The Fecal Microbiota of Healthy Dogs Fed Extruded and Raw Meat-Based Diets
Conventional dog diets, such as extruded diets, remain common; however, the popularity of unconventional options, particularly raw diets, has increased over time and may differentially influence the gut microbiota. In addition, raw diets inherently harbor higher bacterial loads, including potentially pathogenic microorganisms. The aim of the study was to compare the fecal microbial composition of clinically healthy dogs fed extruded diets with that of dogs fed raw meat-based diets (RMBD) and to evaluate how microbiota composition may vary in pets carrying zoonotic bacterial pathogens. Fecal samples from healthy dogs were collected (extruded-fed n = 14; raw-fed n = 10), as well as samples from raw-fed dogs previously characterized as pathogen carriers. The V3-V4 region of the 16S rRNA gene was sequenced and diversity metrics, including alpha and beta diversity were obtained to evaluate intra and inter sample variations. Additionally, this study conducted a comprehensive evaluation of the nutritional profiles of raw and extruded diets consumed by the study participants.  Raw-fed dogs showed a higher abundance and diversity of species as indicated by the alpha metrics, including taxa that are less commonly observed in the canine gut microbiota. Pathogen carriers showed significantly lower microbial diversity in comparison with non-pathogen carriers. RMBDs showed significant differences in macronutrient composition compared to extruded diets, particularly in terms of higher protein and fat contents and lower levels of fiber and non-fiber carbohydrates (NFC). The observed differences in taxa between raw- and extruded-fed dogs were associated with the distinct nutrient proportions characteristic of each diet.