Dietary Fermentation with Lactobacillus sp. and Bacillus sp. Modulates Rumen Transcriptomic and Microbiota Profiles in Bos taurus

Animal feed made from fermented agricultural residues using <i>Lactobacillus</i> sp. <i>and Bacillus</i> 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 <i>Lactobacillus</i> sp. <i>and Bacillus</i> sp. (AF) on gene expression in major metabolic organs and on microbial populations in the rumen of <i>Bos-Taurus</i> 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 (<i>p</i> < 0.05) increased <i>Firmicutes</i> but reduced <i>Bacterioidetes</i> abundances. At the genus level, <i>Faecalicatena</i>, <i>Intestinimonas</i>, <i>Lachnoclostridium</i>, <i>Faecalicatena</i>, and <i>Intestinimonas</i> were significantly higher (<i>p</i> < 0.05) in animals fed with the AF diet. Regarding fungal populations, <i>Neocallimastigomycota</i> accounted for 98.2% in the NF diet and 86.88% in the AF diet. AF feeding increased <i>Orpinomyces</i> and <i>Piromyces</i> but decreased <i>Neocallimastix</i> abundances. These findings highlight the potential of fermented feeds to improve metabolic responses and rumen microbial balance, contributing to enhanced animal performance.