Background: An understanding of the bacterial species comprising the core microbiome in a large cohort of healthy dogs is lacking but required for informing therapeutic efforts aimed at restoring dysbiotic microbiomes. Hypothesis/
Objectives: Identify the bacterial species that constitute the core microbiome in healthy dogs and examine the effects of sex-neuter status, age, body weight, diet, probiotic intake, and geographic region on this core. Animals: Fecal samples were collected from 286 healthy pet dogs with no current or past physical conditions, no clinical signs, and no reported medication use.
Methods: Full-length PacBio16S rRNA gene sequence data from fecal samples were analyzed in R. Core bacterial species were present in at least 33% of dogs. Generalized additive models were used to correlate two core microbiome metrics with host factors.
Results: 27 bacterial species formed part of the core microbiome in healthy dogs, among them Collinsella intestinalis, Megamonas funiformis, Peptacetobacter hiranonis, Prevotella copri, Streptococcus lutetiensis, and Turicibacter sanguinis. Overall, sterilized females had more core taxa (x̄:16.4) than intact males (x̄:15) (GAM p< 0.05). Dogs of intermediate body weight had more core taxa than small or large dogs (GAM p< 0.05). Dogs fed kibble had more core taxa (x̄:17.6) than dogs fed raw (x̄:15.6) or cooked food (x̄:15.08) (GAM p< 0.05). The total sum of core taxa in the fecal microbiome decreased with age. No differences in core microbiome metrics were detected between healthy dogs that did vs. did not receive probiotics.
Conclusions: A common core group of bacteria was identified, some of which are known to decrease in abundance with gut dysbiosis.
