Advertisement

Journal of Microbiology

, Volume 52, Issue 8, pp 646–651 | Cite as

Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines

  • Edward Alain B. Pajarillo
  • Jong Pyo Chae
  • Marilen P. Balolong
  • Hyeun Bum Kim
  • Kang-Seok Seo
  • Dae-Kyung Kang
Microbial Ecology and Environmental Microbiology

Abstract

This study examined the fecal bacterial diversity of 15-weekold pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Keywords

pyrosequencing 16S rRNA genes microbiome pig breeds 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12275_2014_4270_MOESM1_ESM.pdf (102 kb)
Supplementary material, approximately 102 KB.
12275_2014_4270_MOESM2_ESM.xlsx (87 kb)
Supplementary material, approximately 87.2 KB.

References

  1. Brodziak, F., Meharg, C., Blaut, M., and Loh, G. 2013. Differences in mucosal gene expression in the colon of two inbred mouse strains after colonization with commensal gut bacteria. PLoS ONE 8, e72317.CrossRefGoogle Scholar
  2. Campbell, J.H., Foster, C.M., Vishnivetskaya, T., Campbell, A.G., Yang, Z.K., Wymore, A., Palumbo, V., Chesler, E.J., and Podar, M. 2012. Host genetic and environmental effects on mouse intestinal microbiota. ISME J. 6, 2033–2044.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Chmielowiec-Korzeniowska, A., Tymczyna, L., and Babicz, M. 2012. Assessment of selected parameters of biochemistry, hematology, immunology and production of pigs fattened in different seasons. Archiv. Tierzucht. 5, 469–479.Google Scholar
  4. Chun, J., Lee, J.H., Jung, Y., Kim, M., Kim, S., Kim, B.K., and Lim, Y.W. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57, 2259–2261.PubMedCrossRefGoogle Scholar
  5. de Sevilla, X.F., Fàbrega, E., Tibau, J., and Casellas, J. 2008. Effect of leg conformation on survivability of Duroc, Landrace, and Large White sows. J. Anim. Sci. 86, 2392–2400.PubMedCrossRefGoogle Scholar
  6. 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.PubMedCrossRefGoogle Scholar
  7. Gibson, G.R. and Roberfroid, M.B. 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125, 1401–1412.PubMedGoogle Scholar
  8. Guixin, Q., Verstegen, M.W.A., and Bosch, M.W. 1995. Variation of digestive capacity between genetically different pig populations: a review. J. Anim. Physiol. Anim. Nutr. 73, 233–242.CrossRefGoogle Scholar
  9. Hildebrand, F., Nguyen, T., Brinkman, B., Yunta, R.G., Cauwe, B., Vandenabeele, P., Liston, A., and Raes, J. 2013. Inflammationassociated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol. 14, R4.CrossRefGoogle Scholar
  10. Ibáñez-Escriche, N., Reixach, J., Lleonart, N., and Noguera, J.L. 2011. Genetic evaluation combining purebred and crossbred data in a pig breeding scheme. J. Anim. Sci. 89, 3881–3889.PubMedCrossRefGoogle Scholar
  11. Jeon, Y.S., Chun, J., and Kim, B.S. 2013. Identification of household bacterial community and analysis of species shared with human microbiome. Curr. Microbiol. 67, 557–563.PubMedCentralPubMedCrossRefGoogle Scholar
  12. Jeong, J.Y., Park, H.D., Lee, K.H., Weon, H.Y., and Ka, J.O. 2011. Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing. J. Microbiol. 49, 585–594.PubMedCrossRefGoogle Scholar
  13. Jombart, T. and Ahmed, I. 2011. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071. doi: 10.1093/bioinformatics/btr5-1.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Jung, J.Y., Lee, S.H., Kim, J.M., Park, M.S., Bae, J.W., Hahn, Y., Madsen, E.L., and Jeon, C.O. 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77, 2264–2274.PubMedCentralPubMedCrossRefGoogle Scholar
  15. Kerr, K.R., Forster, G., Dowd, S.E., Ryan, E.P., and Swanson, K.S. 2013. Effects of dietary cooked navy bean on the fecal microbiome of healthy companion dogs. PLoS ONE 8, e74998. doi:  10.1371/journal.pone.0074-98.CrossRefGoogle Scholar
  16. Kim, H.B., Borewicz, K., White, B.A., Singer, R.S., Sreevatsan, S., Tu, Z.J., and Isaacson, R.E. 2011. Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Vet. Microbiol. 153, 124–133.PubMedCrossRefGoogle Scholar
  17. Kim, H.B., Borewicz, K., White, B.A., Singer, R.S., Sreevatsan, S., Tu, Z.J., and Isaacson, R.E. 2012a. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. Proc. Natl. Acad. Sci. USA 109, 15485–15490.PubMedCentralPubMedCrossRefGoogle Scholar
  18. Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee, J.H., Yi, H., Won, S., and Chun, J. 2012b. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721.PubMedCrossRefGoogle Scholar
  19. Kim, O.S., Chae, N., Lim, H.S., Cho, A., and Kim, J.H.. 2012c. Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica. J. Microbiol. 50, 1081–1085.CrossRefGoogle Scholar
  20. Kim, T.H., Kim, K.S., Choi, B.H., Yoon, D.H., Jang, G.W., Lee, K.T., Chung, H.Y., Lee, H.Y., Park, H.S., and Lee, J.W. 2005. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J. Anim. Sci. 83, 2255–2263.PubMedGoogle Scholar
  21. Lamendella, R., Li, K.C., Oerther, D., and Santo Domingo, J.W. 2013. Molecular diversity of Bacteroidales in fecal and environmental samples and swine-associated subpopulations. Appl. Environ. Microbiol. 79, 816–824.PubMedCentralPubMedCrossRefGoogle Scholar
  22. Ley, R.E., Peterson, D.A., and Gordon, J.I. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837–848.PubMedCrossRefGoogle Scholar
  23. Loh, G., Brodziak, F., and Blaut, M. 2008. The Toll-like receptors TLR2 and TLR4 do not affect the intestinal microbiota composition in mice. Environ. Microbiol. 10, 709–715.PubMedCrossRefGoogle Scholar
  24. Lu, X.M., Lu, P.Z., and Zhang, H. 2013. Bacterial communities in manures of piglets and adult pigs bred with different feeds revealed by 16S rDNA 454 pyrosequencing. Appl. Microbiol. Biotechnol. doi:  10.1007/s00253-013-5211-4.Google Scholar
  25. Malmuthuge, N., Griebel, P.J., and Guan, L. 2014. Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves. Appl. Environ. Microbiol. 80, 2021–2028.PubMedCrossRefGoogle Scholar
  26. McKnite, A.M., Perez-Munoz, M.E., Lu, L., Williams, E.G., Brewer, S., Andreux, P.A., Bastiaansen, J.W., Wang, X., Kachman, S.D., Auwerx, J., and et al. 2012. Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLoS ONE 7, e39171.CrossRefGoogle Scholar
  27. Na, H., Kim, O.K., Yoon, S.H., Kim, Y., and Chun, J. 2011. Comparative approach to capture bacterial diversity of coastal waters. J. Microbiol. 49, 729–740.PubMedCrossRefGoogle Scholar
  28. O’Hara, A.M. and Shanahan, F. 2006. The gut flora as a forgotten organ. EMBO Rep. 7, 688–693.PubMedCentralPubMedCrossRefGoogle Scholar
  29. Rehman, A., Sina, C., Gavrilova, O., Häsler, R., Ott, S., Baines, J.F., Schreiber, S., and Rosenstiel, P. 2011. Nod2 is essential for temporal development of intestinal microbial communities. Gut 60, 1354–1362.PubMedCrossRefGoogle Scholar
  30. Shan, T., Reng, Y., Liu, Y., Zhu, L., and Wang, Y. 2010. Breed difference and regulation of the porcine Sirtuin 1 by insulin. J. Anim. Sci. 88, 3909–3917.PubMedCrossRefGoogle Scholar
  31. Shepherd, M.L., Swecker, W.S., Jensen, R.V., and Ponder, M.A. 2012. Characterization of the fecal bacteria communities of forage- fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. FEMS Microbiol. Lett. 326, 62–68.PubMedCrossRefGoogle Scholar
  32. Song, Y.G., Shim, S.G., Kim, K.M., Lee, D.H., Kim, D.S., Choi, S.H., Song, J.Y., Kang, H.L., Baik, S.C., Lee, W.K., and et al. 2014. Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing. J. Microbiol. 52, 504–509.PubMedCrossRefGoogle Scholar
  33. Strong, T., Dowd, S., Gutierrez, A.F., and Coffman, J. 2013. Amplicon pyrosequencing of wild duck eubacterial microbiome from a fecal sample reveals numerous species linked to human and animal diseases [v1; ref status: approved with reservations 1, not approved 1, http://f1000r.es/1yy] F1000Research 2013, 2, 224. doi:  10.12688/f1000research.2-224.v1.Google Scholar
  34. Tantasuparuk, W., Lundeheim, N., and Dalin, A.M. 2000. Reproductive performance of purebred Landrace and Yorkshire sows in Thailand with special reference to seasonal influence and parity number. Theriogenology 54, 481–496.PubMedCrossRefGoogle Scholar
  35. Yan, H., Potu, R., Lu, H., de Almeida, V.V., Stewart, T., Ragland, D., Armstrong, A., Adeola, O., Nakatsu, C.H., and Ajuwon, K.M. 2013. Dietary fat content and fiber type modulate hind gut microbial community and metabolic markers in the pig. PLoS ONE 8, e59581. doi: 10.1371.journal.pone.005913;81.CrossRefGoogle Scholar
  36. Yang, L., Bian, G., Su, Y., and Zhu, W. 2014. Comparison of faecal microbial community of lantang, bama, erhualian, meishan, xiaomeishan, duroc, landrace, and yorkshire sows. Asian Australas. J. Anim. Sci. 27, 898–906.PubMedCentralPubMedCrossRefGoogle Scholar
  37. Yu, Z. and Morrison, M. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808–812.PubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Edward Alain B. Pajarillo
    • 1
  • Jong Pyo Chae
    • 1
  • Marilen P. Balolong
    • 1
    • 2
  • Hyeun Bum Kim
    • 1
  • Kang-Seok Seo
    • 3
  • Dae-Kyung Kang
    • 1
  1. 1.Department of Animal Resources ScienceDankook UniversityCheonanRepublic of Korea
  2. 2.Department of BiologyUniversity of the Philippines ManilaManilaPhilippines
  3. 3.Department of Animal Science and TechnologySunchon National UniversitySunchonRepublic of Korea

Personalised recommendations