Microbiome Dynamics and Host-Microbiome Interactions Governing Feed Efficiency in Nigerian Cattle Breeds

This study investigates rumen and gut microbiome composition and dynamics in relation to feed efficiency variation in Nigerian indigenous cattle breeds, contributing an original understanding of host-microbiome interactions that determine feed conversion efficiency in tropical beef cattle. Feed efficiency, the ability to convert feed into body gain with minimal waste, is an important but highly variable trait in beef cattle production. While genetic factors influence efficiency, emerging evidence suggests that rumen microbiome composition explains a significant proportion of feed efficiency variation independent of genetics. In Nigerian cattle, where feed efficiency directly determines financial sustainability of beef production, the microbiome basis of efficiency differences has not been investigated. This study characterises rumen microbiome (16S rRNA V4 amplicon sequencing and metagenomic analysis) in 120 Bunaji, Sokoto Gudali, and Keteku steers that have been precisely phenotyped for residual feed intake (the gold standard feed efficiency metric) over 84-day testing periods at NAPRI and University of Maiduguri. Differential microbiome composition between high and low efficiency animals is identified, and predicted functional pathways are mapped using PICRUSt2. Rumen fluid transplantation experiments test the causal contribution of microbiome differences to efficiency outcomes. Findings reveal a distinct core microbiome signature in high-efficiency animals enriched in Fibrobacter succinogenes and Ruminococcus champanellensis, associated with enhanced cellulose degradation. Methanogen populations are significantly lower in high-efficiency animals, consistent with reduced methane losses. Transplantation studies confirm microbiome causal contribution to efficiency improvement. The study recommends rumen microbiome modulation as a novel feed efficiency management strategy.

Keywords: rumen microbiome, feed efficiency, Nigerian cattle, residual feed intake, methanogen.