Microbiome

Rumen microbiome mediates genetic effects on feed efficiency in beef cattle

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Abstract

Beef production sustainability relies on three key aspects: animal performance, efficiency, and emissions. However, the role of the rumen microbiome and its interaction with the host remains unclear. For example, the extent to which the rumen microbial community mediates host genetic effects on feed efficiency and gas emission traits is still under investigation. This study aimed to quantify the direct genetic effect and indirect effects mediated by the rumen microbiome on feed efficiency traits.We assessed the causal relationships between the microbiome component (M) and phenotypic traits (P) such as residual feed intake (RFI), dry matter intake (DMI), and body weight (BW), assuming no residual correlation between the microbiome and phenotype. The host genome (G) was modeled as influencing both the phenotype (GP→P) and the rumen microbial composition (GM→M), with this also affecting the phenotype (M→P), thereby mediating indirect genetic effects (G→M→P). Data consisted of 537 purebred Hereford bulls and steers evaluated in seven postweaning feed tests. All animals were genotyped using 100k SNP panels, and rumen microbial abundances were profiled via restriction enzyme reduced representation sequencing. We transformed microbial abundances using a centered log-ratio (CLR) transformation, retaining 1,536 amplicon sequence variants (ASVs) for analysis. The use of recursive models revealed significant causal effects of 384, 339 and 479 individual ASVs on RFI, DMI, and BW respectively. We obtained an average microbial heritability of 0.07 (ranging from 0 to 0.36 ± 0.05). From 23 to 32% of ASVs exhibited significant phenotypic effects, though most exhibited low microbial heritability (h2M 2M > 0.10). The total heritability, which accounts for direct and indirect genetic effects, decreased when microbiome information was included, suggesting that mostly ASVs counteract direct genetic effects. The identification of microbial taxa with moderate heritability values and significant causal influence supports their potential for being used in selective breeding. Our findings suggest that the rumen microbiome may mediate part of the genetic variance for feed efficiency traits. Overall, recursive modeling emerges as a powerful tool to disentangle direct and mediated genetic effects, offering new insights into host-microbiome interactions in beef cattle.

Keywords: 2026

How to Cite:

Peraza, P., Martinez-Boggio, G., Naya, H., Sotelo-Silveira, J. & Navajas, E., (2026) “Rumen microbiome mediates genetic effects on feed efficiency in beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2280560. doi: https://doi.org/10.31274/wcgalp.23446

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