The fecal microbiota of healthy dogs fed extruded and raw meat-based diets.

Conventional dog diets, such as extruded diets, remain common. The popularity of unconventional options, particularly raw diets, has increased over time and may differentially influence the gut microbiota. Raw diets inherently harbor higher bacterial loads, including potentially pathogenic microorganisms, raising concerns from a One Health perspective due to the close interaction among pets, humans, and the environment. The study aims were to characterize the nutritional profiles of extruded and raw diets, compare the fecal microbial composition of dogs fed extruded diets with that of dogs fed RMBDs, and evaluate microbiota differences in pathogen-carrying dogs. Extruded (n = 10) and raw (n = 6) diets were analyzed. Fecal samples from extruded-fed (n = 14) and raw-fed dogs (n = 10), including samples from raw-fed dogs previously identified as pathogen carriers (6/10), were analyzed. The V3-V4 region of the 16S rRNA gene was sequenced, and diversity metrics were obtained to evaluate intra- and inter-sample variations. RMBDs showed higher protein and fat contents and lower fiber and non-fiber carbohydrate levels compared to extruded diets. Discrepancies between declared and analyzed nutritional composition were found in 100% of raw diets and 10% of extruded diets. Alpha diversity showed a mixed pattern between dietary groups, with significant differences in Chao1 and Simpson indices but not across all diversity metrics. Raw-fed dogs showed higher microbial diversity and increased relative abundance of specific taxa. Taxa differences between raw- and extruded-fed dogs suggest an association with diet composition. Raw-fed dogs identified as pathogen carriers showed significantly lower microbial diversity than non-carriers. These findings highlight the variability and potential nutritional imbalances of raw diets, confirm diet as a key modulator of canine gut microbiota, and suggest that greater bacterial diversity does not necessarily reflect healthier microbiota.