RNA 16S;

ANIMAL SHELL; ARTICLE; ATRINA PECTINATA; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; DNA DNA HYBRIDIZATION; ENDOZOICOMONAS ATRINAE; ENDOZOICOMONAS ELYSICOLA; FATTY ACID ANALYSIS; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; INTESTINE FLORA; KOREA; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHYLOGENETIC TREE; PRIORITY JOURNAL;

ANIMALS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; BIVALVIA; DNA, BACTERIAL; FATTY ACIDS; GAMMAPROTEOBACTERIA; GASTROINTESTINAL TRACT; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHOSPHOLIPIDS; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; UBIQUINONE;

EID: 84904473195     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.060780-0     Document Type: Article

References (34)

1. Bae, J. W., Rhee, S. K., Park, J. R., Chung, W. H., Nam, Y. D., Lee, I., Kim, H. & Park, Y. H. (2005). Development and evaluation of genomeprobing microarrays for monitoring lactic acid bacteria. Appl Environ Microbiol 71, 8825-8835.
2. Benson, H. J. (1994). Microbiological Applications: a Laboratory Manual in General Microbiology, 6th edn. Dubuque, Iowa: W.C. Brown.
3. Bernardet, J. F., Nakagawa, Y., Holmes, B. & Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049-1070.
4. Chang, H. W., Nam, Y. D., Jung, M. Y., Kim, K. H., Roh, S. W., Kim, M. S., Jeon, C. O., Yoon, J. H. & Bae, J. W. (2008). Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J Microbiol Methods 75, 523-530.
5. Collins, M. D. & Jones, D. (1981a). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45, 316-354.
6. Collins, M. D. & Jones, D. (1981b). A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thinlayer chromatography and high performance liquid chromatography. J Appl Bacteriol 51, 129-134.
7. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
8. Fitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
9. Gonzalez, J. M. & Saiz-Jimenez, C. (2002). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4, 770-773.
10. Goszczynska, T. & Serfontein, J. J. (1998). Milk-Tween agar, a semiselective medium for isolation and differentiation of Pseudomonas syringae pv. syringae, Pseudomonas syringae pv. phaseolicola and Xanthomonas axonopodis pv. phaseoli. J Microbiol Methods 32, 65-72.
11. Hyun, D. W., Shin, N. R., Kim, M. S., Kim, P. S., Jung, M. J., Kim, J. Y., Whon, T. W. & Bae, J. W. (2014). Polaribacter atrinae sp. nov., a bacterium isolated from the intestine of a comb pen shell Atrina pectinata. Int J Syst Evol Microbiol 64, 1654-1661.
12. Kaiser, P., Geyer, R., Surmann, P. & Fuhrmann, H. (2012). LC-MS method for screening unknown microbial carotenoids and isoprenoid quinones. J Microbiol Methods 88, 28-34.
13. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (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.
14. Kurahashi, M. & Yokota, A. (2007). Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata. Syst Appl Microbiol 30, 202-206.
15. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. New York: Wiley.
16. Leisner, J. J., Larsen, M. H., Jørgensen, R. L., Brøndsted, L., Thomsen, L. E. & Ingmer, H. (2008). Chitin hydrolysis by Listeria spp., including L. monocytogenes. Appl Environ Microbiol 74, 3823-3830.
17. Loy, A., Schulz, C., Lücker, S., Schöpfer-Wendels, A., Stoecker, K., Baranyi, C., Lehner, A. & Wagner, M. (2005). 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl Environ Microbiol 71, 1373-1386.
18. MIDI (1999). Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE: MIDI Inc.
19. Nishijima, M., Adachi, K., Katsuta, A., Shizuri, Y. & Yamasato, K. (2013). Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007. Int J Syst Evol Microbiol 63, 709-714.
20. Okutani, T. (1997). Basic data on scarcely wild species in Japan-IV. Jpn Fish Resour Conserv Assoc Tokyo, 43-47.
21. Park, E. J., Kim, M. S., Jung, M. J., Roh, S. W., Chang, H. W., Shin, K. S. & Bae, J. W. (2010a). Agromyces atrinae sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 60, 1056-1059.
22. Park, E. J., Kim, M. S., Roh, S. W., Jung, M. J. & Bae, J. W. (2010b). Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood. Int J Syst Evol Microbiol 60, 914-918.
23. Pike, R. E., Haltli, B. & Kerr, R. G. (2013). Description of Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas. Int J Syst Evol Microbiol 63, 4294-4302.
24. Rochelle, P. A., Fry, J. C., Parkes, R. J. & Weightman, A. J. (1992). DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol Lett 100, 59-65.
25. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
26. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
27. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
28. Teather, R. M. & Wood, P. J. (1982). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43, 777-780.
29. Tindall, B. J. (1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
30. Tittsler, R. P. & Sandholzer, L. A. (1936). The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31, 575-580.
31. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
32. Xin, H., Itoh, T., Zhou, P., Suzuki, K., Kamekura, M. & Nakase, T. (2000). Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 50, 1297-1303.
33. Yang, C. S., Chen, M. H., Arun, A. B., Chen, C. A., Wang, J. T. & Chen, W. M. (2010). Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata. Int J Syst Evol Microbiol 60, 1158-1162.
34. Yurimoto, Y., Watanabe, Y., Nasu, H., Tobase, N., Matsui, S. & Yoshioka, N. (2003). Relationship between environmental food and glycogen contents in pen shells. In Proceedings of 32nd US Japan Symposium on Aquaculture, California, USA, pp. 16-23.