Abstract
Animal feed made from fermented agricultural residues using Lactobacillus sp. and Bacillus sp. has received significant attention. However, interactions between differentially expressed genes (DEGs) in adipose, liver, and muscle tissues and bacteria or fungi in the rumen remain largely unknown. This study determined effects of normal diet feed (NF) and alternative diet feed made by Lactobacillus sp. and Bacillus sp. (AF) on gene expression in major metabolic organs and on microbial populations in the rumen of Bos-Taurus using high-throughput sequencing methods. Rumen bacteria/fungi interaction with DEGs in key metabolic organs was also investigated. According to our findings, 34, 36, and 28 genes were differentially expressed in adipose, liver, and muscle tissues, respectively. Most DEGs were associated with osteoclast differentiation and immune functions. Microbial dynamics analysis showed that the AF diet significantly (p < 0.05) increased Firmicutes but reduced Bacterioidetes abundances. At the genus level, Faecalicatena, Intestinimonas, Lachnoclostridium, Faecalicatena, and Intestinimonas were significantly higher (p < 0.05) in animals fed with the AF diet. Regarding fungal populations, Neocallimastigomycota accounted for 98.2% in the NF diet and 86.88% in the AF diet. AF feeding increased Orpinomyces and Piromyces but decreased Neocallimastix abundances. These findings highlight the potential of fermented feeds to improve metabolic responses and rumen microbial balance, contributing to enhanced animal performance.