Several studies have evaluated the effects of live yeast supplementation on rumen microbial population; however, its effect on differential microbial genes and their functional potential has not been described. Thus, this study applied shotgun metagenomic sequencing to evaluate the effects of live yeast supplementation on genetic and functional potential of the rumen microbiota in beef cattle. Eight rumen-cannulated Holstein steers were randomly assigned to two treatments in a cross-over design with two 25-day experimental periods and a 10-day wash-out between the two periods. The steers were housed in individual pens and fed 50% concentrate-mix and 50% red clover/orchard hay ad libitum . Treatments were (1) control (CON; basal diet without additive) and (2) yeast (YEA; basal diet plus 15 g/d of live yeast product). Rumen fluid samples were collected at 3, 6, and 9 h after feeding on the last d of each period. Sequencing was done on an Illumina HiSeq 2500 platform. Dietary yeast supplementation increased the relative abundance of carbohydrate-fermenting bacteria (such as Ruminococcus albus , R . champanellensis , R. bromii , and R. obeum ) and lactate-utilizing bacteria (such as Megasphaera elsdenii , Desulfovibrio desulfuricans , and D. vulgaris ). A total of 154 differentially abundant genes (DEGs) were obtained (false discovery rate < 0.01). Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of the DEGs revealed that 10 pathways, including amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, lipopolysaccharide biosynthesis, pantothenate and coenzyme A biosynthesis, glutathione metabolism, beta-alanine metabolism, polyketide sugar unit biosynthesis, protein export, ribosome, and bacterial secretory system, were enriched in steers fed YEA. Annotation analysis of the DEGs in the carbohydrate-active enzymes (CAZy) database revealed that the abundance of genes coding for enzymes belonging to glycoside hydrolases, glycosyltransferases, and carbohydrate binding modules were enriched in steers fed YEA. These results confirm the effectiveness of a live S. cerevisiae product for improving rumen function in beef steers by increasing the abundance of cellulolytic bacteria, lactic acid-utilizing bacteria, and carbohydrate-active enzymes in the rumen. Electronic supplementary material The online version of this article (10.1186/s40104-019-0378-x) contains supplementary material, which is available to authorized users.

Simple SummaryMonensin can enhance the efficiency of feed utilization by modulating rumen fermentation; however, its effects on rumen function has not been fully described. Thus, this study integrated metagenomics and metabolomics analysis to identify differences in functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Our results showed differences in relative abundance of functional genes involved in lipid metabolism and amino acid metabolism as well as changes in rumen fluid metabolites and their metabolic pathways. This study revealed a better understanding of the effects of monensin, which may enable more effective use of this additive for beef cattle production.AbstractTo identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Eight rumen-fistulated steers were used in the study for a period of 53 days. Rumen fluid samples were collected on the last day of the experiment. Monensin increased the relative abundance of Selenomonas sp. ND2010, Prevotella dentalis, Hallella seregens, Parabacteroides distasonis, Propionispira raffinosivorans, and Prevotella brevis, but reduced the relative abundance of Robinsoniella sp. KNHs210, Butyrivibrio proteoclasticus, Clostridium botulinum, Clostridium symbiosum, Burkholderia sp. LMG29324, and Clostridium butyricum. Monensin increased the relative abundance of functional genes involved in amino acid metabolism and lipid metabolism. A total of 245 metabolites were identified. Thirty-one metabolites were found to be differentially expressed. Pathway analysis of the differentially expressed metabolites revealed upregulated metabolic pathways associated with metabolism of linoleic acid and some amino acids. These findings confirm that monensin affects rumen fermentation of forage-fed beef cattle by modulating the rumen microbiome, and by reducing amino acid degradation and biohydrogenation of linoleic acid in the rumen.

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This study utilized 16S ribosomal ribonucleic acid (rRNA) sequencing and liquid chromatography-mass spectrometry (LC-MS)-based metabolomic profiling to evaluate the effects of a live yeast product on ruminal bacterial diversity and metabolome of beef steer. Eight rumen-cannulated Holstein steers were assigned randomly to 1 of 2 treatment sequences in a study with two 25-d experimental periods and a crossover design. The steers were fed 50% concentrate-mix and 50% red clover hay ad libitum. Dietary treatments were (1) control (CON; basal diet) and (2) yeast (YEA; basal diet plus 15 g/d of live yeast product; PMI, Arden Hills, MN, USA). Bacterial diversity was examined by sequencing of the V3-V4 region of the 16S rRNA gene. Metabolome analysis was performed using an ultra-performance LC-MS system. Relative abundance of bacteria was analyzed using the GLIMMIX procedure of SAS and a model that included the effects of treatment, period, and their interaction. Significant differences were declared at P ≤ 0.05. Differential metabolites were filtered using significance estimate of P ≤ 0.10 using Metaboanalyst 4.0. Pearson correlation was used to examine associations between the relative abundance of ruminal bacteria and rumen metabolites. Yeast supplementation increased (P ≤ 0.05) the relative abundance of Ruminococcaceae NK4A214, Christensenellaceae R-7, Ruminococcaceae UCG-010, Ruminococcus 2, and Ruminococcaceae UCG-005, Candidatus saccharimonas, Anaerovorax, and Lachnospiraceae. Yeast supplementation increased (P ≤ 0.10) the concentrations of 4-cyclohexanedione and β-d-glucopyranoside, and decreased concentrations of threonic acid, xanthosine, deoxycholic acid, lauroylcarnitine, methoxybenzoic acid, and pentadecylbenzoic acid. Bacteroidales BS11, Christensenellaceae R-7, and Candidatus saccharimonas showed positive correlations with metabolites involved in amino acid biosynthesis and 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.