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Helpful information about the unique nutritional needs of dogs and cats with certain lifestyles or health challenges.


Managing the Gut Microbiome

Advanced molecular microbiology techniques have found the gastrointestinal (GI) tract of dogs and cats harbors a diverse, dynamic, and complex microbial community. The GI or gut microbiota is comprised of trillions of microorganisms including bacteria, archaea, fungi, protozoa and viruses (mostly bacteriophages) — there are at least as many microbial cells present in the gut as there are cells in the entire body.1 Bacteria make up the largest segment, accounting for approximately 98% of the microbiota in dogs and cats,2,3 and play key roles in host health. GI bacteria provide essential functions that contribute to metabolism, protect against potential intestinal pathogens, prime the immune system, and promote healthy intestinal structure.4 As for the other microbial species present within the GI microbiome, scientists are just beginning to understand their roles and significance. 

GI microbiota composition can be influenced — even profoundly altered — by a variety of factors, including diet, environment, age, host genetics, medications and diseases.5─8 While some of these factors cannot be controlled, diet provides a daily opportunity to influence the gut microbiome and, ultimately, pet health. 

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The intestine of mammals is estimated to contain approximately 1010 to 1014 microorganisms.17

Key Messages

  • Food not only nourishes dogs and cats but also feeds the gut microbiota, influencing its composition and bacterial metabolite production.9 Microbial metabolites can affect an animal’s GI tract or be absorbed to impact the pet’s health at locations beyond the GI tract.
    • The microbiome may be affected by ingredients, macronutrient concentrations and digestibility, and processing procedures of the diet.4,9─12 These factors influence nutrient digestion and absorption, and affect what substrates are available for microbial metabolism.9,10 
  • Nondigestible carbohydrates, including dietary fiber, are the preferred fuel of gut microbes. However, the microbiota can and does use protein and fat when available.12,13 
    • Gut bacteria ferment nondigestible carbohydrates to produce short-chain fatty acids (SCFAs) such as acetate, propionate and butyrate. SCFAs are an important energy source for intestinal epithelial cells and for other bacteria, act as signaling molecules, promote epithelial barrier function, regulate intestinal motility, and exert an anti-inflammatory effect. 
    • Dietary protein and amino acids that escape digestion and absorption in the small intestine can be fermented by the gut microbiota. Some metabolites produced from amino acid metabolism are beneficial, while others have been implicated in certain inflammatory diseases.9 
  • Other options for feeding and influencing the GI microbiome include probiotics and prebiotics
    • Prebiotics, such as inulin, chicory root, wheat aleurone, psyllium and other oligosaccharides, are fermentable, nondigestible carbohydrates that selectively promote the growth or activity of potentially beneficial microorganisms without significantly altering food digestibility.14 
    • Probiotics are live microorganisms that can provide benefits directly or indirectly by:15 
      • stimulating growth of resident bacteria through metabolic interactions 
      • reducing the abundance of potentially pathogenic bacteria 
      • interacting with the intestinal epithelium and gut immune system 
    • Synbiotics blend probiotics and prebiotics. A combination may be complementary, in which the prebiotic and probiotic have independent mechanisms and benefits, or synergistic, in which the prebiotic is the preferred substrate for the accompanying probiotic.16 
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"Like us, pets have a complex and diverse community of microorganisms living in their digestive system that is closely linked to pet health. Food can have a profound impact — positive or negative — on the gut microbiome. Choosing a food that includes complex carbohydrates, prebiotic fiber or adding a probiotic supplement can help increase the levels of beneficial bacteria present in the GI tract."

To Share With Pet Owner:


Probiotics offer many benefits, but with so many options available, pet owners may not know how to select the best quality and most appropriate one for their pet's needs

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Purina was the first to use prebiotics in pet food and is a leader in the field. What are the benefits of prebiotics to pets?

View Hot Topic 6 min to 10 min


  1. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533. doi: 10.1371/journal.pbio.100253 
  2. Swanson, K. S., Dowd, S. E., Suchodolski, J. S., Middelbos, I. S., Vester, B. M., Barry, K. A., Nelson, K. E., Torralba, M., Henrissat, B., Coutinho, P. M., Cann, I. K. O., White, B. A., & Fahey, G. C., Jr. (2011). Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. The ISME Journal, 5(4), 639─649. doi: 10.1038/ismej.2010.162 
  3. Tun, H. M., Brar, M. S., Khin, N., Jun, L., Hui, R. K., Dowd, S. E., & Leung, F. C. (2012). Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. Journal of Microbiological Methods, 88(3), 369─376. doi: 10.1016/j.mimet.2012.01.001 
  4. Pilla, R., & Suchodolski, J. S. (2021). The gut microbiome of dogs and cats, and the influence of diet. Veterinary Clinics of North America: Small Animal Practice, 51(3), 605─621. doi: 10.1016/j.cvsm.2021.01.002​ 
  5. Barko, P. C., McMichael, M. A., Swanson, K. S., & Williams, D. A. (2018). The gastrointestinal microbiome: A review. Journal of Veterinary Internal Medicine, 32(1), 9─25. doi: 10.1111/jvim.14875 
  6. Garcia-Mazcorro, J. F., & Minamoto, Y. (2013). Gastrointestinal microorganisms in cats and dogs: A brief review. Archivos de Medicina Veterinaria, 45(2), 111─124. doi: 10.4067/S0301-732X2013000200002 
  7. Belas, A., Marques, C., & Pomba, C. (2020). The gut microbiome and antimicrobial resistance in companion animals. In A. F. Duarte & L. Lopes da Costa (Eds.), Advances in animal health, medicine and production (pp. 233─245). Springer, Cham. doi: 10.1007/987-3-030-61981-7_12 
  8. Vilson, Å., Ramadan, Z., Li, Q., Hedhammar, Å., Reynolds, A., Spears, J., Labuda, J., Pelker, R., Björkstén, B., Dicksved, J., & Hansson-Hamlin, H. (2018). Disentangling factors that shape the gut microbiota in German Shepherd dogs. PLoS ONE, 13(3), e0193507. doi: 10.1371/journal.pone.0193507 
  9. Wernimont, S. M., Radosevich, J., Jackson, M. I., Ephraim, E., Badri, D. V., MacLeay, J. M., Jewell, D. E., & Suchodolski, J. S. (2020). The effects of nutrition on the gastrointestinal microbiome of cats and dogs: Impact on health and disease. Frontiers in Microbiology, 11, Article 1266. doi: 10.3389/fmicb.2020.01266 
  10. Do, S., Phungviwatnikul, T., de Godoy, M. R. C., & Swanson, K. (2021). Nutrient digestibility and fecal characteristics, microbiota, and metabolites in dogs fed human-grade foods. Journal of Animal Science, 99(2), 1─13. doi: 10.1093/jas/skab028 
  11. Bermingham, E. N., Young, W., Kittelmann, S., Kerr, K. R., Swanson, K. S., Roy, N. C., & Thomas, D. G. (2013). Dietary format alters fecal bacterial populations in the domestic cat (Felis catus). MicrobiologyOpen, 2(1), 173─181. doi: 10.1002/mbo3.60 
  12. Mori, A., Goto, A., Kibe, R., Oda, H., Kataoka, Y., & Sako, T. (2019). Comparison of the effects of four commercially available prescription diet regimens on the fecal microbiome in healthy dogs. The Journal of Veterinary Medical Science, 81(12), 1783─1790. doi: 10.1292/jvms.19-0055 
  13. Schauf, S., de la Fuente, G., Newbold, C. J., Salas-Mani, A., Torre, C., Abecia, L., & Castrillo, C. (2018). Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs. Journal of Animal Science, 96(9), 3684─3698. doi: 10.1093/jas/sky264 
  14. Grieshop, C. M., Flickinger, E. A., Bruce, K. J., Patil, A. R., Czarnecki-Maulden, G. L., & Fahey, G. C., Jr. (2004). Gastrointestinal and immunological responses of senior dogs to chicory and mannan-oligosaccharides. Archives of Animal Nutrition, 58(6), 483─493. doi: 10.1080/00039420400019977 
  15. Derrien, M., & van Hylckama Vlieg, J. E. T. (2015). Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends in Microbiology, 23(6), 354─366. doi: 10.1016/j.tim.2015.03.002 
  16. Cunningham, M., Azcarate-Peril, M. A., Barnard, A., Benoit, V., Grimaldi, R., Guyonnet, D., Holscher, H. D., Hunter, K., Manurung, S., Obis, D., Petrova, M. I., Steinert, R. E., Swanson, K. S., van Sinderen, D., Vulevic, J., & Gibson, G. R. (2021). Shaping the future of probiotics and prebiotics. Trends in Microbiology. Advance online publication. doi: 10.1016/j.tim.2021.01.003 
  17. Suchodolski, J. S. (2011). Intestinal microbiota of dogs and cats: A bigger world than we thought. Veterinary Clinics of North America: Small Animal Practice, 41(2), 261─272. doi: 10.1016/j.cvsm.2010.12.006