Background The gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown. Methods Healthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM. Results Dogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006). Conclusion Owners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity.

Commercial fresh cooked foods have started gaining popularity among American dog owners in recent years. However, nutrient digestibility and the estimation of metabolizable energy (ME) of commercial fresh dog foods remain inadequately understood, even though both measures are critical to provide the intended calories for the target animal. In this preliminary study, different cohorts of normal-weight dogs were fed one of five test diets of comparable macronutrient composition: a chicken-based extruded dry kibble diet (n=12), and chicken- (n=12), beef- (n=6), pork- (n=6), or turkey-based fresh food (n=6) for 10 days. Daily food intake and fecal characteristics were recorded, and fecal samples were collected for nutrient analysis. Despite comparable dry matter (DM) and caloric intakes between the two chicken-based diets, the fresh diet led to lower defecation frequency (1.2±0.2 vs 1.7±0.5 times/d, adjusted p&lt;0.001), lower fecal DM (24±8 vs 47±10 g/d, adjusted p&lt;0.001), and lower fecal calories (92±31 vs 189±43 kcal/d, adjusted p&lt;0.001) than the kibble diet. The apparent total tract digestibility of DM, protein, fat, nitrogen-free extract, and calories of the kibble diet were all significantly lower than any of the fresh diets (adjusted p&lt;0.001 for all). Measured ME per food DM in all of the fresh diets, except that being pork-based, was significantly higher than that of the kibble diet (adjusted p&lt;0.001 for all). For the kibble diet, the modified Atwater calculation underestimated the ME and the NRC 2006 calculation was the most accurate predictor of ME. The standard Atwater calculation performed best for the two fresh diets that had the highest fat content (chicken, beef) and the NRC 2006 calculation performed best for the fresh diet that had the highest protein content (pork). ME of the turkey-based diet was equally overestimated and underestimated with the standard Atwater and NRC 2006 methods, respectively. We propose that commercial and home-prepared fresh diets should be assessed using standard Atwater factors as commonly done in human nutrition, or preferably for commercial products, by direct measurement in conforming feeding trials.

Dogs have the ability to consume and utilize energy from both animal-based products (meat, organ meat, eggs and dairy products) and a variety of edible plant-based foods (fruits, vegetables, legumes, grains, nuts and seeds). The National Research Council (NRC) of the U.S. National Academy of Sciences provides a summary of the evidence and basis of essential nutrient recommendations for dogs; these are largely incorporated into the regulatory guidelines of the Association of American Feed Control Officials (AAFCO), which establishes nutrient profiles for different life stages, including adult dogs for maintenance, growth and/or reproduction

Most canine microbiome trials are conducted in a controlled environment, with an unverified assumption that identical findings can be extrapolated to household dogs. In this study, the fecal microbiome of healthy beagles living in household or controlled environments was characterized with shotgun metagenomic sequencing and compared. Beagles were recruited from U.S. households (Pet, n = 54), a private kennel (Kennel, n = 39), and the University of Illinois at Urbana-Champaign (UIUC, n = 34). Dogs were fed an identical diet (fresh chicken, non-extruded and cooked) or diet type (kibble, various brands) for ≥ 7 days. Shannon diversity index was significantly higher in Kennel than Pet when fed both fresh and kibble, and significantly higher than UIUC when fed fresh only. β-Diversity was significantly different among the three cohorts on both diets. Mainly, species belonging to Actinobacteriota, Bacteroidota, Firmicutes_A, Firmicutes, and Proteobacteria were differentially abundant among the cohorts. Likewise, significant discriminant features in the functional data were observed among the cohorts after controlling for diet type. The findings demonstrate the living environment as an important factor in microbial composition, and further draw attention to possible limitations in the translation of findings between dogs in controlled versus free-living environments.

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