miRNA‒microbiome correlations in Bos indicus feed efficiency.

The fecal microbiome is emerging as an essential component of the gut microbiota and host metabolism, whereas in cattle, fecal microbiome characterization is still needed. Recent evidence indicates that small RNAs, such as miRNAs, may be isolated from feces and involved in host-microbe interactions. In this study, fecal samples were collected from the rectal ampulla of Nelore bulls that were phenotypically divergent in terms of residual feed intake (RFI). miRNA sequencing and 16S rRNA gene (V3-V4 region) sequencing were performed to reveal the associations between host miRNAs and microbiome composition and their relationships with the feed efficiency phenotype. Among the 162 identified fecal miRNAs, seven were more expressed in the inefficient group: bta-miR-27b, bta-miR-30a, bta-miR-126, bta-miR-143, bta-miR-155, bta-miR-205 and bta-miR-196a. Using metabarcoding sequencing, we identified 5,005 bacterial ASVs, and after filtering, we used 357 ASVs in subsequent analyses. Weighted gene coexpression network analysis (WGCNA) was used to identify miRNA and microbiome interactions. We observed significant correlations between fecal miRNA expression and microbiota composition. The differentially expressed fecal miRNAs were correlated with some taxa, such as Prevotella, Anaerorhabdus furcosa, Bifidobacterium, Bacillales, Succinispira mobilis, Peptostreptococcaceae and Coriobacteriaceae, suggesting that the host is mediating its effect on the microbiome through miRNA expression. Fecal miRNAs and the identified taxa play roles in biological processes, e.g. muscle development, metabolic homeostasis and inflammatory processes related to feed efficiency, serving as potential candidates for exploring host-microbe interactions. Although limited by the sample size, our findings may serve as a basis for future studies on developing strategies to manipulate the microbiome and improve feed efficiency traits in cattle.