Canine microbiome comparison between different diets

Background: While many studies have explored the impact of raw diets on the microbiome in dogs, research on gently cooked, fresh diets remains limited. 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 fecal 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 characterize the bacterial composition of the fecal sample, representing 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, including the phylum Proteobacteria and the genus Sutterella, were higher in kibble-fed dogs. Biochemical pathway analysis with the PICRUSt2 toolkit identified several pathways that were more abundant in fresh-fed than in 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 that 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 of the effects of fresh and kibble diets on the canine gut microbiome. To strengthen the findings of this preliminary research, future studies should incorporate metabolomic analysis, shotgun sequencing, and stricter control of the brand and quality of kibble diets.