Milk Composition Changes and Alterations in Bacteria, Serum, and Gut Metabolome Over Time in Lactating Naks and Simmental Cows.

Objective: This study aimed to elucidate the mechanisms underlying milk composition divergence between naks (female yaks) and Simmental cows (S-cows) by integrating longitudinal multi-omics analyses of gut microbiota and metabolomes.

Methods: We determined the gut microbiota and metabolites of both species over a 54-day period (day 26 to 80 of lactation), with ten naks and ten S-cows. Gut microbiota dynamics were assessed via 16S rRNA sequencing, while serum and fecal metabolomes were profiled using UHPLC-MS/MS. Statistical analyses included Wilcoxon rank-sum tests, LEfSe (LDA > 2, p < 0.05), and Spearman correlations (r > 0.70).

Results: Milk yield was lesser (0.53-0.91 vs. 2.07-3.88 kg/d) but concentrations of fat (5.63-6.30% vs. 3.30-3.74%), protein (5.66-6.30% vs. 3.39-3.74%), and conjugated linoleic acid（CLA） (1.74-2.35% vs. 1.40-1.75%) were greater (p < 0.001) in nak than S-cow milk. Species-specific microbial signatures emerged. In naks, the g-Family-XIII-AD3011-group and g-norank-Ruminococcaceae were correlated with bile acid metabolism and CLA synthesis via 13-hydroxyoctadecadienoic acid transport. Additionally, the naks gut had a greater concentration of 13-hydroxyoctadecadienoic acid, a precursor of CLA, which may be transported to mammary cells via phosphatidylcholine and converted to CLA under the catalysis of fatty acid desaturase2(FADS2). S-cows harbored g-Succinivibrio and g-Eubacterium-ruminantium-group, which are linked to galactose utilization and mTOR-mediated amino acid allocation. Metabolomics revealed naks-enriched steroid biosynthesis and taurine pathways (FDR < 0.05), while S-cows exhibited a lactating network associated with greater milk yield.

Conclusions: Host-specific gut microbiota mediated nutrient allocation trade-offs. Naks optimized lipid-rich milk through bile acid and CLA metabolic networks, whereas S-cows enhanced yield via microbial-galactose synergies. This research underscores the pivotal role of the gut microbiome in mediating milk composition and suggests that microbiome manipulation could be a promising strategy to enhance milk quality in ruminants.