Compound microbial intelligent membrane fermentation reshapes the virome and reduces various resistance genes in duck litter.

Contamination of duck litter is a major contributor to frequent disease outbreaks in the scaled dry-litter rearing system, posing serious threats to duck health. Although compound microbial intelligent membrane fermentation has multiple advantages, its impacts on the litter virome and resistome remain poorly characterized. This study employed metaviromics to examine the effects of compound microbial intelligent membrane high-temperature fermentation on duck litter from four treatment groups: deep-layer fermentation (DL-D), shallow-layer fermentation (DL-S-NAF), shallow-layer without fermentation (DL-S), and shallow-layer from an antibiotic-using farm without fermentation (DL-S-ANF). We observed that fermentation treatments (DL-D and DL-S-NAF) significantly reduced RNA viral abundance, with a corresponding decreasing trend for DNA viruses. Fermentation treatments also markedly decreased the loads of antibiotic resistance genes (ARGs) including sul1, sul2, tetB(P), and qacEdelta1; metal resistance genes (MRGs) including arsC, arsM, merA, copR, and corR; biocide resistance genes including mdeA, actP, smdB, cpxA, and galE; and bacterial virulence factors including ggroEL2 and lirB. In duck litter, viral communities were dominated by Uroviricota and Nucleocytoviricota (DNA viruses) and Pisuviricota and Lenarviricota (RNA viruses), with Caudoviricetes and Megaviricetes as the predominant DNA virus classes. Single-sample metavirome analysis identified 34 viral operational taxonomic units (vOTUs) and 343 viral genes. ARG abundance followed a hierarchical trend of DL-D < DL-S-NAF < DL-S < DL-S-ANF, while MRG abundance showed DL-D < DL-S-NAF < DL-S-ANF < DL-S. Compound microbial intelligent membrane fermentation effectively reduced both DNA and RNA viral abundance, diminished resistance gene loads, and attenuated virulence factors in duck litter. These data indicate that RNA viruses, particularly Pisuviricota, are sensitive bioindicators for ecological health assessment. Additionally, this antibiotic-free fermentation system may provide an important strategy for curbing dissemination of antimicrobial resistance at its source.