Quantifying differences in the canine gut microbiome between fresh and processed diets: A home-based, cross- sectional study with demographic diversity

Background: A number of studies have demonstrated a significant impact of diet on the gut microbiome. We aimed to conduct the largest and most demographically diverse home-based exploratory cross-sectional study to date on the effects of different diet types on the canine microbiome. Although a range of diets were fed to the dogs in our study, the major focus was on comparing the impact of a gently cooked (fresh) diet with a conventional dry processed (kibble) diet. Methods: A total of 103 dogs were recruited for this study. Each participant provided a single faecal microbiome sample along with a completed questionnaire on their dog’s health and nutritional history. Microbial DNA was extracted and sequenced using 16S rRNA gene analysis to characterise the bacterial composition of the faecal sample, which is representative of the gut microbiome. Results: The study revealed several significant trends, providing a deeper and more complete understanding of the effects of feeding methods on the canine microbiome. Microbiome metrics, such as alpha diversity and richness, were lower in fresh-fed dogs, while levels of opportunistic and potentially pathogenic bacteria, such as the Sutterellagenus, were higher in kibble-fed dogs. Biochemical pathway analysis using the Picrust2 toolkit identified several pathways that were more abundant in fresh-fed compared with kibble-fed dogs, such as the combined protein degradation pathway and the synthesis of butyrate from amino acids. We subsequently developed a simple classifier model which differentiated microbiome samples from fresh-fed and kibble-fed dogs, with pathways such as POLYAMSYN, HISDEG and PWY0.1296 emerging as strong predictors for distinguishing between the two dietary cohorts. Conclusions: This study provides a robust and statistically significant investigation into the effects of fresh and kibble diets on the canine gut microbiome. To strengthen the findings and robustness of this preliminary research, we recommend that future studies incorporate metabolomic analysis, shotgun sequencing, and stringent control of the brand or quality of kibble diet.