16S amplicon sequencing and untargeted metabolomics reveal changes in rumen microorganisms and metabolic pathways involved in the reduction of methane by cordycepin

As a major contributor to methane production in agriculture, there is a need for a suitable methane inhibitor to reduce ruminant methane emissions and minimize the impact on the climate. This work aimed to explore the influence of cordycepin on rumen fermentation, gas production, microbiome and their metabolites. A total of 0.00, 0.08, 0.16, 0.32, and 0.64 g L^–1 cordycepin were added into fermentation bottles containing 2 g total mixed ration for in vitro ruminal fermentation, and then the gas produced and fermentation parameters were measured for each bottle. Samples from the 0 and 0.64 g L^–1 cordycepin addition were selected for 16S rRNA gene sequencing and metabolome analysis. The result of this experiment indicated that the addition of cordycepin could linearly increase the concentration of total volatile fatty acid, ammonia nitrogen, the proportion of propionate, valerate, and isovalerate, and linearly reduce ruminal pH and methane, carbon dioxide, hydrogen and total gas production, as well as the methane proportion, carbon dioxide proportion and proportion of butyrate. In addition, there was a quadratic relationship between hydrogen and cordycepin addition. At the same time, the relative abundance of Succiniclasticum, Prevotella, Rikenellaceae_RC9_gut_group, NK4A214_group, Christensenellaceae_R_7_group, unclassified_F082, Veillonellaceae_UCG_001, Dasytricha, Ophryoscolex, Isotricha, unclassified_Eukaryota, Methanobrevibacter, and Piromyces decreased significantly after adding the maximum dose of cordycepin. In contrast, the relative abundance of Succinivibrio, unclassified_Succinivibrionaceae, Prevotellaceae_UCG_001, unclassified_Lachnospiraceae, Lachnospira, Succinivibrionaceae_UCG_002, Pseudobutyrivibrio, Entodinium, Polyplastron, unclassified_Methanomethylophilaceae, Methanosphaera, and Candidatus_Methanomethylophilus increased significantly. Metabolic pathways such as biosynthesis of unsaturated fatty acids and purine metabolism and metabolites such as arachidonic acid, adenine, and 2´-deoxyguanosine were also affected by the addition of cordycepin. Based on this, we conclude that cordycepin is an effective methane emission inhibitor that can change the rumen metabolites and fermentation parameters by influencing the rumen microbiome, thus regulating rumen methane production. This experiment may provide a potential theoretical reference for developing Cordyceps byproduct or additives containing cordycepin as methane inhibitors.