Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources

Improving nitrogen (N) utilization efficiency in ruminant livestock is vital for coping with global protein scarcity and lowering environmental pollution. The biogeographically stratified microorganisms in the gastrointestinal tract (GIT) fulfill the pivotal role of metabolizing dietary N into bioavailable nutrients. In this study, we deciphered the microbial N utilization dynamics in the rumen and colon under different protein source interventions, soybean meal (SBM) and corn gluten meal (CGM) which differed in rumen degradation rate and amino acid (AA) profile, using goats as a model. Goats fed with the SBM diet exhibited greater N utilization efficiency, as characterized by greater average daily gain (ADG), nutrient digestibility, and the concentration of free amino acids (AAs) in the GIT. The SBM diet, with its higher rumen-degradable protein (RDP) content, selectively enriched protein degraders Sodaliphilus, Limivicinus, and RUG472 spp., and upregulated genes encoding key peptidases (pepT, pepDA/B) in the rumen. Conversely, aligning with its higher rumen-undegradable protein (RUP) content, the CGM diet promoted the enrichment of proteolytic bacteria Alistipes spp. in the colon. Notably, in response to dietary AA deficiency, the CGM diet enriched AA producers—Ruminococcus, RUG563, UBA1179 spp. in the rumen, Treponema, UBA737, and Firm-07 spp. in the colon. This is accompanied by greater abundances of genes involved in de novo biosynthesis of aromatic AAs (trpA, trpB), lysine (dapA), and histidine (hisG), suggesting a microbial compensatory response for dietary deficiencies, though insufficient to fully offset the nutritional shortfall. This study depicts the microbial nitrogen metabolic landscapes integrating protein degradation, AA biosynthesis, and AA catabolism under distinct dietary protein sources, and provides potential microbial targets for optimizing N utilization efficiency in ruminants.