Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.

UNLABELLED: The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (AD) and on-farm slurry lagoon treatment affect microbial community composition and relative AMR gene abundance in livestock waste. Samples were collected before and after treatment from three AD sites and two on-farm slurry lagoon sites. Taxonomic profiles and diversity metrics were generated from short-read Illumina sequencing, and AMR gene presence and relative abundance were assessed using APHA SeqFinder, an in-house analysis pipeline. AD treatment led to decreased microbial richness and evenness, and reduced the relative abundance of several high-prevalence taxa, including members of the Enterobacteriaceae. On-farm slurry lagoon treatment had a comparatively minor effect on microbial composition. AD was also associated with significant reductions in the relative abundance of genes conferring resistance to macrolides, aminoglycosides, fusidic acid, and beta-lactams. These findings suggest that AD and on-farm slurry lagoon treatment exert distinct effects on microbial communities and AMR gene profiles. The results provide preliminary evidence that AD may contribute to reducing AMR gene burden in agricultural waste, although further investigation across broader temporal scales and treatment methods is needed.

IMPORTANCE: Antimicrobial resistance is a major global health challenge, and agricultural waste is a key environmental reservoir of resistance genes. This study examined how two livestock waste treatments (anaerobic digestion and on-farm slurry lagoon storage) affect microbial communities and relative antimicrobial resistance gene (ARG) abundance. The findings show that anaerobic digestion reduces both microbial diversity and the relative abundance of several resistance genes, while on-farm slurry lagoon treatment has a limited impact. These results highlight the potential for treatment strategies to reduce the environmental spread of resistance.