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Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle.


Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n=10; inefficient, n=10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic datasets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalki, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. Through comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed efficiency animals (P < 0.10) and one archaeal taxa (Methanomassiliicoccale) tended to more abundant in efficient cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score > 2 with P < 0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZymes were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle may have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.Importance This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome with feed efficiency (residual feed intake) in beef cattle. The data generated from current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in feed efficiency. The findings on the active rumen microbiome that may contribute to variations in feed efficiency of beef cattle highlight the possibility to enhance nutrient utilization and improve cattle feed efficiency through altering rumen microbial functions.