Ruminal archaea and bacteria metatranscriptomic responses to supplementation in steers fed low-quality forage

A basal diet of low-quality forage (LQF) results in decreased forage utilization and animal performance. Protein and starch supplementation can ameliorate these effects by providing additional nitrogen and energy to ruminal microbes. However, the effect of protein and starch supplementation on ruminal microbial gene expression, specifically pathways involved in methanogenesis, is not well-documented. We aimed to evaluate the effect of supplement composition on ruminal microbial gene expression before and after supplementation in steers consuming a basal diet of LQF. Five ruminally-cannulated Angus steers (BW 375 ± 45 kg) were used in a 4 × 4 Latin square and fed a basal diet of King Ranch Bluestem Hay (3.5% CP, 73% NDF), and one of four isonitrogenous (130 mg nitrogen/kg BW) supplements. Ruminal samples collected from the steers provided the two most divergent supplements, 2% starch (43% CP; 100% soybean meal) and 56% starch (21% CP; 78% corn, 19% soybean meal, 2.4% urea) were used for metatranscriptomic analysis. Samples were collected via cannula prior to and 4 h post-supplementation; total RNA was sequenced. Differentially expressed genes (DEG) were identified and functionally annotated; pathway enrichment analysis was completed. Sampling time exerted a greater effect than starch concentration (∼78 vs. 17% in both archaea and bacteria). All methanogenesis pathways were differentially regulated by time (P < 0.05) with upregulated genes primarily expressed by Thermoplasmata and downregulated genes primarily expressed by Methanobrevibacter. Acetoclastic and methylotrophic methanogenesis pathways were differentially regulated by starch supplementation (P < 0.05) with upregulated genes primarily expressed by Thermoplasmatales and downregulated genes primarily expressed by Methanomethylophilus alvus. The majority of bacterial DEG were expressed by Clostridia, but unclassified Bacteroidetes was the predominant bacteria responsible for expression of carbohydrate active enzymes (CAZymes). Time relative to feeding, rather than starch supplementation, resulted in a greater number of bacterial CAZymes expressed. Supplement composition elicited changes in the taxa involved in methanogenesis and carbohydrate metabolism, suggesting the potential for effects on CH4 emissions. Further research is needed to directly quantify CH4 emissions in response to supplementation to potentially optimize supplementation strategies and improve sustainability of beef cattle production.