Microbiome

Establishing an across-country breeding metagenome for methane mitigation in cattle

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Abstract

Reducing enteric methane emissions from ruminants is a key objective for sustainable livestock production. The rumen microbiome plays a central role in methanogenesis, yet its composition and host genetic drivers may differ across production environments. This study characterised the rumen and oral microbiome of cattle from three countries involved in the Re-Livestock project (Horizon Europe grant agreement No 101059609) to quantify taxonomic and functional diversity across countries: the Netherlands (NL; n = 961 Holstein cows), Spain (ES; n = 445 Holstein cows), and Australia (AUS; n = 218 Brahman/Brahman-cross animals). A central objective was to estimate the heritability of microbiome-derived aggregate traits and their genetic correlations with methane missions in the NL and ES Holstein populations, where methane concentration phenotypes and host genomic data were available. The AUS dataset was used to quantify microbiome composition and inter-country variation. Rumen fluid samples (NL, ES) and oral swabs (AUS) were sequenced on Oxford Nanopore Technologies platforms using whole metagenome DNA libraries (shotgun). Taxonomic and functional (KEGG) profiles were generated and filtered for 90% within-population prevalence. Principal component (PC) analyses were used to derive aggregated microbial phenotypes within country representing the principal dimensions of microbial community structure. Linear mixed models were applied in ASReml 4.2 to estimate heritabilities and genetic correlations within and between countries for five microbial PCs and methane concentration. Prevotella dominated the NL and ES rumen samples, comprising on average 37.2% (±7.9%) of classified reads, whereas Moraxella was most abundant in AUS samples (13.7% ±6.4%) and Prevotella averaged only 1.6%. Across the NL and ES datasets, 4,794 microbial genera were detected; 64% were shared, while 31% and 5% were unique to NL and ES, respectively. The AUS dataset contained 5,162 genera, 63% of which were unique, reflecting differences in host-breed, production system and sampling method. In NL and ES Holstein populations, heritability of methane concentration measured with sniffers was 0.18 (±0.11) and 0.25 (±0.13), respectively. Microbial PCs showed low-to-moderate heritabilities: 0.14-0.36 (mean SE ±0.10) in NL and 0.01-0.44 (mean SE ±0.13) in ES. Genetic correlations between methane concentration and microbial PCs ranged from |0.07-0.78| (SE 0.32-0.41; NL) and |0.15-0.98| (SE 0.29-0.66; ES), indicating that specific microbial aggregates capture host-genetic variation linked to methane production. Preliminary results of cross-country genetic correlations for microbial PCs are promising and ranged from |0.07-0.65| (SE 0.35-0.74), suggesting potential to share rumen metagenome information across countries. These results demonstrate that rumen microbiome-derived PCs are heritable and genetically associated with methane concentration in Holstein cattle, supporting their use in breeding low-methane emitting cattle. Ongoing work within the Global Methane Genetics microHub project will expand this work to functional PCs, individual taxa, and additional populations to develop a core, cross-country breeding metagenome for reducing methane emissions.

Keywords: 2026

How to Cite:

Gredler-Grandl, B., Bouwman, A., Flossdorf, D., Manzanilla-Pech, C., Ong, C., Ross, E., Hayes, B., Zetouni, L., de Haas, Y. & González-Recio, O., (2026) “Establishing an across-country breeding metagenome for methane mitigation in cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286971. doi: https://doi.org/10.31274/wcgalp.24183

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