Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches

Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.