[논문]Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus

Yang, Jhung-Ahn; Yang, Sung-Hyun; Kim, Junghee; Kwon, Kae Kyoung; Oh, Hyun-Myung

doi:10.1007/s12275-017-7172-2

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus 원문보기

The journal of microbiology, v.55 no.7, 2017년, pp.583 - 591

Yang, Jhung-Ahn , Yang, Sung-Hyun , Kim, Junghee , Kwon, Kae Kyoung , Oh, Hyun-Myung

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Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

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BMC Genomics R.K. Aziz 9 75 2008 10.1186/1471-2164-9-75 Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75.

상세보기
Appl. Environ. Microbiol. G. Braker 64 3769 1998 10.1128/AEM.64.10.3769-3775.1998 Braker, G., Fesefeldt, A., and Witzel, K.P. 1998. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64, 3769-3775.

상세보기
PLoS One D. Castillo 11 0152515 2016 Castillo, D., Christiansen, R.H., Dalsgaard, I., Madsen, L., Espejo, R., and Middelboe, M. 2016. Comparative genome analysis provides insights into the pathogenicity of Flavobacterium psychrophilum. PLoS One 11, e0152515.
Food Rev. Int. C. Cho 6 333 1990 10.1080/87559129009540876 Cho, C. 1990. Fish nutrition, feeds, and feeding: with special emphasis on salmonid aquaculture. Food Rev. Int. 6, 333-357.

상세보기
Vet. Res. A.M. Declercq 44 27 2013 10.1186/1297-9716-44-27 Declercq, A.M., Haesebrouck, F., Van den Broeck, W., Bossier, P., and Decostere, A. 2013. Columnaris disease in fish: a review with emphasis on bacterium-host interactions. Vet. Res. 44, 27.

상세보기
Int. J. Biol. Sci. Q. Du 7 41 2011 10.7150/ijbs.7.41 Du, Q., Wang, H., and Xie, J. 2011. Thiamin (Vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int. J. Biol. Sci. 7, 41-52.

상세보기
Nat. Biotechnol. E. Duchaud 25 763 2007 10.1038/nbt1313 Duchaud, E., Boussaha, M., Loux, V., Bernardet, J.F., Michel, C., Kerouault, B., Mondot, S., Nicolas, P., Bossy, R., Caron, C., et al. 2007. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat. Biotechnol. 25, 763-769.

상세보기
Int. J. Syst. Evol. Microbiol. Y. Fu 61 205 2011 10.1099/ijs.0.018846-0 Fu, Y., Tang, X., Lai, Q., Zhang, C., Zhong, H., Li, W., Liu, Y., Chen, L., Sun, F., and Shao, Z. 2011. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 61, 205-209.

상세보기
PeerJ. R. Gil-Solsona 5 2920 2017 10.7717/peerj.2920 Gil-Solsona, R., Nácher-Mestre, J., Lacalle-Bergeron, L., Sancho, J.V., Calduch-Giner, J.A., Hernández, F., and Pérez-Sánchez, J. 2017. Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata). PeerJ. 5, e2920.

상세보기
Acad. Sci. USA S.J. Giovannoni 109 13888 2012 10.1073/pnas.1211722109 Giovannoni, S.J. 2012. Vitamins in the sea. Proc. Natl. Acad. Sci. USA 109, 13888-13889.

상세보기
BMC Genomics D. Helen 17 155 2016 10.1186/s12864-016-2465-0 Helen, D., Kim, H., Tytgat, B., and Anne, W. 2016. Highly diverse nirK genes comprise two major clades that harbour ammoniumproducing denitrifiers. BMC Genomics 17, 155.

상세보기
Int. J. Syst. Evol. Microbiol. H. Jang 65 1866 2015 10.1099/ijs.0.000188 Jang, H., Yang, S.H., Seo, H.S., Lee, J.H., Kim, S.J., and Kwon, K.K. 2015. Amphritea spongicola sp. nov., isolated from a marine sponge, and emended description of the genus Amphritea. Int. J. Syst. Evol. Microbiol. 65, 1866-1870.

상세보기
Int. J. Syst. Evol. Microbiol. S. Jit 58 1665 2008 10.1099/ijs.0.65578-0 Jit, S., Dadhwal, M., Prakash, O., and Lal, R. 2008. Flavobacterium lindanitoleran sp. nov., isolated from hexachlorocyclohexanecontaminated soil. Int. J. Syst. Evol. Microbiol. 58, 1665-1669.

상세보기
Biochem. J. S. Jitrapakdee 413 369 2008 10.1042/BJ20080709 Jitrapakdee, S., St Maurice, M., Rayment, I., Cleland, W.W., Wallace, J.C., and Attwood, P.V. 2008. Structure, mechanism and regulation of pyruvate carboxylase. Biochem. J. 413, 369-387.

상세보기
ISME J. A. Kabisch 8 1492 2014 10.1038/ismej.2014.4 Kabisch, A., Otto, A., Konig, S., Becher, D., Albrecht, D., Schuler, M., Teeling, H., Amann, R.I., and Schweder, T. 2014. Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803. ISME J. 8, 1492-1502.

상세보기
Int. J. Syst. Evol. Microbiol. S.T. Khan 56 959 2006 10.1099/ijs.0.64055-0 Khan, S.T., Nakagawa, Y., and Harayama, S. 2006. Sandarakinotalea sediminis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 56, 959-963.

상세보기
PLoS One M. Kolton 8 76704 2013 10.1371/journal.pone.0076704 Kolton, M., Sela, N., Elad, Y., and Cytryn, E. 2013. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 8, e76704.

상세보기
Genome Announc. M. Kopel 2 00793 2014 Kopel, M., Helbert, W., Henrissat, B., Doniger, T., and Banin, E. 2014. Draft genome sequence of Nonlabens ulvanivorans, an ulvan-degrading bacterium. Genome Announc. 2, e00793-14.
Genome Biol. Evol. S.K. Kwon 5 187 2013 10.1093/gbe/evs134 Kwon, S.K., Kim, B.K., Song, J.Y., Kwak, M.J., Lee, C.H., Yoon, J.H., Oh, T.K., and Kim, J.F. 2013. Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. Genome Biol. Evol. 5, 187-199.

상세보기
Nucleic Acids Res. K. Lagesen 35 3100 2007 10.1093/nar/gkm160 Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T., and Ussery, D.W. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108.

상세보기
Int. J. Syst. Evol. Microbiol. S.C. Lau 55 2497 2005 10.1099/ijs.0.63824-0 Lau, S.C., Tsoi, M.M., Li, X., Plakhotnikova, I., Dobretsov, S., Wong, P.K., and Qian, P.Y. 2005. Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 55, 2497-2500.

상세보기
Genome Biol. T. Lefébure 8 R71 2007 10.1186/gb-2007-8-5-r71 Lefébure, T. and Stanhope, M.J. 2007. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8, R71.

상세보기
Nucleic Acids Res. T.M. Lowe 25 955 1997 10.1093/nar/25.5.0955 Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.

상세보기
Int. J. Syst. Evol. Microbiol. O.I. Nedashkovskaya 55 391 2005 10.1099/ijs.0.63314-0 Nedashkovskaya, O.I., Kim, S.B., Lysenko, A.M., Frolova, G.M., Mikhailov, V.V., Bae, K.S., Lee, D.H., and Kim, I.S. 2005. Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int. J. Syst. Evol. Microbiol. 55, 391-394.

상세보기
Int. J. Syst. Evol. Microbiol. O.I. Nedashkovskaya 53 1281 2003 10.1099/ijs.0.02302-0 Nedashkovskaya, O.I., Suzuki, M., Vysotskii, M.V., and Mikhailov, V.V. 2003. Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides. Int. J. Syst. Evol. Microbiol. 53, 1281-1286.

상세보기
D.L. Nelson 653 2013 Lehninger principles of biochemistry Nelson, D.L. and Cox, M.M. 2013. Lehninger principles of biochemistry, p. 653.
Antonie van Leeuwenhoek S. Park 102 669 2012 10.1007/s10482-012-9765-4 Park, S., Yoshizawa, S., Chiura, H.X., Muramatsu, Y., Nakagawa, Y., Kogure, K., and Yokota, A. 2012. Nonlabens marinus sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean. Antonie van Leeuwenhoek 102, 669-676.

상세보기
J. Fish. Board Can. H. Poston 33 1803 1976 10.1139/f76-230 Poston, H. 1976. Optimum level of dietary biotin for growth, feed utilization, and swimming stamina of fingerling lake trout (Salvelinus namaycush). J. Fish. Board Can. 33, 1803-1806.

상세보기
Front. Microbiol. C. Ramírez 8 271 2017 10.3389/fmicb.2017.00271 Ramírez, C. and Romero, J. 2017. Fine flounder (Paralichthys adspersus) microbiome showed important differences between wild and reared specimens. Front. Microbiol. 8, 271.

상세보기
Essentiality of biotin for channel catfish (Ictalurus punctatus) fed lipid and lipid-free diets. J. Nutrit. E. Robinson 108 1600 1978 Robinson, E. and Lovell, R. 1978. Essentiality of biotin for channel catfish (Ictalurus punctatus) fed lipid and lipid-free diets. J. Nutrit. 108, 1600-1605.
Proc. Natl. Acad. Sci. USA S.A. Sañudo-Wilhelmy 109 14041 2012 10.1073/pnas.1208755109 Sañudo-Wilhelmy, S.A., Cutter, L.S., Durazo, R., Smail, E.A., Gómez-Consarnau, L., Webb, E.A., Prokopenko, M.G., Berelson, W.M., and Karl, D.M. 2012. Multiple B-vitamin depletion in large areas of the coastal ocean. Proc. Natl. Acad. Sci. USA 109, 14041-14045.

상세보기
Ann. Rev. Mar. Sci. S.A. Sañudo-Wilhelmy 6 339 2014 10.1146/annurev-marine-120710-100912 Sañudo-Wilhelmy, S.A., Gómez-Consarnau, L., Suffridge, C., and Webb, E.A. 2014. The role of B vitamins in marine biogeochemistry. Ann. Rev. Mar. Sci. 6, 339-367.

상세보기
Bull. Jap. Soc. Sci. Fish. T. Saisho 49 939 1983 10.2331/suisan.49.939 Saisho, T., Noguchi, T., Koyama, K., Uzu, A., Kikuta, T., and Hashimoto, K. 1983. Examination of stomach contents in xanthid crabs. Bull. Jap. Soc. Sci. Fish. 49, 939-947.

상세보기
J. Appl. Microbiol. M.K. Sang 113 383 2012 10.1111/j.1365-2672.2012.05330.x Sang, M.K. and Kim, K.D. 2012. The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J. Appl. Microbiol. 113, 383-398.

상세보기
Int. J. Syst. Evol. Microbiol. M. Suzuki 51 1639 2001 10.1099/00207713-51-5-1639 Suzuki, M., Nakagawa, Y., Harayama, S., and Yamamoto, S. 2001. Phylogenetic analysis and taxonomic study of marine Cytophagalike bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int. J. Syst. Evol. Microbiol. 51, 1639-1652.

상세보기
Nucleic Acids Res. R.L. Tatusov 28 33 2000 10.1093/nar/28.1.33 Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36.
Appl. Environ. Microbiol. M. Touchon 77 7656 2011 10.1128/AEM.05625-11 Touchon, M., Barbier, P., Bernardet, J.F., Loux, V., Vacherie, B., Barbe, V., Rocha, E.P., and Duchaud, E. 2011. Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl. Environ. Microbiol. 77, 7656-7662.

상세보기
PLoS Genet. M. Touchon 5 1000344 2009 10.1371/journal.pgen.1000344 Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, E., Bonacorsi, S., Bouchier, C., Bouvet, O., et al. 2009. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344.

상세보기
ISME J. P. Xing 9 1410 2015 10.1038/ismej.2014.225 Xing, P., Hahnke, R.L., Unfried, F., Markert, S., Huang, S., Barbeyron, T., Harder, J., Becher, D., Schweder, T., Glöckner, et al. 2015. Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME J. 9, 1410-1422.

상세보기
Mar. Genomics J.A. Yang 26 5 2016 10.1016/j.margen.2015.11.012 Yang, J.A., Kang, I., Moon, M., Ryu, U.C., Kwon, K.K., Cho, J.C., and Oh, H.M. 2016. Complete genome sequence of Celeribacter marinus IMCC12053T, the host strain of marine bacteriophage P12053L. Mar. Genomics 26, 5-7.

상세보기
Genome Announc. J.A. Yang 5 01551 2017 Yang, J.A., Kwon, K.K., and Oh, H.M. 2017. Complete genome sequence of Flavobacteriales bacterium strain UJ101 isolated from a Xanthid Crab. Genome Announc. 5, e01551-16.
Agricul. Biol. Chem. D. Yasumura 50 593 1986 Yasumura, D., Oshima, Y., Yasumoto, T., Alcala, A.C., and Alcala, L.C. 1986. Tetrodotoxin and paralytic shellfish toxins in Philippine crabs. Agricul. Biol. Chem. 50, 593-598.
Int. J. Syst. Evol. Microbiol. S.H. Yoon 67 1613 2016 10.1099/ijsem.0.001755 Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2016. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613-1617.

상세보기
Int. J. Syst. Evol. Microbiol. J.H. Yoon 55 793 2005 10.1099/ijs.0.63416-0 Yoon, J.H., Kang, S.J., and Oh, T.K. 2005. Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea. Int. J. Syst. Evol. Microbiol. 55, 793-798.

상세보기
BMC Genomics Y. Zhang 16 38 2015 10.1186/s12864-015-1275-0 Zhang, Y., Liu, J., Tang, K., Yu, M., Coenye, T., and Zhang, X.H. 2015. Genome analysis of Flaviramulus ichthyoenteri Th78T in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine. BMC Genomics 16, 38.

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Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus 원문보기

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Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus 원문보기

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