We were taught in school that the genes we inherit from our parents are the biggest driver of health outcomes. Since Antonie van Leewenhoek’s discoveries in the 1680’s that there are visible differences in microbes from the mouth vs. feces, the microbiome and its influence on health and behavior is slowly being realized (cardiovascular, neural development, metabolism, immune regulation, bacterial infection and anxiety to name a few), yet there is so much that remains unknown. [1-6]
We know that the cellular power of the microbiome outweighs its canine host by 10 times. We know that the microbiome’s genetic power significantly outweighs the canine host and that the microbes’ ability to respond to stimuli can be 1-5 minutes, compared to 15-120 minutes for mammalian cells response time. 
We know from academic studies, that “germ-free” mice, rats, pigs, flies and fishes can live
absent a gut microbiome. However, there are measurable differences in behavior, learning and stress responses. 
In several interesting studies looking at over 1,500 twin pairs (both identical and fraternal), host genetics appear to influence the composition of the microbiome, with 5.3-8.8% of the gut microbiome showing heritable conservation. [8-9]
Several decades of studies characterizing the gut, skin and oral microbiomes of animals and humans with defined disease states (obesity, cardiovascular disease, periodontal disease, dermatitis, etc) have shown how significant the presence, absence and relative abundance of bacterial species in these disease states can be. For example, in a dog study, Porphyromonas abundance increases 2.7x in periodontal disease and coincides with increases in Bacteroides and Fusobacterium and correlates strongly with a shift in microbial metabolism towards sugar fermentation, anaerobic glycolysis and the production of endotoxin in the gum tissue. 
In a preliminary study with working dog vs general dog breeds, the presence of Lactobacillus spp., acetate and butyrate-producing bacteria associated with increased cowardice scores, while increased motivation scores were positively associated with Prevotella spp. Increased sociability scores were associated with Lachnospiraceae and Bacteroides. Also, high aggression scores were positively associated with increased abundance of Balutia, Bradyrhizobium and Rhuminococcaceae. Also interesting, high obedience scores were associated with low Clostridium perfringens abundance. 
All this is to say that we are still learning about whether genetics or the microbiome plays the bigger role in driving physiology and health outcomes. There is evidence suggesting microbes play many roles in its host animals and that more work needs to be done to fully elucidate the role that host genetics and microbiome play in sculpting health and behavior in our pets.
1. van Leeuwenhoek, A. An abstract of a Letter from Antonie van Leeuwenhoek Sep. 12,
2. van Leeuwenhoek, A. About animals in the scrurf of the teeth, Philosophical
Transactions of the Royal Society of London, 14 (1684), 568–74.
3. Buffington, S. Dissecting the contribution of host genetics and the microbiome in
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4. Backhed et al. Host-bacterial mutualism in the human intestine. (2005) Science.
5. Tremaroli, V. and Backhed, F. (2012) Functional interactions between the gut microbiota
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6. Cryan, J. and Dinan, T. (2012) Mind-altering microorganisms: the impact of the gut
microbiota on brain and behavior. Nat Rev Neurosci. 13:701-712.
7. Luczynski, P. et al. (2016) Growing up in a bubble. Using germ-free animals to assess
the influence of the gut microbiota on brain and behavior. Int J Neuropsychopharmacol.
8. Goodrich, J. et al. (2016) Cross-species comparisons of host genetic associations with
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9. Goodrich, J. et al. (2014) Human genetics shape the gut microbiome. Cell. 159:789-799.
10. Craddock, H. et al. (2022) Phenotypic correlates of the working dog microbiome. Npj
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11. Santibanez, R. et al. (2021) Assessment of changes in the oral microbiome that occur in
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12. Pilla, R. and Suchodolski, J. (2020) The role of the canine gut microbiome and
metabolome in health and gastrointestinal disease. Front Vet Sci. doi.org/10.3389