Ruminant production is under strong societal pressure because of emissions of the greenhouse gas methane (CH4). Methanogenesis occurs during feed fermentation and nutritional strategies appear to be an effective and sustainable way to reduce emissions without adverse effects. This work aimed to enhance our understanding of the mechanisms in rumen methanogenesis by highlighting similarities or dissimilarities between two animal species, cows and goats, in microbial responses to diet supplementation. Four Holstein cows and 4 Alpine goats received similar rations based on meadow hay and concentrate containing no supplemental (CTL) or supplemented with corn oil (COS), marine algae powder (MAP) or hydrogenated palm oil (HPO). CH4 emissions were measured in respiratory chambers. Total RNA from rumen content was extracted and subjected to RNASeq sequencing on Illumina platform. Raw data were analyzed using an open-source pipeline (MetaTrans) and mapped against a homemade rumen metagenome database. To identify biologically relevant features, we developed a five-step biostatistical pipeline: 1) identification of differentially expressed OTUs and KEGGs (deOTUs, deKEGGs), 2) bipartite network deduction, 3) clustering analysis, 4) pathway enrichment analysis and 5) sPLS regression, to associate the deKEGGs and deOTUs variables with CH4 emissions by species. The key features extracted from comparisons of COS vs CTL, COS vs MAP and COS vs HPO were considered for a metabolic network reconstruction and an integration analysis by logical modelling. Only, the COS diet reduced enteric CH4 emissions in both species compared to CTL. Differential analysis between COS vs CTL identified 380 deKEGGs and 16 deOTUs in cows and 133 deKEGGs and 10 deOTUs in goats. These results suggests that the diet mainly affected microbial functions rather than taxonomy. Further, sPLS analysis highlighted a correlation between the reduction in CH4 emissions and differentially regulated genes related to CH4 metabolism (such as the methyl coenzyme M reductase in both species) and to carbohydrate metabolism (class I fructose bisphosphate aldolase (fba) in cows and Fructose 1,6-bisphosphatase (fbp) in goats). Integrally, the metabolic network related to COS vs HPO were highly different to the others comparisons in cows, while in goats the metabolic reactions between COS vs CTL and COS vs HPO diets were similar. We identified key elements of methanogenesis attenuation processes that have been integrated into a model for predicting and validating key microbiome determinants of enteric methanogenesis in ruminants.