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., <i>Limosilactobacillus reuteri</i> and <i>Lactobacillus johnsonii</i>) and the enrichment of bacteria linked to metabolic dysfunction (e.g., <i>Streptococcus alactolyticus</i>). 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.