Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
권호 표지
DOI QR코드

DOI QR Code

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

16S rRNA 유전자의 454 파이로서열 분석을 이용한 해삼(Apostichopus japonicas)과 새우(Litopenaeus vannamei)의 장내 세균의 다양성 연구

  • 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)
  • Received : 2013.07.02
  • Accepted : 2013.09.25
  • Published : 2013.09.30
Download PDF
⟨ Previous Next ⟩

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.

16S rRNA 유전자를 대상으로 454 파이로서열 분석법을 이용하여 해삼(Apostichopus japonicus)과 새우(Litopenaeus vannamei)의 장내 세균의 다양성을 분석하였다. 해삼의 경우, 대부분의 서열은 두 개의 속과 연관성이 있는 것으로 나타났다. 하나는 Fusobacteria 문의 Propionigenium 속이며, 다른 하나는 Bacteroidetes 문의 Flavobacteriaceae 과에 속하는 미분류 속이었다. 새우는 해삼에 비해 다양한 속들을 포함하고 있었으며 Lactococcus, Leuconostoc, Prochlorococcus, Vibrio 속들과 Flavobacteriaceae, Rhodobacteraceae, Desulfobulbaceae, Helicobacteraceae 과와 Mycoplasmatales 목에 속하는 미분류 속들을 포함하고 있었다. 해삼과 새우의 속들의 절반 이상이 환경에서 비배양적으로 얻어진 서열만 존재하는 미분류된 속인 것으로 확인되었다. 대용량 454 파이로서열 분석법을 통하여 해삼과 새우의 장내 세균의 다양성을 밝힐 수 있었으며, 그 결과 해삼과 새우는 아직까지 밝혀지지 않는 새로운 미생물을 많이 포함하고 있는 것을 알 수 있었다.

Keywords

References

  1. 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. https://doi.org/10.1016/j.soilbio.2008.07.022
  2. 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.
  3. 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.
  4. 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. https://doi.org/10.1371/journal.pone.0000197
  5. 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.
  6. 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. https://doi.org/10.1111/j.1523-5378.2006.00413.x
  7. 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. https://doi.org/10.2323/jgam.52.273
  8. 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.
  9. 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. https://doi.org/10.1016/j.aquaculture.2008.10.015
  10. 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. https://doi.org/10.1089/fpd.2008.0107
  11. 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. https://doi.org/10.1186/1471-2164-7-57
  12. Ercolini, D. 2004. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Methods 56, 297-314. https://doi.org/10.1016/j.mimet.2003.11.006
  13. 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. https://doi.org/10.1128/AEM.70.6.3724-3732.2004
  14. 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. https://doi.org/10.1007/s00248-002-1011-6
  15. 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. https://doi.org/10.1016/j.aquaculture.2007.08.045
  16. 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.
  17. 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. https://doi.org/10.1007/BF02568731
  18. 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.
  19. 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. https://doi.org/10.1007/s12275-012-1214-6
  20. 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. https://doi.org/10.1007/s12275-012-1340-1
  21. Lightner, D.V. 2011. Virus diseases of farmed shrimp in the Western Hemisphere (the Americas): a review. J. Invertebr. Pathol. 106, 110-130. https://doi.org/10.1016/j.jip.2010.09.012
  22. 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. https://doi.org/10.1038/nature03959
  23. 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. https://doi.org/10.1038/ismej.2011.139
  24. 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. https://doi.org/10.1080/14888386.2010.9712666
  25. 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. https://doi.org/10.1038/nature12352
  26. 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. https://doi.org/10.1016/j.ijfoodmicro.2010.08.016
  27. 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. https://doi.org/10.1038/ismej.2009.83
  28. 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. https://doi.org/10.1128/AEM.01541-09
  29. 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. https://doi.org/10.1038/ismej.2011.116
  30. 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.
  31. 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. https://doi.org/10.1128/MMBR.64.4.655-671.2000
  32. 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. https://doi.org/10.1099/ijs.0.65060-0