Moderate increase in dietary fat induces alterations of microbiota and metabolome along the digestive tract prior to systemic metabolic changes: insights from a pig model

The small intestine is a key site for nutrient sensing and host–microbiota interactions, yet how it functionally adapts to dietary changes remains poorly understood. Using a translational porcine model, we investigated the impact of moderate dietary fat increase on the gut microbiota and metabolome across five locations in the digestive tract. Pigs were fed either a low-fat (3%) or a medium-fat (12%) diet for 12 weeks without developing obesity. Multiomics profiling revealed significant dietary effects on bile and duodenojejunal metabolomic profiles, particularly lipid and stachydrine, with notable sex-specific responses. These metabolite shifts were accompanied by segment- and sex-specific changes in microbial communities, including the depletion of metabolically beneficial taxa (e.g., Limosilactobacillus reuteri and Lactobacillus johnsonii) and the enrichment of bacteria linked to metabolic dysfunction (e.g., Streptococcus alactolyticus). In the small intestine lumen, multiple bacterial–metabolite associations correlated with host metabolic markers, suggesting early diet-induced alterations with potential relevance for metabolic disease onset. Our findings position the small intestine as a critical site for early diet-induced microbial and metabolic remodeling, potentially influencing metabolic disease risk and shaping the downstream intestinal environment. This study also underscores the importance of considering both region- and sex-specific responses in diet–microbiota–metabolome research.