Given that the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome plays a key role in determining host feed efficiency and methane (CH₄) emissions. Some reports suggests that a less diverse rumen microbiome is associated with improved feed efficiency, while other studies suggest that microbial diversity does not differ between low- and high-efficiency cattle of the same breed, fed identical diets. While reducing enteric CH₄ emissions offers a dual benefit in terms of improved feed efficiency and a reduced environmental footprint; recent findings indicate that these outcomes are not always consistent in ruminants. The composition of the rumen microbiome is mainly determined by diet but is also influenced by host genetics and physiological parameters such as rumen volume, rate of passage and rumination. Reduced microbial diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture are the energetic foundation of the rumen microbiome, and considerable resources have been invested in developing additives that redirect hydrogen flow toward alternative sinks and away from the reduction of CO₂ to CH₄. These additives reduce enteric CH₄ emissions by 30-80%, yet the anticipated gains in feed efficiency remain inconsistent. Strategies to improve the feed efficiency of cattle production must consider the multifaceted interactions among the host, rumen microbiome, and diet to ensure the sustainable intensification of cattle production while maintaining the social license for milk and meat production.

Enhancing crop residue digestibility can boost the available energy for growth and milk yield and improve the sustainability of ruminant production systems. As the natural diet of bison is high in lignocellulose, bison have developed a microbiome that efficiently digests cellulose and hemicellulose. This study compared the rumen metatranscriptomes of bison and beef heifers and investigated the effects of inoculating heifers with bison rumen contents. Gene Ontology, molecular function, and Kyoto Encyclopedia of Genes and Genomes orthology terms identified through gene set enrichment analysis successfully captured differences in gene expression of rumen microbiome between heifers and bison fed different diets. Specifically, differences in nitrogen metabolism was detected between heifers and bison rumen microbiomes. Heifer rumen microbiomes demonstrated a higher dissimilatory nitrate reduction, while bison microbiomes tended to suppress this pathway. In contrast, bison microbiomes expressed higher levels of glutamate dehydrogenase 2 (GDH2) genes. However, glutamate dehydrogenase gene expression was observed to be strictly regulated in heifers, as inoculation with bison rumen contents had no effect on expression. Moreover, the transfer of bison rumen contents led to a persistent downregulation of microbial nitrogen metabolism in heifers after 27 days of transfer. In addition, gene set enrichment analysis also identified the crucial regulatory role of serine/threonine kinase in heifer rumen microbial metabolism and differences in ion transport between heifers and bison. These findings provide valuable insights into the complex interplay between diet and the rumen microbiome. IMPORTANCE: Ruminants play a key role in the conversion of cellulolytic plant material into high-quality meat and milk protein for humans. The rumen microbiome is the driver of this conversion, yet there is little information on how gene expression within the microbiome impacts the efficiency of this conversion process. The current study investigates gene expression in the rumen microbiome of beef heifers and bison and how transplantation of ruminal contents from bison to heifers alters gene expression. Understanding interactions between the host and the rumen microbiome is the key to developing informed approaches to rumen programming that will enhance production efficiency in ruminants.

Efficient utilization of lignocellulosic biomass by the rumen microbiome is critical for improving feed efficiency in ruminants, yet the development of stable, functionally specialized microbial consortia remains limited. This study aimed to assemble substrate-adapted rumen microbial consortia using an ecology-guided enrichment approach. Rumen fluid collected from cannulated Angus × Hereford heifers was sequentially enriched over 10 generations on four substrates with distinct cell wall characteristics: alfalfa, barley straw, carboxymethyl cellulose (CMC), and xylan. Fermentation parameters, including gas production and volatile fatty acids (VFAs), and bacterial community dynamics were analyzed, and selected consortia (alfalfa and xylan) were evaluated for stability following one month of cryopreservation. Across enrichments, total VFA concentrations declined (e.g., xylan: 109.8 mM (G0) to 56.37 mM (G10)), accompanied by reduced gas production and decreased alpha diversity, indicating substrate-driven selection. Distinct functional profiles emerged, including increased propionate in alfalfa consortia, higher acetate in barley straw, lactate–propionate cross-feeding with CMC, and caproate production (6.3 mM at G10) in xylan enrichments associated with Caproiciproducens and Megasphaera. Cryopreserved consortia retained core community structure and fermentation characteristics upon revival. These results demonstrate that substrate-driven enrichment can generate stable, functionally specialized rumen consortia and provide a framework for developing ecologically compatible microbial communities with potential applications in improving rumen fermentation efficiency.