Microbiome Fundamentals

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Genetics play a significant role in microbiome composition.1 The gut microbiomes of genetically related dogs was more similar to each other than to unrelated dogs, despite geographical separation after weaning.2

Microbial colonization of the intestinal tract is first influenced by the maternal microbiome, environment and nutrition.

Puppies’ microbiomes were more similar to their mothers’ microbiomes at 7 weeks of age compared to their composition at birth.2 The gut microbiome of puppies increases in microbial diversity and species richness from 2 to 56 days after birth, but is relatively stable by 42 days after birth.3 In contrast, kittens may exhibit a reduction in diversity from 4 weeks to 8 weeks of age.4

One metagenomics study suggested the kitten microbiome undergoes little change between 8 and 16 weeks,5 and a separate study observed shifts in structural and functional diversity between 18 and 30 weeks of age but no significant change from 30 to 42 weeks.6

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factors influencing the microbiomes icon

With age, disease, medical treatments and other stressors, the balance of bacteria in the gut can shift toward larger populations of potentially pathogenic bacteria.3,7,8

The pet’s living environment can also dramatically impact the gut microbiome. The microbiomes of dogs living in households differed from those living in shelters, with the shelter dogs displaying a more diverse microbiome population.1 Dogs living in larger cities show a more diverse microbiome than those in smaller cities or in rural settings.2

A number of disease states are associated with dysbiosis of the gut microbiome, although whether the dysbiosis is the cause or a consequence of the disease state has not been definitively determined.1

Dysbiosis has been found in dogs with chronic enteropathies, chronic diarrhea, and acute diarrhea.9,10

Medications may affect the microbiome.

Antimicrobials in particular (such as metronidazole and tylosin) can profoundly alter the microbiome.1,11,12 Proton pump inhibitors, such as omeprazole, also exert negative effects on the microbiome.1,13

Obesity is associated with changes in the microbiome, but the role of the microbiome as the cause or consequence of obesity remains unknown.14,15

The microbiome of obese dogs responds differently to diet and is less resilient than than the microbiome of lean dogs.15,16

The composition of the gut microbiota is largely affected by diet.

The microbiome may be affected by ingredient profile, nutrient concentrations and digestibility, and processing procedures of the diet.17-24 Macronutrient composition appears to be the most significant dietary factor driving changes in composition of the microbiome.17,24-29 Diets high in protein increase abundance of proteolytic microbes, whereas diets high in carbohydrates increase abundance of saccharolytic microbes.23

The gut microbiome changes quickly in response to diet,17,30,31 indicating great flexibility in its composition. However, these changes are reversible, and the microbiome will revert to its original composition when dogs are returned to their original diet.30,31

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  1. Belas, A., Marques, C., & Pomba, C. (2020). The gut microbiome and antimicrobial resistance in companion animals. In Duarte, A. & Lopes da Costa, L. (Eds.), Advances in Animal Health, Medicine and Production (1st ed.), pp. 233–245. Springer International Publishing
  2. Vilson, Å., Ramadan, Z., Li, Q., Hedhammar, Å., Reynolds, A., Spears, J.,…Hansson-Hamlin, H. (2018). Disentangling factors that shape the gut microbiota in German Shepherd dogs. PLoS ONE, 13(3), e0193507. doi:1371/journal.pone.0193507
  3. Guard, B. C., Mila, H., Steiner, J. M., Mariani, C., Suchodolski, J. S., & Chastant-Maillard, S. (2017). Characterization of the fecal microbiome during neonatal and early pediatric development in puppies. PLoS ONE, 12(4), e0175718. doi:10.1371/journal.pone.0175718
  4. Jia, J., Frantz, N., Khoo, C., Gibson, G. R., Rastall, R. A., & McCartney, A. L. (2011). Investigation of the faecal microbiota of kittens: monitoring bacterial succession and effect of diet. FEMS Microbiology Ecology, 78, 395–404. doi:10.1111/j.1574-6941.2011.01172.x
  5. Deusch, O., O’Flynn, C., Colyer, A., Morris, P., Allaway, D., Jones, P. G., & Swanson, K. S. (2014). Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PLoS ONE, 9(7), e101021. doi:10.1371/ journal.pone.0101021
  6. Deusch, O., O’Flynn, Colyer, A., Swanson, K. S., Allaway, D., & Morris, P (2015). A longitudinal study of the feline faecal microbiome identifies changes in to early adulthood irrespective of sexual development. PLoS ONE, 10(12), e0144881. doi: 10.1371/journal.pone.0144881
  7. Romano-Keeler, J., & Weitkamp, J. H. (2015). Maternal influences on fetal microbial colonization and immune development. Pediatric Research, 77(1–2), 189–95. doi:10.1038/pr.2014.163
  8. Young, W., Moon, C. D., Thomas, D. G., Cave, N. J., & Bermingham, E. N. (2016). Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances. Scientific Reports, 6, 34668. doi:10.1038/srep34668
  9. Honneffer, J. B., Minamoto, Y., & Suchodolski, J. S. (2014). Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs. World Journal of Gastroenterology, 20(44), 16489–16497. doi:10.3748/wjg.v20.i44.16489
  10. Suchodolski, J. S., Markel, M. E., Garcia-Mazcorro, J. F., Unterer, S., Heilmann, R. M., Dowd, S. E.,…Toresson, L. (2012). The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease. PLoS ONE, 7(12), e51907. doi:10.1371/journal.pone.0051907
  11. Igarashi, H., Maeda, S., Ohno, K., Horigome, A., Odamaki, T., & Tsujimoto, H. (2014). Effect of oral administration of metronidazole or prednisolone on fecal microbiota in dogs. PLoS ONE, 9(9), e107909. doi:10.1371/journal.pone.0107909
  12. Suchodolski, J. S., Dowd, S. E., Westermarck, E., Steiner, J. M., Wolcott, R. D., Spillmann, T., & Harmoinen, J. A. (2009). The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing. BMC Microbiology, 9, 210. doi:10.1186/1471-2180/9/201
  13. Garcia-Mazcorro, J. F., Suchodolski, J. S., Jones, J. R., Clark-Price, S. C., Dowd, S. E., Minamoto, Y.,…Dossin, O. (2012). Effect of the proton pump inhibitor omeprazole on the gastrointestinal bacterial microbiota of healthy dogs. FEMS Microbiology Ecology, 80, 624-636.
  14. Handl, S., German, A. J., Holden, S. L., Dowd, S. E., Steiner, J. M., Heilman, R. M.,…Suchodolski, J. S. (2013). Faecal microbiota in lean and obese dogs. FEMS Microbiology Ecology, 84, 332343. doi: 10.1111/1574-6941.12067
  15. Li, Q., Lauber, C. L., Czarnecki-Maulden, G., Pan, Y., & Hannah, S. S. (2017). Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions. MBio, 8(1), e01703–16. doi:10.1128/mBio.01703-16.
  16. Xu, J., Verbrugghe, A., Lourenco, M., Cools, A., Lui, D. J. X., Van de Wiele, T.,…Hesta, M. (2017). The response of canine faecal microbiota to increased dietary protein is influenced by body condition. BMC Veterinary Research, 13, 374. doi:10.1186/s12917-017-1276-0
  17. Do, S., Phungviwatnikul, T., de Godoy, M. R. C., & Swanson, K. S. (2021). Nutrient digestibility and fecal characteristics, microbiota, and metabolites in dogs fed human-grade foods. Journal of Animal Science, Epub ahead of print. doi:10.1093/jas/skab028/6123189
  18. Bermingham, E. N., Young, W., Kittelman, 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). Microbiology Open, 2(1), 173–181. doi:10.1002/mbo3.60
  19. Kim, J., An, J.-U., Kim, W., Lee, S., & Cho, S. (2017). Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform. Gut Pathogens, 9, 68. doi:10.1186/s13099-017-0218-5
  20. Sandri, M., Dal Monego, S., Conte, G., Sgorlon, S., & Stefanon, B. (2017). Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs. BMC Veterinary Research, 13, 65. doi:10.1186/s12917-017-0981-z
  21. Algya, K. M., Cross, T.-W. L., Leuck, K. N., Kastner, M. E., Baba, T., Lye, L., de Godoy, M. R. C., & Swanson, K. S. (2018). Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets. Journal of Animal Science, 96, 3670-3683. doi:10.1093/jas/sky235
  22. Hill, S. R., Rutherfurd-Markwick, K. J., Ravindran, G., & Thomas, D. G. (2015). The effects of differing proportions of dietary macronutrients on the digestibility and post-prandial endocrine responses in domestic cats (Felis catus). Journal of Applied Animal Nutrition, 3, e4. doi:10.1017/ jan.2015.2
  23. Schmidt, M., Unterer, S., Suchodolski, J. S., Honneffer, J. B, Guard, B. C., Lidbury, J. A.,…Kölle, P. (2018). The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PLoS ONE, 13(8), e0201279. doi:10.1371/journal.pone.0201279
  24. 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
  25. Vester, B. M., Dalsing, B. L., Middlebos, I. S., Apanavicius, C. J., Lubbs, D. C., & Swanson, K. S. (2009). Faecal microbial populations of growing kittens fed high- or moderate-protein diets. Archives of Animal Nutrition, 63(3), 254–265.
  26. Hooda, S., Vester Boler, B. M., Dowd, S. E., Swanson, K. S. (2012). The gut microbiome of kittens is affected by dietary protein:carbohydrate ratio and correlated with blood metabolite and hormone concentrations. British Journal of Nutrition, 109, 1637–1646. doi:10.1017/S0007114512003479
  27. Bermingham, E. N., Kittelman, S., Young, W., Kerr, K. R.. Swanson, K. S., Roy, N. C., & Thomas, D. G. (2013). Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus). PLoS ONE, 8(11), e80992. doi:10.1371/ journal.pone.0080992
  28. Bermingham, E. N., Maclean, P., Thomas, D. G., Cave, N. J., & Young, W. (2017). Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ, 5, e3019. doi:10.7717/peerj.3019
  29. 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. Journal of Veterinary Medical Science, 81(12), 1783–1790. doi:10.1292/jvms.19-0055
  30. Herstad, K. M. V., Gajardo, K., Bakke, A. M., Moe, L., Ludvigsen, J., Rudi, K.,…Skancke, E. (2017). A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs. BMC Veterinary Research, 13, 147. doi:10.1186/s12917-017-1073-9
  31. Allaway, D., Haydock, R., Lonsdale, Z. N,, Deusch, O. D., O’Flynn, C., & Hughes, K. R. (2020). Rapid reconstitution of the faecal microbiome after extended diet-induced changes indicate a stable gut microbiome in healthy adult dogs. Applied Environmental Microbiology, Epub ahead of print. doi:10.1128/AEM.00562-20