Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle

SIMPLE SUMMARY: Grass-fed beef industry is booming in the USA. Compared to grain-fed, the rumen microbiome profiles and features in a grass-fed regimen have yet to be identified. In this study, we found that the rumen microbiome in the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity than that of grain-fed cattle. The abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. A rumen microbial predictor accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. The results of this study provided deep insights into microbial interactions in the rumen under different feed schemes, which will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains in beef practice. ABSTRACT: The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle’s rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R(2) = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.