Fecal Microbiota and Metabolites of Adult Dogs Fed Extruded, Mildly Cooked, and Raw Diets

The pet food market continues to produce diets with novel formats and unique processing methods. Although extruded and canned diets are still the most popular diet choice, lightly cooked and raw diets are other options. Unfortunately, there is little research on these diets and how they may alter fecal characteristics. The objective of this study was to determine fecal microbiota and metabolite concentrations of adult dogs fed the following commercial dog diets: 1) Freshpet Vital Balanced Complete Nutrition (CO); 2.) Freshpet Roasted Meals (RM); 3) Freshpet Vital Raw (VR); and 4) Purina Dog Chow (DC). Eight dogs (mean age = 3.6; mean BW = 12.9 kg) were used in replicated 4x4 Latin square design. Each period consisted of 28 d, with a 21-d adaptation phase followed by a total and fresh fecal collection phase. All samples were scored based on a 5 point scale (1 = hard, dry pellets; 5 = watery liquid). A fresh fecal sample was collected for pH, moisture, microbiota and metabolite measurements. Microbiota was assessed using 16S rRNA-based amplicon sequencing using Illumina, Qiime, and linear discriminant analysis effect size (LEfSe). Dogs fed CO had a higher (P<0.05) fecal pH than dogs fed VR, with dogs fed RM and DC being intermediate. Dogs fed DC, CO or RM had lower (P<0.05) fecal moisture than dogs fed VR, but fecal scores were not affected. Dogs fed VR had a higher (P<0.05) fecal acetate concentration than dogs fed RM, with dogs fed CO and DC being intermediate. Dogs fed RM had a higher (P<0.05) fecal indole and total phenol: indole ratio than with dogs fed CO, VR and DC. Dogs fed VR had a higher (P<0.05) fecal ammonia concentration than dogs fed RM, CO and DC. Dogs fed RM had a higher (P<0.05) ammonia concentration than dogs fed DC, with dogs fed CO being intermediate. All other fecal metabolites were not affected by treatment. Dogs fed CO or VR had a lower (P<0.05) alpha diversity of fecal microbes than dogs fed DC. Dogs fed CO or VR also shifted from dogs fed DC when unweighted and weighted beta diversity was evaluated. LEfSe demonstrated that each diet tended to be enriched in different microbial taxa: DC (Firmicutes; Actinobacteria); CO (Proteobacteria); VR (Bacteroides; Pediococcus); and RM (Fusobacteria). All diets were well tolerated and dogs remained healthy throughout the study. Diet-induced differences in fecal microbiota and metabolites should be further studied.