Background and objectives Breastfeeding, the gold standard for infant nutrition, results in a higher abundance of Bifidobacteria. In a prospective, open label study of an infant formula with unique whey protein concentrate enriched in α-lactalbumin, osteopontin and gangliosides, after 6 weeks of intervention, we explored the bifidogenic effect and changes in the microbial-derived metabolites, compared to a breastfed reference group. Methods Chinese infants were enrolled between 3 and 28 days and assigned to predominantly formulRegorafenib抑制剂a-fed(FF)(N= 60) or breastfed(BF) group(N=60) per their feeding biogas technologypracTezacaftor体外tice, for 6 weeks. Fecal samples were collected at baseline and after week 6. Fecal metagenomic data was processed using MetaPhlAn3. Bacteria relative abundances was analyzed with a zero-inflated negative binomial(ZINB) model. Bacteria genus and species were compared for FF versus BF group at week 6. Short chain fatty acids(SCFAs) and branched-chain fatty acids(BCFAs) were analyzed by ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MSMS) and results expressed as μmol/g of dry feces. Both microbiota and SCFAs analyses were adjusted for covariates including baseline age, sex, delivery mode, site and baseline measures. Results Bifidobacterium genus relative abundance was not significantly different(p=0.686) between the FF and BF groups at end of trial. Bifidobacterium bifidum species increased over time with intervention formula(p=0.0105). After 6 weeks, total SCFAs were significantly higher(p=0.048) in the FF versus BF group. The increase in SCFAs level was mainly driven by the increased levels of, valeric and propanoic acids(p<0.05 for both). Also, after 6 weeks, total BCFAs, isobutyric and isovaleric acids were significantly higher in FF vs BF(p<0.05 for all). Conclusions Our study provides evidence on the effectiveness of a unique infant formula in modulating the gut microbiome and promoting Bifidobacteria abundance similar to that of the BF group.