Elucidating gut microbiota and metabolite patterns shaped by goat milk-based infant formula feeding in mice colonized by healthy infant feces

•Infant formula (IF) were prepared with different milk bases.•Goat milk-based IF increased beneficial microbes Blautia, Roseburia, Alistipes and Muribaculum.•Goat milk-based IF emphasizes unique metabolic pathways.•Metabolites are associated with gut microbes. The gut microbiota plays an evolutionarily conserved role in host metabolism, which is influenced by diet. Here, we investigated differences in shaping the gut microbiota and regulating metabolism in cow milk-based infant formula, goat milk-based infant formula, and mix milk-based infant formula compared with pasteurized human milk. 16S rRNA results showed that goat milk-based infant formula selectively increased the relative abundance of Blautia, Roseburia, Alistites and Muribaculum in the gut compared to other infant formulas. Metabolomics identification indicated that goat milk-based infant formula mainly emphasized bile acid biosynthesis, arachidonic acid metabolism and steroid biosynthesis metabolic pathways. Metabolites associated with these metabolic pathways were positively associated with increased microorganisms in goat milk-based infant formula, particularly Alistipes. Furthermore, we found a deficiency of Akkermansia abundance in three infant formula-fed compared to pasteurizedhuman milk-fed. This study presents new insights into the improvement and application of goat milk-based infant formulas in terms of intestinal microecology.