Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs

The gut microbiome has an important role in health and disease, developing through early life and, in humans, stabilising around 3 years of age. Diet represents a key lever for shaping of the gut microbiome across all stages of life and the observed long-term health effects of maternal milk consumption in neonates is suggestive of pliability in the infant gut microbiome enabling diet in early life to drive enduring change. The ability to drive lasting change in the adult gut microbiome through dietary intervention is less understood. We studied the effect of an extreme dietary shift on the faecal microbiome of 46 Labrador retriever dogs over 11 months. Dogs were fed a nutritionally complete commercially available, complex diet (CD) for a minimum of 5 weeks, followed by highly purified diets (PD) for 36 weeks and the initial CD for at least a further 4 weeks. Faecal samples were collected at regular intervals for DNA extraction. Analysing 16S rDNA genotypes and the metagenomes, we observed minor effects on microbial diversity; but major changes in bacterial taxa and genetic potential when PD was fed. When dogs returned to CD, no significant differences were found with the initial time point. These findings are consistent with the gut microbiome being rapidly adaptable, but capable of being reconstituted when provided with similar diets. These data highlight that long term changes in the adult dog gut microbiome may only be achieved through long-term maintenance on a specified diet, rather than through feeding a transitionary diet.