In a single full-scale campaign evaluating an integrated anaerobic digestion-composting system treating cattle slurry, comprehensive viromic and metagenomic analyses revealed that the relative abundance of total antibiotic resistance genes (RPKG) was higher in cattle slurry digestate than in raw cattle slurry, yet was lower in mature compost than in compost feedstock. The analyses also established that the relative abundance of virulence factor gene (VFG)-carrying contigs (RPKM), as well as mean ARG and VFG abundances (RPKG), were lower in mature compost than in compost feedstock, addressing critical knowledge gaps regarding agricultural waste treatment within the One Health framework.
Despite the overall reduction of total resistance gene abundance in the final compost, specific high-risk resistance genes demonstrated extreme recalcitrance. In particular, the resistance genes aac(3)-VIIa and sul1, alongside tet(M), remained detectable in the mature compost. Metagenomic profiling identified that at the maturation stage, thermotolerant bacterial taxa dominated by Bacillota and Actinomycetota constituted the ultimate high-risk antibiotic-resistant bacteria, with ARG-carrying metagenome-assembled genomes (MAGs) affiliated with these two phyla persisting through the completion of composting.
Crucially, the carriage of specific quorum sensing regulatory genes, LuxR and DGC, within the ultimate high-risk antibiotic-resistant bacteria exhibited a highly significant positive correlation (R2 > 0.82, P < 0.001) with ARG and VFG abundances. Quorum sensing involving luxR and DGC was associated primarily with persistence and potential horizontal gene transfer. Meanwhile, although lytic phages dominated the viral community, phages functioned predominantly as ecological predators and rarely carried ARGs. During the thermophilic stage, researchers observed a marked decoupling of phage and host abundance trajectories, consistent with reduced viral abundance under thermal stress, indicating that resistant-bacteria persistence coincided with weaker virus–host coupling at high temperatures rather than viral transduction.
Based on these findings, the authors highlighted biologically targeted interventions, such as quorum sensing inhibitors or sequential phage inoculation, as potential candidate management strategies. However, the study noted that the feasibility and efficacy of such interventions remain to be rigorously tested across different feedstocks, seasons, and full-scale operating conditions before general operational recommendations can be made.
Subject of Research: Antibiotic resistance gene dynamics in anaerobic digestion and composting
Article Title: Viromic and metagenomic analyses reveal distribution and dissemination of antibiotic resistance genes in anaerobic digestion-composting systems: roles of quorum sensing and viruses
Article References: Lin, L., Xu, P., Li, H., Liu, N., Liu, C., Su, J., & Yang, X. (2026). Viromic and metagenomic analyses reveal distribution and dissemination of antibiotic resistance genes in anaerobic digestion-composting systems: roles of quorum sensing and viruses. Microbiome. https://doi.org/10.1186/s40168-026-02573-9
Image Credits: AI Generated
DOI: 10.1186/s40168-026-02573-9
Keywords: antibiotic resistance genes, anaerobic digestion, composting, quorum sensing, bacteriophages, cattle slurry, metagenomics, viromics, Viromic, metagenomic, analyses, reveal
News Source: William Thompson. (November 5, 2026). Study Tracks Antibiotic Resistance Dynamics Across Cattle Slurry Digestion and Composting. Scienmag.
