Journal of Animal Environmental Science (한국축산시설환경학회지)

The Korean Society of Animal Environmental Science & Technology (한국축산환경학회)
권호 표지
DOI QR코드

DOI QR Code

Application of Next Generation Sequencing to Investigate Microbiome in the Livestock Sector

Next Generation Sequencing을 통한 미생물 군집 분석의 축산분야 활용

  • Kim, Minseok (Animal Nutrition and Physiology Team, National Institute of Animal Science) ;
  • Baek, Youlchang (Animal Nutrition and Physiology Team, National Institute of Animal Science) ;
  • Oh, Young Kyoon (Animal Nutrition and Physiology Team, National Institute of Animal Science)
  • 김민석 (농촌진흥청 국립축산과학원) ;
  • 백열창 (농촌진흥청 국립축산과학원) ;
  • 오영균 (농촌진흥청 국립축산과학원)
  • Received : 2015.07.09
  • Accepted : 2015.08.12
  • Published : 2015.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

Keywords

References

  1. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R., 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7, 335-336. https://doi.org/10.1038/nmeth.f.303
  2. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A,, Turnbaugh, P.J., Fierer, N., Knight, R., 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U. S. A. 108 Suppl 1, 4516-4522. https://doi.org/10.1073/pnas.1000080107
  3. Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., Sun, Y., Brown, C.T., Porras-Alfaro, A., Kuske, C.R., Tiedje, J. M., 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic. Acids. Res. 42, D633- D642. https://doi.org/10.1093/nar/gkt1244
  4. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G.L., 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072. https://doi.org/10.1128/AEM.03006-05
  5. Eden, P.A., Schmidt, T.M., Blakemore, R. P., Pace, N.R., 1991. Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int. J. Syst. Bacteriol. 41, 324-325. https://doi.org/10.1099/00207713-41-2-324
  6. Freetly HC, Lindholm-Perry AK, Hales KE, Brown-Brandl TM, Kim M, Myer PR, Wells JE. 2015. Methane production and methanogen levels in steers that differ in residual gain. J. Anim. Sci. 93, 2375-2381. https://doi.org/10.2527/jas.2014-8721
  7. Hwang, O.H., Raveendar, S., Kim, Y.J., Kim, J.H., Choi, J.W., Kim, T.H., Choi, D.Y., Jeon, C.O., Cho, S.B., Lee, K.T., 2014. Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis. J. Microbiol. 52, 918-929. https://doi.org/10.1007/s12275-014-4251-5
  8. Kim, M., Morrison, M., Yu, Z., 2011a. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS. Microbiol. Ecol. 76, 49-63. https://doi.org/10.1111/j.1574-6941.2010.01029.x
  9. Kim, M., Morrison, M., Yu, Z., 2011b. Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments. Folia. Microbiol. 56, 453-458. https://doi.org/10.1007/s12223-011-0066-5
  10. Kim, M., Morrison, M., Yu, Z., 2011c. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J. Microbiol. Methods. 84, 81-87. https://doi.org/10.1016/j.mimet.2010.10.020
  11. Kim, M., Yu, Z., 2012. Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets. J. Anim. Sci. Biotechnol. 3, 28. https://doi.org/10.1186/2049-1891-3-28
  12. Kim, M., Wang, L., Morrison, M., Yu, Z., 2014a. Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities. J. Appl. Microbiol. 117, 949-960. https://doi.org/10.1111/jam.12598
  13. Kim, M., Kim, J., Kuehn, L.A., Bono, J.L., Berry, E.D., Kalchayanand, N., Freetly, H.C., Benson, A.K., Wells, J.E., 2014b. Investigation of bacterial diversity in the feces of cattle fed different diets. J. Anim. Sci. 92, 683-694. https://doi.org/10.2527/jas.2013-6841
  14. Kumari, P., Choi, H.L., Sudiarto, S.I., 2015. Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry. PLoS. One. 10, e0139437. https://doi.org/10.1371/journal.pone.0139437
  15. Mosher, J.J., Bowman, B., Bernberg, E.L., Shevchenko, O., Kan, J., Korlach, J., Kaplan, L.A., 2014. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. J. Microbiol. Methods. 104, 59-60. https://doi.org/10.1016/j.mimet.2014.06.012
  16. Myer, P.R., Smith, T.P., Wells, J.E., Kuehn, L.A., Freetly, H.C., 2015. Rumen microbiome from steers differing in feed efficiency. PLoS One. 10, e0129174. https://doi.org/10.1371/journal.pone.0129174
  17. Park, S.J., Kim, J., Lee, J.S., Rhee, S.K., Kim, H., 2014. Characterization of the fecal microbiome in different swine groups by high-throughput sequencing. Anaerobe. 28, 157-162. https://doi.org/10.1016/j.anaerobe.2014.06.002
  18. Ruff-Roberts, A.L., Kuenen, J.G., Ward, D.M., 1994. Distribution of cultivated and uncultivated cyanobacteria and Chloroflexuslike bacteria in hot spring microbial mats. Appl. Environ. Microbiol. 60, 697-704.
  19. Schloss, P.D., Handelsman, J., 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68, 686-691. https://doi.org/10.1128/MMBR.68.4.686-691.2004
  20. 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., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J., Weber, C. F., 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
  21. Wei, S., Morrison, M., Yu, Z., 2013. Bacterial census of poultry intestinal microbiome. 92, 671-683. https://doi.org/10.3382/ps.2012-02822
  22. Woese, C.R., Fox, G.E., 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U. S. A. 74, 5088-5090. https://doi.org/10.1073/pnas.74.11.5088
  23. Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., Glockner, F.O., 2014. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic. Acids. Res. 42, D643-D648. https://doi.org/10.1093/nar/gkt1209
  24. Yu, Z., Morrison, M., 2004a. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70, 4800-4806. https://doi.org/10.1128/AEM.70.8.4800-4806.2004
  25. Yu, Z., Morrison, M., 2004b. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 36, 808-812.
  26. Zhou, M., Hernandez-Sanabria, E., Guan, L.L., 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl. Environ. Microbiol. 75, 6524-6533. https://doi.org/10.1128/AEM.02815-08