We observed significant correlations between fecal miRNA expression and microbiota composition.
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 identi?ed 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, indicating that they may play a role in the expression of feed efficiency-related miRNAs. Our results provide a new perspective for exploring host-microbiome interactions that a?ect FE traits. Taken together, these results point to the miRNAs and taxa identified here as potential regulators of feed efficiency, which may provide the knowledge needed to develop future strategies to manipulate the microbiome.