Skip to main content Accessibility help

The intestinal microbiome of the pig

  • Richard Isaacson (a1) and Hyeun Bum Kim (a1)

The intestinal microbiome has been the subject of study for many decades because of its importance in the health and well being of animals. The bacterial components of the intestinal microbiome have closely evolved as animals have and in so doing contribute to the overall development and metabolic needs of the animal. The microbiome of the pig has been the subject of many investigations using culture-dependent methods and more recently using culture-independent techniques. A review of the literature is consistent with many of the ecologic principles put forth by Rene Dubos. Animals develop an intestinal microbiome over time and space. During the growth and development of the pig, the microbiome changes in composition in a process known as the microbial succession. There are clear and distinct differences in the composition of the pig intestinal microbiome moving from the proximal end of the intestinal tract to the distal end. The majority (>90%) of the bacteria in the pig intestinal microbiome are from two Phyla: Firmicutes and Bacteroidetes. However, the ileum has a high percentage of bacteria in the phylum Proteobacterium (up to 40%). Perturbations to the microbiome occur in response to many factors including stresses, treatment with antibiotics, and diet.

Corresponding author
*Corresponding author. E-mail:
Hide All
Allen, HK, Looft, T, Bayles, DO, Humphrey, S, Levine, UY, Alt, D and Stanton, TB (2011). Antibiotics in feed induce prophages in swine fecal microbiomes. mBio 2.
Allison, MJ, Robinson, IM, Bucklin, JA and Booth, GD (1979). Comparison of bacterial populations of the pig cecum and colon based upon enumeration with specific energy sources. Applied and Environmental Microbiology 37: 11421151.
Backhed, F, Ley, RE, Sonnenburg, JL, Peterson, DA and Gordon, JI (2005). Host–bacterial mutualism in the human intestine. Science 307: 19151920.
Berg, RD (1996). The indigenous gastrointestinal microflora. Trends in Microbiology 4: 430435.
Brogden, KA, Guthmiller, JM and Taylor, CE (2005). Human polymicrobial infections. Lancet 365: 253255.
Bryant, MP (1972). Commentary on the Hungate technique for culture of anaerobic bacteria. American Journal of Clinical Nutrition 25: 13241328.
Collier, CT, Smiricky-Tjardes, MR, Albin, DM, Wubben, JE, Gabert, VM, Deplancke, B, Bane, D, Anderson, DB and Gaskins, HR (2003). Molecular ecological analysis of porcine ileal microbiota responses to antimicrobial growth promoters. Journal of Animal Science 81: 30353045.
Dethlefsen, L, Huse, S, Sogin, ML and Relman, DA (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology 6: e280.
Dowd, SE, Callaway, TR and Morrow-Tesch, J (2007). Handling may cause increased shedding of Escherichia coli and total coliforms in pigs. Foodborne Pathogens and Disease 4: 99–102.
Dowd, SE, Sun, Y, Wolcott, RD, Domingo, A and Carroll, JA (2008). Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathogens and Disease 5: 459472.
Dubos, R, Schaedler, RW, Costello, R and Hoet, P (1965). Indigenous, normal, and autochthonous flora of the gastrointestinal tract. Journal of Experimental Medicine 122: 6776.
Fox, G, Stackebrandt, E, Hespell, R, Gibson, J, Maniloff, J, Dyer, TA, Wolfe, RS, Balch, WE, Tanner, RS, Magrum, LJ, Zablen, LB, Blakemore, R, Gupta, R, Bonen, L, Lewis, BJ, Stahl, DA, Luehrsen, KR, Chen, KN and Woese, CR (1980). The phylogeny of prokaryotes. Science 209: 457463.
Gilliland, SE and Speck, ML (1977). Deconjugation of bile acids by intestinal lactobacilli. Applied and Environmental Microbiology 33: 1518.
International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature 431: 931945.
Isaacson, R, Borewicz, K, Kim, HB, Vannucci, F, Gebhart, C, Singer, R, Sreevatsan, S and Johnson, T (2011). Lawsonia interacellularis increases Salmonella enterica levels in the intestines of pigs. In Conference of Research Workers in Animal Diseases, Chicago, Illinois, abstract #107.
Isaacson, RE, Firkins, LD, Weigel, RM, Zuckermann, FA and DiPietro, JA (1999). Effect of transportation and feed withdrawal on shedding of Salmonella Typhimurium among experimentally infected pigs. American Journal of Veterinary Research 60: 11551158.
Janczyk, P, Pieper, R, Smidt, H and Souffrant, WB (2007). Changes in the diversity of pig ileal lactobacilli around weaning determined by means of 16S rRNA gene amplification and denaturing gradient gel electrophoresis. FEMS Microbiology Ecology 61: 132140.
Kim, HB, Borewicz, K, White, BA, Singer, RS, Sreevatsan, S, Tu, ZJ and Isaacson, RE (2011). Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Veterinary Microbiology 153: 124133.
Lamendella, R, Domingo, JW, Ghosh, S, Martinson, J and Oerther, DB (2011). Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiology 11: 103.
Lederberg, J and McCray, AT (2001). ‘Ome sweet’ omics – a genealogical treasury of words. The Scientist 15: 8.
Leser, TD, Amenuvor, JZ, Jensen, TK, Lindecrona, RH, Boye, M and Moller, K (2002). Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Applied and Environmental Microbiology 68: 673690.
Leser, TD, Lindecrona, RH, Jensen, TK, Jensen, BB and Moller, K (2000). Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae. Applied and Environmental Microbiology 66: 32903296.
Leslie, M (2012). Immunology. Gut microbes keep rare immune cells in line. Science 335: 1428.
Looft, T, Johnson, TA, Allen, HK, Bayles, DO, Alt, DP, Stedtfeld, RD, Chai, B, Cole, JR, Hashsham, SA, Tiedje, JM and Stanton, TB (2012). In-feed antibiotic effects on the swine intestinal microbiome. Proceedings of the National Academy of Sciences, USA 109: 16911696.
Luckey, TD (1972). Introduction to intestinal microecology. American Journal of Clinical Nutrition 25: 12921294.
Mazmanian, SK, Liu, CH, Tzianabos, AO and Kasper, DL (2005). An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107118.
Nocker, A, Burr, M and Camper, AK (2007). Genotypic microbial community profiling: a critical technical review. Microbial Ecology 54: 276289.
Olsen, GJ and Woese, CR (1993). Ribosomal RNA: a key to phylogeny. FASEB Journal 7: 113123.
Peterson, J, Garges, S, Giovanni, M, McInnes, P, Wang, L, Schloss, JA, Bonazzi, V, McEwen, JE, Wetterstrand, KA, Deal, C, Baker, CC, Di Francesco, V, Howcroft, TK, Karp, RW, Lunsford, RD, Wellington, CR, Belachew, T, Wright, M, Giblin, C, David, H, Mills, M, Salomon, R, Mullins, C, Akolkar, B, Begg, L, Davis, C, Grandison, L, Humble, M, Khalsa, J, Little, AR, Peavy, H, Pontzer, C, Portnoy, M, Sayre, MH, Starke-Reed, P, Zakhari, S, Read, J, Watson, B and Guyer, M (2009). The NIH Human Microbiome Project. Genome Research 19: 23172323.
Phillips, I, Casewell, M, Cox, T, De Groot, B, Friis, C, Jones, R, Nightingale, C, Preston, R and Waddell, J (2004). Does the use of antibiotics in food animals pose a risk to human health? A critical review of published data. Journal of Antimicrobial Chemotherapy 53: 2852.
Pieper, R, Janczyk, P, Urubschurov, V, Korn, U, Pieper, B and Souffrant, WB (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. International Journal of Food Microbiology 130: 227232.
Pryde, SE, Richardson, AJ, Stewart, CS and Flint, HJ (1999). Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Applied and Environmental Microbiology 65: 53725377.
Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C, Nielsen, T, Pons, N, Levenez, F, Yamada, T, Mende, DR, Li, J, Xu, J, Li, S, Li, D, Cao, J, Wang, B, Liang, H, Zheng, H, Xie, Y, Tap, J, Lepage, P, Bertalan, M, Batto, JM, Hansen, T, Le Paslier, D, Linneberg, A, Nielsen, HB, Pelletier, E, Renault, P, Sicheritz-Ponten, T, Turner, K, Zhu, H, Yu, C, Li, S, Jian, M, Zhou, Y, Li, Y, Zhang, X, Li, S, Qin, N, Yang, H, Wang, J, Brunak, S, Doré, J, Guarner, F, Kristiansen, K, Pedersen, O, Parkhill, J, Weissenbach, J; MetaHIT Consortium, Bork, P, Ehrlich, SD and Wang, J (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 5965.
Rakoff-Nahoum, S, Paglino, J, Eslami-Varzaneh, F, Edberg, S and Medzhitov, R (2004). Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118: 229241.
Ramotar, K, Conly, JM, Chubb, H and Louie, TJ (1984). Production of menaquinones by intestinal anaerobes. Journal of Infectious Diseases 150: 213218.
Rettedal, E, Vilain, S, Lindblom, S, Lehnert, K, Scofield, C, George, S, Clay, S, Kaushik, RS, Rosa, AJ, Francis, D and Brözel, VS (2009). Alteration of the ileal microbiota of weanling piglets by the growth-promoting antibiotic chlortetracycline. Applied and Environmental Microbiology 75: 54895495.
Robinson, IM, Allison, MJ and Bucklin, JA (1981). Characterization of the cecal bacteria of normal pigs. Applied and Environmental Microbiology 41: 950955.
Robinson, IM, Whipp, SC, Bucklin, JA and Allison, MJ (1984). Characterization of predominant bacteria from the colons of normal and dysenteric pigs. Applied and Environmental Microbiology 48: 964969.
Roediger, WE (1980). Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut 21: 793798.
Russell, EG (1979). Types and distribution of anaerobic bacteria in the large intestine of pigs. Applied and Environmental Microbiology 37: 187193.
Savage, DC (1977). Microbial ecology of the gastrointestinal tract. Annual Reviews in Microbiology 31: 107133.
Schloss, PD and Handelsman, J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 71: 15011506.
Schuster, SC (2008). Next-generation sequencing transforms today's biology. Nature Methods 5: 1618.
Sellon, RK, Tonkonogy, S, Schultz, M, Dieleman, LA, Grenther, W, Balish, E, Rennick, DM and Sartor, RB (1998). Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice. Infection and Immunity 66: 52245231.
Shan, T, Li, L, Simmonds, P, Wang, C, Moeser, A and Delwart, E (2011). The fecal virome of pigs on a high-density farm. Journal of Virology 85: 1169711708.
Shimada, K, Bricknell, KS and Finegold, SM (1969). Deconjugation of bile acids by intestinal bacteria: review of literature and additional studies. Journal of Infectious Diseases 119: 273281.
Simpson, JM, Kocherginskaya, S, Aminov, RI, Skerlos, LT, Bradley, TM, Mackie, RI and White, BA (2002). Comparative microbial diversity in the gastrointestinal tracts of food animal species. Integrative and Comparative Biology 42: 327331.
Simpson, JM, McCracken, VJ, White, BA, Gaskins, HR and Mackie, RI (1999). Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. Journal of Microbiological Methods 36: 167.
Turnbaugh, PJ and Gordon, JI (2008). An invitation to the marriage of metagenomics and metabolomics. Cell 134: 708713.
Urubschurov, V, Janczyk, P, Souffrant, WB, Freyer, G and Zeyner, A (2011). Establishment of intestinal microbiota with focus on yeasts of unweaned and weaned piglets kept under different farm conditions. FEMS Microbiology Ecology 77: 493502.
Vahjen, W, Pieper, R and Zentek, J (2010). Bar-coded pyrosequencing of 16S rRNA gene amplicons reveals changes in ileal porcine bacterial communities due to high dietary zinc intake. Applied and Environmental Microbiology 76: 66896691.
Varel, VH, Robinson, IM and Jung, HJ (1987). Influence of dietary fiber on xylanolytic and cellulolytic bacteria of adult pigs. Applied and Environmental Microbiology 53: 2226.
Woese, CR and Fox, GE (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, USA 74: 50885090.
Yolton, D and Savage, DC (1976). Influence of certain indigenous gastrointestinal microorganisms on duodenal alkaline phosphatase of mice. Applied and Environmental Microbiology 31: 880888.
Zhu, WY, Williams, BA, Konstantinov, SR, Tamminga, S, De Vos, WM and Akkermans, AD (2003). Analysis of 16S rDNA reveals bacterial shift during in vitro fermentation of fermentable carbohydrate using piglet faeces as inoculum. Anaerobe 9: 175180.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Animal Health Research Reviews
  • ISSN: 1466-2523
  • EISSN: 1475-2654
  • URL: /core/journals/animal-health-research-reviews
Please enter your name
Please enter a valid email address
Who would you like to send this to? *



Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed