Rumen microbial diversity and functional annotation in cattle fed yeast supplements using shotgun metagenomics

This study evaluated the effect of yeast supplementation on rumen microbial diversity and fermentation potential in cattle. Four rumen-fistulated cattle were assigned to four treatments: T0(control), T1(150 mL LEBAS®/kg feed), T2(300 mL LEBAS®/kg feed) and T3(12 g lyophilized yeast/day) across four 15-day periods in a 4 × 4 Latin square design. Due to the removal of one animal for health reasons, the final dataset was analyzed as an unbalanced design. The DNA from ruminal fluid was analyzed using shotgun metagenomic sequencing to assess bacterial, archaeal, fungal, protozoal and viral communities, as well as functional and CAZyme annotations. A total of 429,682 high-quality sequences were used for taxonomic and functional analyses. Across all treatments, archaea were dominated by Methanobrevibacter and Methanosarcina, bacteria by Butyrivibrio and Prevotella, fungi by Aspergillus and Penicillium, protozoa by Plasmodium and Symbiodinium and viruses by Myoviridae and Podoviridae; no significant differences were observed among all microbial communities (P > 0.05). Functional annotations were mainly associated with carbohydrate metabolism, with no significant differences (P > 0.05). Enzymatic analysis identified families involved in cellulose, hemicellulose and starch degradation. Alpha diversity indices did not differ among treatments (P > 0.05). In summary, LEBAS® supplementation did not significantly alter the rumen microbial composition, diversity or functional potential under the experimental conditions.