Compound microbial intelligent membrane fermentation reshapes the bacterial community and reduces antibiotic, metal, and biocide resistance genes and virulence factors in duck litter
- 1Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University
- 2Gut Microbiome Research Center, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou
Abstract
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.
Related
- Effects of monensin residues on microbial community and the attenuation of antibiotic resistance genes during chicken manure composting
- Urbanization shapes the landscape of antibiotic resistance genes and water quality microbial markers across an urban watershed
- Identification of antibiotic resistance genes and their bacterial hosts in samples collected from wastewater treatment plants in Palestine
- Antibiotic resistance genes in aquaculture: Molecular detection, environmental dynamics, and biological control strategies
- Response to comment on “Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper”
BibTeX
@article{sun2026compound,
title = {{Compound microbial intelligent membrane fermentation reshapes the bacterial community and reduces antibiotic, metal, and biocide resistance genes and virulence factors in duck litter}},
author = {Tiecheng Sun and Guiheng Mei and Meiqin Li and Junru Mo and Chengwei Zhang and Yanmei Ma and Jiamei Zhao and Song Peng and Fengqiang Lin and Ji-Long Chen and Zhaolong Li},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1997145},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1997145/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Compound microbial intelligent membrane fermentation reshapes the bacterial community and reduces antibiotic, metal, and biocide resistance genes and virulence factors in duck litter
AU - Tiecheng Sun
AU - Guiheng Mei
AU - Meiqin Li
AU - Junru Mo
AU - Chengwei Zhang
AU - Yanmei Ma
AU - Jiamei Zhao
AU - Song Peng
AU - Fengqiang Lin
AU - Ji-Long Chen
AU - Zhaolong Li
PY - 2026
DA - 2026/10/26
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1997145
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1997145/full
AB - 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.
SN - 1664-302X
ER -