Application of multi-omics to investigate the effect of Pinus koraiensis cone essential oil on rumen methane emission, microbial community, and metabolites

Abstract

Background Enteric methane (CH4) excreted by ruminants is a major source of anthropogenic greenhouse gas emissions in the global environment. Pinus koraiensis cone essential oil (PEO) contains functional compounds such as monoterpene hydrocarbons, which can directly affect the microbiota and their function in the rumen. Previously, we found that PEO oral administration during the growing phases of goats reduced CH4 emissions and was associated with the rumen prokaryotic microbiota. However, a more comprehensive analysis of the rumen microbiota and metabolites are needed. The objective was to elucidate the potential microbial features that underpin CH4 mitigation in goats using metataxonomics (prokaryotes, protozoa, and fungi) and metabolomics (rumen fluid and serum). Ten fattening Korean native goats were divided into two dietary groups: control (CON; basal diet without additives) and PEO (basal diet + 1.5 g/d of PEO), using a 2 × 2 crossover design for 11 weeks. Methane measurements were conducted every four consecutive days for 24–27 d. Results Oral administration of PEO reduced CH4 concentrations in the exhaled gas from eructation by 12.0–13.6% (P < 0.05). Although the microbiota structure, including prokaryotes, protozoa, and fungi, was not altered after PEO administration, MaAsLin2 analysis revealed that Selenomonas, Christensenellaceae R-7, and Anaerovibrio were enriched in the PEO group (Q < 0.1). Co-occurrence network analysis revealed that the Bacteroidales RF16 group and Anaerovibrio were the keystone genera in the CON and PEO groups, respectively, with fungal genera exclusively found in the PEO group but not identified as keystone taxa. Predicted function analysis using CowPI, CH4 metabolism was enriched in the CON group, whereas metabolism of sulfur (P < 0.001) and propionate (P < 0.1) were enriched in the PEO group. Random forest analysis identified eight ruminal metabolites, including propionate, that were altered after PEO administration, with predictive accuracy ranging from 0.75 to 0.88. Selenomonas was positively correlated with propionate and co-occurred with it. Conclusions The results provide an understanding of how PEO oral administration affects the ruminal microbial community and its functions in the rumen, as well as its linkages with rumen metabolites and host health, ultimately leading to the reduced CH4 emissions.