The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets

Abstract

IntroductionFeeding a Bones and Raw Food (BARF) diet has become an increasing trend in canine nutrition. Bones and Raw Food diets contain a high amount of animal components like meat, offal, and raw meaty bones, combined with comparatively small amounts of plant ingredients like vegetables and fruits as well as different sorts of oil and supplements. While many studies have focused on transmission of pathogens via contaminated meat and on nutritional imbalances, only few studies have evaluated the effect of BARF diets on the fecal microbiome and metabolome. The aim of the study was to investigate differences in the fecal microbiome and the metabolome between dogs on a BARF diet and dogs on a commercial diet (canned and dry dog food).MethodsNaturally passed fecal samples were obtained from 27 BARF and 19 commercially fed dogs. Differences in crude protein, fat, fiber, and NFE (Nitrogen-Free Extract) between diets were calculated with a scientific nutrient database. The fecal microbiota was analyzed by 16S rRNA gene sequencing and quantitative PCR assays. The fecal metabolome was analyzed in 10 BARF and 9 commercially fed dogs via untargeted metabolomics approach.ResultsDogs in the BARF group were fed a significantly higher amount of protein and fat and significantly lower amount of NFE and fiber. There was no significant difference in alpha-diversity measures between diet groups. Analysis of similarity (ANOSIM) revealed a significant difference in beta-diversity (p < 0.01) between both groups. Linear discriminant analysis effect size (LefSe) showed a higher abundance of Lactobacillales, Enterobacteriaceae, Fusobacterium and, Clostridium in the BARF group while conventionally fed dogs had a higher abundance of Clostridiaceae, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae. The qPCR assays revealed significantly higher abundance of Escherichia coli (E. coli) and Clostridium (C.). perfringens and an increased Dysbiosis Index in the BARF group. Principal component analysis (PCA) plots of metabolomics data showed clustering between diet groups. Random forest analysis showed differences in the abundance of various components, including increased 4-hydroxybutryric acid (GBH) and 4-aminobutyric acid (GABA) in the BARF group. Based on univariate statistics, several metabolites were significantly different between diet groups, but lost significance after adjusting for multiple comparison. No differences were found in fecal bile acid concentrations, but the BARF group had a higher fecal concentration of cholesterol in their feces compared to conventionally fed dogs.ConclusionMicrobial communities and metabolome vary significantly between BARF and commercially fed dogs.

Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners’ motivation

“…In the present study, dogs fed with RMBD were more likely to be positive for C. perfringens (p = 0.008) ( Table 1) than those receiving commercial dry feed. This result corroborates previous reports of metagenomic studies showing that dogs fed with natural diet were more likely to be positive for C. perfringens than those fed with commercial dry diet [55,56]. These results suggest that raw meat-based diet alters the C. perfringens population in the gut.…”

The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease

“…Most of those genera are associated with digestion of dietary fiber and SCFA production, indicating a decrease in fermentation of fiber and carbohydrates due to their decreased intake. In contrast, other bacterial taxa were found to increase in abundance, including Proteobacteria and Fusobacteria (genus Fusobacterium), and two genera from phylum Firmicutes (Lactobacillus and Clostridium) (19,23).…”

“…A few studies have evaluated the impact of meat-based raw diets in the gut microbiome of healthy dogs in comparison with kibble-fed dogs. In one study (23), dogs were fed home-prepared Bones and Raw Food (BARF) diets consisting of a combination of raw meat, organs, meaty bones, and vegetables. Overall, compared to the kibble-fed control group, BARF diets included more protein and fat, and less fiber and carbohydrates.…”

“…Interestingly, one of the Clostridiaceae strains was later identified as Clostridium hiranonis, a bacterial species associated with normal bile acid (BA) metabolism (25,26). A study (23) reported normal BA metabolism in healthy dogs fed BARF diets, with no significant difference from kibble-fed controls. BA metabolism is an important pathway not only for lipid digestion, but also for regulation of intestinal inflammation, and is commonly altered in chronic gastrointestinal diseases (26,27).…”

“…Another bacterium known to produce butyrate from protein sources is Fusobacterium varium (31), which was more abundant in a group of dogs fed meat-based raw diets for at least 1 year, suggesting an adaptation of the microbiome to the long-term diet (24). In addition, members of the Fusobacteriaceae family have been found to be more abundant in other carnivore species [cats: (18,32), wolves: (33,34), other carnivora: (17,35)], and dogs fed raw diets (19,23,36).…”