Browse > Article
http://dx.doi.org/10.7845/kjm.2013.3044

Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes  

Noh, Eun Soo (Department of Microbiology, Pukyong National University)
Kim, Young-Sam (Department of Microbiology, Pukyong National University)
Kim, Dong-Hyun (Department of Microbiology, Pukyong National University)
Kim, Kyoung-Ho (Department of Microbiology, Pukyong National University)
Publication Information
Korean Journal of Microbiology / v.49, no.3, 2013 , pp. 237-244 More about this Journal
Abstract
Bacterial diversities in the guts of sea cucumbers (Apostichopus japonicus) and shrimps (Litopenaeus vannamei) were investigated using barcoded or tag-encoded 454 pyrosequencing of 16S rRNA genes. In sea cucumbers, most of sequences were related to two genera, the genus Propionigenium in the phylum Fusobacteria and an unclassified genus in the family Flavobacteriaceae of phylum Bacteroidetes. Shrimps showed various kinds of genera including Lactococcus, Leuconostoc, Prochlorococcus, and Vibrio as well as the unclassified genera in the families, Flavobacteriaceae, Rhodobacteraceae, Desulfobulbaceae, and Helicobacteraceae and in the order Mycoplasmatales. Unclassified genera containing environmental sequences only are more than half of genera from sea cucumbers and shrimps. Sea cucumbers and shrimps could be unexplored sources of novel microbes and the bacterial diversity of them was revealed by high throughput 454 pyrosequencing.
Keywords
bacterial diversity; sea cucumber; shrimp; tag-encoded 454 pyrosequencing;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
연도 인용수 순위
1 Dowd, S.E., Sun, Y., Wolcott, R.D., Domingo, A., and Carroll, J.A. 2008. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 5, 459-472.   DOI   ScienceOn
2 Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander Jr, E.C., and Rohwer, F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7, 57.   DOI   ScienceOn
3 Ercolini, D. 2004. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Methods 56, 297-314.   DOI   ScienceOn
4 Roh, S.W., Kim, K.H., Nam, Y.D., Chang, H.W., Park, E.J., and Bae, J.W. 2010. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J. 4, 1–16.   DOI   ScienceOn
5 Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., and et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541.   DOI   ScienceOn
6 Schmitt, S., Tsai, P., Bell, J., Fromont, J., Ilan, M., Lindquist, N., Perez, T., Rodrigo, A., Schupp, P.J., Vacelet, J., and et al. 2012. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J. 6, 564-576.   DOI
7 Seo, J.Y., Kim, D.G., Kim, G.U., Cho, S.S., Park, H.G., and Lee, S.M. 2009. Effect of different substrates in the rearing tank on growth and body composition of juvenile sea cucumber Apostichopus japonicus. J. Aquaculture 22, 118-121.
8 Verschuere, L., Rombaut, G., Sorgeloos, P., and Verstraete, W. 2000. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. Rev. 64, 655-671.   DOI   ScienceOn
9 Yang, S.J., Choo, Y.J., and Cho, J.C. 2007. Lutimonas vermicola gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine polychaete Periserrula leucophryna. Int. J. Syst. Evol. Microbiol. 57, 1679-1684.   DOI   ScienceOn
10 Acosta-Martinez, V., Dowd, S., Sun, Y., and Allen, V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol. Biochem. 40, 2762-2770.   DOI   ScienceOn
11 Amann, R.I., Ludwig, W., and Schleifer, K.H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
12 Bernardet, J.-F. and Nakagawa, Y. 2006. An Introduction to the Family Flavobacteriaceae. Vol. 7, pp. 455-480. The Prokaryotes: A Handbook on the Biology of Bacteria. In Rosenberg, E., Stackebrandt, E., Thompson, F., Lory, S., and DeLong, E.F. (eds.), Springer, New York, USA.
13 Binladen, J., Gilbert, M.T., Bollback, J.P., Panitz, F., Bendixen, C., Nielsen, R., and Willerslev, E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2, e197.   DOI
14 Both, B., Kaim, G., Wolters, J., Schleifer, K.H., Stackebrandt, E., and Ludwig, W. 1991. Propionigenium modestum: a separate line of descent within the eubacteria. FEMS Microbiol. Lett. 62, 53-58.
15 Bury-Mone, S., Kaakoush, N.O., Asencio, C., Megraud, F., Thibonnier, M., De Reuse, H., and Mendz, G.L. 2006. Is Helicobacter pylori a true microaerophile? Helicobacter 11, 296–303.   DOI   ScienceOn
16 Castroverde, C.D., San Luis, B.B., Monsalud, R.G., and Hedreyda, C.T. 2006. Differential detection of vibrios pathogenic to shrimp by multiplex PCR. J. Gen. Appl. Microbiol. 52, 273-280.   DOI   ScienceOn
17 Kuczynski, J., Stombaugh, J., Walters, W.A., Gonzalez, A., Caporaso, J.G., and Knight, R. 2012. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Microbiol. Chapter 1, Unit 1E 5.
18 Crab, R., Lambert, A., Defoirdt, T., Bossier, P., and Verstraete, W. 2010. The application of bioflocs technology to protect brine shrimp (Artemia franciscana) from pathogenic Vibrio harveyi. J. Appl. Microbiol. 109, 1643-1649.
19 Deng, H., He, C., Zhou, Z., Liu, C., Tan, K., Wang, N., Jiang, B., Gao, X., and Liu, W. 2009. Isolation and pathogenicity of pathogens from skin ulceration disease and viscera ejection syndrome of the sea cucumber Apostichopus japonicus. Aquaculture 287, 18–27.   DOI   ScienceOn
20 Janssen, P.H. and Liesack, W. 1995. Succinate decarboxylation by Propionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment. Arch. Microbiol. 164, 29-35.   DOI
21 Lee, J.H., Yi, H., Jeon, Y.S., Won, S., and Chun, J. 2012. TBC: a clustering algorithm based on prokaryotic taxonomy. J. Microbiol. 50, 181-185.   DOI
22 Li, X., Yu, Y., Feng, W., Yan, Q., and Gong, Y. 2012. Host species as a strong determinant of the intestinal microbiota of fish larvae. J. Microbiol. 50, 29-37.   DOI
23 Lightner, D.V. 2011. Virus diseases of farmed shrimp in the Western Hemisphere (the Americas): a review. J. Invertebr. Pathol. 106, 110-130.   DOI   ScienceOn
24 Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., and et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.   DOI
25 McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., DeSantis, T.Z., Probst, A., Andersen, G.L., Knight, R., and Hugenholtz, P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618.   DOI   ScienceOn
26 Fieseler, L., Horn, M., Wagner, M., and Hentschel, U. 2004. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl. Environ. Microbiol. 70, 3724-3732.   DOI   ScienceOn
27 Pangastuti, A., Suwanto, A., Lestari, Y., and Suhartono, M.T. 2010. Bacterial communities associated with white shrimp (Litopenaeus vannamei) larvae at early developmental stages. Biodiversitas 11, 65–68.   DOI
28 Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.F., Darling, A., Malfatti, S., Swan, B.K., Gies, E.A., and et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437.   DOI   ScienceOn
29 Robert-Pillot, A., Copin, S., Gay, M., Malle, P., and Quilici, M.L. 2010. Total and pathogenic Vibrio parahaemolyticus in shrimp: fast and reliable quantification by real-time PCR. Int. J. Food Microbiol. 143, 190-197.   DOI   ScienceOn
30 Holben, W.E., Williams, P., Gilbert, M., Saarinen, M., Sarkilahti, L.K., and Apajalahti, J.H. 2002. Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microb. Ecol. 44, 175-185.   DOI   ScienceOn
31 Hovdaa, M.B., Lunestadc, B.T., Fontanillasd, R., and Rosnesa, J.T. 2007. Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture 272, 581-588.   DOI   ScienceOn
32 Jang, I., Kim, J., Cho, K., Seo, H., Cho, Y., Gopalakannan, A., and Kim, B. 2008. Intensive culture of the Pacific white shrimp, Litopenaeus vannamei, under limited water exchange. I. Indoor nursery culture of postlarvae. J. Aquaculture 21, 339-345.