Nutritional gradients orchestrate spatiotemporal microbial assembly and adaptive evolution in the neonatal mammalian gut

Nutritional cues during early life play a pivotal role in shaping the gastrointestinal microbiome, yet the evolutionary forces governing this process remain poorly understood. Using neonatal calves as a mammalian model, we established a genome-resolved catalog encompassing 386 closed genomes and 2,147 species-level genome bins, markedly expanding available resources. Microbial communities displayed a three-stage developmental trajectory, with deterministic selection dominating in the stomach and hindgut, while stochastic drift was more evident in the small intestine. Genome-wide single-nucleotide variant analyses revealed pervasive positive selection on carbohydrate-active pathways. Functional validation demonstrated that variants of E. coli lacZ and Cryptobacteroides sp900316045 bglB-4 exhibited altered enzymatic activities, consistent with adaptive responses to nutritional shifts. Comparative genomics further uncovered age-dependent divergence among coexisting Prevotella species, reflecting niche specialization between milk-adapted and fiber-adapted lineages. Together, these findings provide a mechanistic framework for how nutritional gradients orchestrate spatiotemporal assembly and microevolution of the neonatal gut microbiome, and deliver a broadly applicable genomic resource for exploring microbial adaptation across mammalian hosts.