Compound microbial intelligent membrane fermentation reshapes the bacterial community and reduces antibiotic, metal, and biocide resistance genes and virulence factors in duck litter

Background Contaminated duck litter is a leading cause of flock disease and a bottleneck for the sustainable development of large-scale dry-rearing systems. Methods We applied shotgun metagenomics to litter from four positions within each of three independent compound microbial intelligent membrane fermentation beds, with unfermented litter from the same three batches as the control. We investigated the bacterial community alongside the abundance of antibiotic, metal and biocide resistance genes (ARGs, MRGs and BRGs) and of virulence factor genes (VFGs). Results Fermented litter was consistently enriched in thermophilic and thermotolerant taxa and in beneficial genera such as Paenibacillus and Bacillus , while opportunistic pathogens including Streptococcus , Mycobacterium and Escherichia were clearly reduced. The total burden of the ARG and VFG classes fell in every fermented position, and representative determinants were consistently depleted: floR , qacEdelta1 and sul2 among the ARGs, ruvB among the MRGs, mexF , ideR and sodA among the BRGs, and htpB , clpV and katA among the VFGs. A small number of genes, tet(L) , fexA and bacA among them, rose in the most active zones, indicating structural remodeling of the resistance reservoir rather than uniform removal. Fermentation was not spatially uniform: the upper and edge layers were more active, and the center-lower layer remained closest to the unfermented control. Conclusion Intelligent membrane fermentation reduced the overall abundance of resistance and virulence determinants in the litter microbiome, and spatial uniformity is important for the process. Because these data are DNA-based, they describe the abundance of resistance and virulence determinants and not resistance or virulence phenotypes.