Fermented agricultural by-products improve growth performance in indigenous chickens in association with altered ileal microbiota, microbial functional potential, and mucosal responses.

Fermented agricultural by-products may improve poultry health through microbiota-host interactions, but the underlying microbial and transcriptional responses remain incompletely understood. We assigned 160 Wuliangshan black-bone chickens to diets containing 0%, 5%, 10%, or 15% fermented feed from 8 to 120 d of age. The fermented feed was produced from soybean hulls, rapeseed meal, and vegetable waste by sequential fermentation with Bacillus subtilis, Lactiplantibacillus plantarum, and Limosilactobacillus reuteri. Ileal microbial communities were profiled by 16S rRNA gene sequencing, followed by shotgun metagenomics and ileal mucosal transcriptomics in the control and 10% groups. Fermented feed increased average daily gain (ADG) and ileal villus height and reduced feed conversion ratio (FCR). The 10% diet increased the relative abundance of Lactiplantibacillus from 1.05% to 74.47%, while reducing Enterococcus, Streptococcus, Staphylococcus, and Escherichia-Shigella. Metagenomic analysis revealed enrichment of microbial pathways and carbohydrate-active enzymes associated with starch and plant cell-wall polysaccharide degradation. Ileal butyrate concentration increased, whereas predicted virulence determinants, including cereulide, β-hemolysin/cytolysin, and LPS/LOS-related factors, decreased. The resistome shifted toward efflux-related determinants without broad enrichment of antimicrobial resistance genes. Ileal mucosal transcriptomics revealed lower expression of proinflammatory and innate immune genes and higher expression of genes involved in growth signaling and nutrient transport. Spearman correlation analysis showed that Lactiplantibacillus abundance and butyrate concentration were associated with higher ADG, villus height, and expression of growth-related genes and with lower FCR. Lactiplantibacillus abundance was also positively correlated with selected nutrient transport genes and negatively correlated with selected immune-related genes, whereas the depleted potentially opportunistic genera generally showed opposite correlation patterns. Collectively, fermented feed improved growth performance and intestinal health in association with Lactiplantibacillus enrichment, reduced predicted microbial virulence potential, attenuated mucosal immune activation, and enhanced host responses related to growth and nutrient transport.