Species-specific rumen microbial responses to dietary inhibition of methanogenesis in cows and goats

Introduction Methane, a greenhouse gas, is produced in the rumen microbiome of ruminants. Various nutritional strategies can reduce enteric methane (CH 4 ) emissions from livestock, but it is unclear whether diet affects rumen microbiome similarly across ruminant species. The objective of this study was to determine whether cows and goats differ in their rumen microbial functional responses to dietary strategies based on starch and/or lipid supplementation, and whether these differences explain diet-associated variation in CH 4 emissions under comparable experimental conditions. Methods Experiments were conducted simultaneously, and both species received the same diet based on grassland hay and concentrate as the Control diet (CTL) or supplemented with corn oil and wheat starch (COS), marine algae powder (MAP) or hydrogenated palm oil (HPO). To identify biologically relevant features from the rumen microbial metatranscriptomes, we followed a five-step integrative statistical and network analysis pipeline, combining a network-based approach with clustering and supervised model fitting to associate differentially expressed genes and taxa with CH 4 emissions in the rumen. Results The COS diet lowered CH 4 emissions in both cows and goats and altered their rumen microbiomes. However, the number of differentially expressed KEGG orthologs and differentially abundant OTUs identified in the COS vs CTL comparison was greater in cows than in goats. Moreover, clustering analysis revealed differences in network topology between ruminant species. In goats, CH 4 emission reduction was strongly associated with genes involved in carbohydrate metabolism and methylotrophic and hydrogenotrophic pathways of methanogenesis; whereas in cows, hydrogenotrophic pathways were prominent. Additionally, sparse Partial Least Squares (sPLS) analysis identified species-specific discriminant microbial features. Discussion Overall, these results show that host species modulates rumen microbial responses to diet and suggest that microbial interactions underlying CH₄ mitigation differ between cows and goats, although validation in independent studies involving larger sample sizes is required.