Microbiome

Do host genetics and the rumen microbiome shape adaptive immunity in beef cattle?

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Abstract

Immune competence is essential for disease resistance and vaccine efficacy in cattle, yet the relative contributions of host genetics and the rumen microbiome to variation in immune function remain unresolved. We integrated data on host genetic background, rumen microbiome composition, and immune phenotypes to evaluate their interrelationships. To do this, we immunized multibreed Angus-Brahman (MAB; n=76) and purebred Brahman (BRA; n=60) heifers with keyhole limpet hemocyanin (KLH) on day 0 and administered a booster on day 14. KLH-specific IgG concentrations were quantified by ELISA on days 0, 14, and 28. We assessed delayed-type hypersensitivity (DTH) on day 28 by intradermal injections at two KLH sites and one phosphate-buffered saline (PBS) control site. Skinfold thickness was recorded immediately before challenge (baseline) and 24 hours post-challenge, and DTH was defined as the average change at the KLH sites minus the change at the PBS site. Rumen fluid collected on day 28 underwent 16S rRNA V4 amplicon sequencing (Illumina MiSeq, paired-end). Reads were quality-filtered, trimmed, denoised, merged, and chimera-removed using DADA2 to infer amplicon sequence variants (ASVs). Taxonomy was assigned with SILVA v138.2, and mitochondrial and chloroplast ASVs were removed. Because the BRA and MAB herds were raised on different farms, analyses were performed separately to avoid farm-level confounding and to provide a clearer understanding of within-herd relationships. Within the MAB group, we used univariate linear models to test the effect of breed composition on day-28 IgG concentration and DTH response. Associations between microbial structure and either Brahman breed percentage or immune traits were evaluated using three complementary approaches: (1) alpha diversity metrics analyzed with generalized linear models; (2) beta diversity assessed by PERMANOVA; and (3) differential abundance tested using a linear regression framework in ANCOM-BC2. In MAB heifers, a higher proportion of Brahman breed composition was associated with lower IgG concentrations at day 28 (P P = 0.13). Microbial alpha diversity was not associated with breed composition or immune traits. Notably, adaptive immune phenotypes were not associated with either compositional or phylogenetic beta diversity in either cohort, suggesting that variation in adaptive immune responses is not reflected in overall structure of rumen microbial community. Conversely, beta diversity was significantly associated with breed composition in the MAB cohort. Differential abundance analyses identified rumen taxa associated with breed composition, IgG, and DTH in MAB heifers (PFDR < 0.05). Overall, our results demonstrate that host genetics contribute to variation in adaptative immune responses, and that rumen microbial community structure is linked to both host genetic background. The identification of microbial taxa associated with immune responses provides potential targets for interventions aimed at improving vaccine responsiveness and immune health in beef cattle.

Keywords: 2026

How to Cite:

Cavender, C., Boscollo, P., Alvarado-Vargas, A., Ladeira, G., Alvares, L., Perdomo, M., Nelson, C., Jeong, K. & Rezende, F., (2026) “Do host genetics and the rumen microbiome shape adaptive immunity in beef cattle?”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286794. doi: https://doi.org/10.31274/wcgalp.24121

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