Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

  • Pajarillo, Edward Alain B. (Department of Animal Resources Science, Dankook University) ;
  • Chae, Jong Pyo (Department of Animal Resources Science, Dankook University) ;
  • Balolong, Marilen P. (Department of Animal Resources Science, Dankook University) ;
  • Kim, Hyeun Bum (Department of Animal Resources Science, Dankook University) ;
  • Seo, Kang-Seok (Department of Animal Science and Technology, Sunchon National University) ;
  • Kang, Dae-Kyung (Department of Animal Resources Science, Dankook University)
  • Received : 2014.08.25
  • Accepted : 2014.11.03
  • Published : 2015.04.01


This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.


Supported by : Rural Development Administration


  1. Brossard, L., J. -Y. Dourmad, J. Rivest, and J. van Milgen. 2009. Modelling the variation in performance of a population of growing pig as affected by lysine supply and feeding strategy. Animal 3:1114-1123.
  2. Canibe, N., O. Hojberg, S. Hojsgaard, and B. B. Jensen. 2005. Feed physical form and formic acid addition to the feed affect the gastrointestinal ecology and growth performance of growing pigs. J. Anim. Sci. 83:1287-1302.
  3. Chun, J., J. -H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y. W. Lim. 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.
  4. Dougal, K., G. de la Fuente, P. A. Harris, S. E. Girdwood, E. Pinloche, R. J. Geor, B. D. Nielsen, H. C. Schott II, S. Elzinga, and C. J. Newbold. 2014. Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing. PLoS One 9(2):e87424.
  5. Dowd, S. E., Y. Sun, R. D. Wolcott, A. Domingo, and J. A. Carroll. 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.
  6. Gao, Z., C. H. Tseng, Z. Pei, and M. J. Blaser. 2007. Molecular analysis of human forearm superficial skin bacterial biota. Proc. Natl. Acad. Sci. USA. 104:2927-2932.
  7. Georgsson, L. and J. Svendsen. 2002. Degree of competition at feeding differentially affects behavior and performance of group-housed growing-finishing pigs of different relative weights. J. Anim. Sci. 80:376-383.
  8. Guan, L. L., J. D. Nkrumah, J. A. Basarab, and S. S. More. 2008. Linkage of microbial ecological to phenotype: Correlation of rumen microbial ecology to cattle's feed efficiency. FEMS Microbiol. Lett. 288:85-91.
  9. Hong, S. M., J. H. Hwang, and I. H. Kim. 2012. Evaluation of the effect of low dietary fermentable carbohydrate content on growth performance, nutrient digestibility, blood characteristics, and meat quality in finishing pigs. Asian Australas. J. Anim. Sci. 25:1294-1299.
  10. Iino, T., K. Mori, K. Tanaka, K. Suzuki, and S. Harayama. 2007. Oscillibacter valericigenes gen. nov., sp. nov., a valerateproducing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam. Int. J. Syst. Evol. Microbiol. 57:1840-1845.
  11. Ige, B. A. 2013. Probiotics use in intensive fish farming. Afr. J. Microbiol. Res. 7:2701-2711.
  12. Kim, H. B., K. Borewicz, B. A. White, R. S. Singer, S. Sreevatsan, Z. J. Tu, and R. E. Isaacson. 2011. Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Vet. Microbiol. 153:124-133.
  13. Kim, H. B., K. Borewicz, B. A. White, R. S. Singer, S. Sreevatsan, Z. J. Tu, and R. E. Isaacson. 2012. 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.
  14. Laerke, H. N. and B. B. Jensen. 1999. D-Tagatose has low small intestinal digestibility but high large intestinal fermentability in pigs. J. Nutr. 129:1002-1009.
  15. Lamendella, R., J. W. S. Domingo, S. Ghosh, J. Martinson, and D. B. Oerther. 2011. Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol. 11:103-120.
  16. Lu, X. -M., P. -Z. Lu, and H. Zhang. 2013. Bacterial communities in manures of piglets and adult pigs bred with different feeds revealed by 16 rDNA 454 pyrosequencing. Appl. Microbiol. Biotechnol. 98:2657-2665.
  17. Mosenthin, R. 1998. Physiology of small and large intestine of swine - Review -. Asian Australas. J. Anim. Sci. 11:608-619.
  18. Pajarillo, E. A. B., J. P. Chae, M. P. Balolong, H. B. Kim, K. -S. Seo, and Kang D.-K. 2014a. Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines. J. Microbiol. 52:646-651.
  19. Pajarillo, E. A. B., J. P. Chae, M. P. Balolong, H. B. Kim, and D. -K. Kang. 2014b. Assessment of fecal bacterial diversity among healthy piglets during the weaning transition. J. Gen. Appl. Microbiol. 60:140-146.
  20. Park, J. C., S. H. Lee, J. K. Hong, J. H. Cho, I. H. Kim, and S. K. Park. 2014. Effect of dietary supplementation of procyanidin on growth performance and immune response in pigs. Asian Australas. J. Anim. Sci. 27:131-139.
  21. Pieper, R., P. Janczyk, V. Urubschurov, U. Korn, B. Pieper, and W. B. Souffrant. 2009. Effect of a single oral administration of Lactobacillus plantarum DSMZ 8862/8866 before and at the time point of weaning on intestinal microbial communities in piglets. Int. J. Food Microbiol. 130:227-232.
  22. Politis, D. N. and J. P. Romano. 1993. On the sample variance of linear statistics derived from mixing sequences. Stoch. Process. Appl. 45:155-167.
  23. Richards, J. D., J. Gong, and C. F. M. de Lange. 2005. The gastrointestinal microbiota and its role in monogastric nutrition and health with an emphasis on pigs: Current understanding, possible modulations, and new technologies for ecological studies. Can. J. Anim. Sci. 85:421-435.
  24. Schwab, C. R. 2007. Quantitative and Molecular Genetic Components of Selection for Intramuscular Fat in Duroc Swine. Ph.D. Thesis, Iowa State University, Ames, IA, USA.
  25. Siavoshian, S., H. M. Biottiere, E. Le Foll, B. Kaeffer, C. Cherbut, and J. P. Galmiche. 1997. Comparison of the effect of short chain fatty acids on the growth and differentiation of human colonic carcinoma cell lines in vitro. Cell Biol. Int. 21:281-287.
  26. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
  27. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
  28. Yang, L., G. Bian, Y. Su, and W. Zhu. 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.
  29. Zhou, X., R. Westman, R. Hickey, M. A. Hansmann, C. K. Kennedy, T. W. Osborn, and L. J. Forney. 2009. Vaginal microbiota of women with frequent vulvovaginal candidiasis. Infect. Immun. 77:4130-4135.

Cited by

  1. High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite vol.16, pp.1, 2016,
  2. sp. in swine: insights from gut microbiota vol.122, pp.3, 2017,
  3. Porcine intestinal microbiota is shaped by diet composition based on rye or triticale vol.123, pp.6, 2017,
  4. Protective effects of Bacillus subtilis against Salmonella infection in the microbiome of Hy-Line Brown layers vol.30, pp.9, 2017,
  5. Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth vol.6, pp.1, 2018,
  6. Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios vol.111, pp.9, 2018,