Influence of host genetics on the functional composition of the Rumen metagenome

Authors: LAKAMP, ANDREW - University Of Nebraska; ADAMS, SEIDU - University Of Nebraska; Wells, James; Snelling, Warren; Kuehn, Larry; HALES, KRISTIN - Texas Tech University; Neville, Bryan; FERNANDO, SAMODHA - University Of Nebraska; SPANGLER, MATTHEW - University Of Nebraska

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2026
Publication Date: N/A
Citation: N/A

Interpretive Summary: The gastrointestinal tract of animals contains a vast array of microorganisms that impact the animal’s productivity, well-being, and pathogen carriage. These microorganism express genes important to the host, but the potential for the host to influence the genetic composition of the microorganisms has not been studied. Utilizing a large group of animals, samples of rumen digesta were collected and analyzed. More than 10% of the microbial genes detected were considered at minimal moderately heritable within the cattle populations, indicating that the host might influence the genetic composition of the microbial populations present. Host genes in the cattle related to immune function and host-microbiome cross talk were correlated with a variety of microbial genes considered to be highly heritable within the cattle populations. The study indicates that the animal host is associated with and might be influencing the microbial genetic composition in the gastrointestinal tract.

Technical Abstract: Background Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. It is known the rumen microbiome composition plays a role in economically important traits. One avenue to alter the functional composition of the rumen microbiome may be genetic selection of the host. Previous studies relating the rumen microbiome to host genetics have either been limited to prokaryotic organisms or relatively limited in sample size. The objectives of this study were to determine the host genetic influence on functional features of the rumen metagenome, examine host genes associated with rumen metagenome composition, and identify metagenomic features which may be targets for host genetic selection in the future. Results Rumen samples were taken from 717 beef cattle on four diets, two high-concentrate and two high-forage. Rumen samples were sequenced using shotgun sequencing from which open reading frames (ORF) were predicted. Animal genotypes were generated from imputation based on either low-pass whole genome sequencing or array data. The log-transformed relative abundance of 16,583 ORF were used as phenotypes in linear mixed models with the random effect of host genotype. Over 50% of the ORF had nonzero heritability estimates and more than 10% had estimates greater than 0.20. Highly heritable ORF functions included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORF were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome cross talk. Conclusions Host genetics influence the rumen metagenome making genetic selection of the host to alter metagenome composition possible. Moreover, a portion of the highly heritable ORFs is genetically correlated with feed efficiency traits making them viable selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host. Additionally, the host genetic influence of the metagenome includes ORF with a variety of functions.