Integrating 16S rRNA Sequencing and LC–MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle

SIMPLE SUMMARY: Live yeast products are used in ruminant nutrition to improve feed efficiency and performance. The effects of yeast on animal performance are mediated via alteration in the rumen microbial population and fermentation; however, the types of metabolites produced from feeding yeast additives have not been described. This study integrated 16S rRNA sequencing and LC–MS-based metabolomics to evaluate rumen bacterial diversity and metabolome of beef steers fed no or 15 g/d of live yeast product. Our findings confirm that live yeast supports the growth of fiber digesters, optimizes the utilization of oxygen and lactic acid, and inhibits the growth of pathogenic Salmonella in the rumen. In addition, some bacteria with unknown functions in relation to the effects of live yeast showed positive correlations with metabolites involved in the metabolism of amino acid and energy substrates. This study enhances our understanding of the effects of live yeast in the rumen. ABSTRACT: We evaluated the effects of live yeast on ruminal bacterial diversity and metabolome of beef steer. Eight rumen-cannulated Holstein steers were assigned randomly to one of two treatment sequences in a study with two 25-d experimental periods and a crossover design. The steers were housed in individual pens. The dietary treatments were control (CON) or yeast (YEA; CON plus 15 g/d of live yeast product). Bacterial diversity was examined by sequencing the V3-V4 region of 16S rRNA gene. The metabolome analysis was performed using a liquid chromatograph and a mass spectrometry system (LC–MS). Live yeast supplementation increased the relative abundance of eight cellulolytic bacterial genera as well as Anaerovorax and Lachnospiraceae. Proteiniclasticum, Salmonella, and Lactococcus were not detected in the YEA treatment. Live yeast supplementation increased the concentrations of 4-cyclohexanedione and glucopyranoside and decreased the concentrations of threonic acid, xanthosine, deoxycholic acid, lauroylcarnitine, methoxybenzoic acid, and pentadecylbenzoic acid. The bacteroidales BS11, Christensenellaceae R-7, and Candidatus saccharimonas showed positive correlations with the metabolites involved in amino acid biosynthesis and the metabolism of energy substrates; the functions of these bacteria are not fully understood in relation to the mode of action of yeast. This study confirms the usefulness of LC–MS-based metabolomics in deciphering the mode of action of live yeast in the rumen.