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
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