Illumina Sequencing and Metabolomic Analysis Explored the Effects of the Mixed Silage of Rice Straw and Chinese Cabbage Waste on Fecal Microorganisms and Metabolites in Hu Sheep

Silage is the most important component of a ruminant diet and has important production and health significance in ruminant production. The aim of the research was to investigate how the mixed silage of Chinese cabbage waste and rice straw (mixed silage) impacts the fecal microorganisms and metabolites in Hu sheep using Illumina sequencing and metabolomic analysis. A total of 16 Hu sheep (8 rams and 8 ewes) weighing about 39 kg and 5.5 months old were used as experimental sheep and divided into two groups (4 rams and 4 ewes, n = 8) using the principle of randomized trials: the control group with peanut sprouts, corn husks, and sorghum husks as roughage and the silage group with the mixed silage as roughage. There were no significant differences in the average daily gain (ADG), dry matter intake (DMI), or feed conversion rate (FCR) between the control group and the mixed silage groups (p > 0.05). Microbiome results showed that 15 microorganisms such as Ruminococcaceae UCG 010, Breznakia, Erysipelothrix, Desulfovibrio, Succiniclasticum, and Shuttleworthia were significantly different between the two groups. In addition, metabolomics showed that the mixed silage modulated the concentrations and metabolic pathways of metabolites in the manure. Significantly different metabolites were mainly enriched in amino acid anabolism (“glycine, serine, and threonine metabolism”, “valine, leucine, and isoleucine biosynthesis”, “arginine biosynthesis”, etc.), nucleic acid metabolism (pyrimidine metabolism). In conclusion, the addition of mixed silage to the diet of Hu sheep can alter the structure of the hindgut microflora and regulate the metabolism of amino acids and nucleotides, which affects health performance.