Horizontal gene transfer between bacteriophages and their hosts is a key factor in the bloom of antibiotic resistance genes in Metaphire californica

Earthworm guts are a reservoir for antibiotic resistance genes (ARGs). However, the role of horizontal gene transfer (HGT) between bacteriophages and their hosts in amplifying ARG proliferation within this niche remains limited. To address this knowledge gap, we analyzed paired metagenomes from Metaphire californica guts and surrounding soil collected from farmland in Zhejiang, China. Earthworm guts harbored greater ARG diversity than soil (323 vs 303 subtypes), with significantly elevated abundances of macrolide-lincosamide-streptogramin (MLS), novobiocin, rifamycin, and tetracycline resistance determinants. Consistent with this, viral diversity was also higher in the earthworm gut comparing with soil. We recovered 67 microbial metagenome-assembled genomes (MAGs) and 5,703 viral operational taxonomic units (vOTUs), which enabled us to evaluate the contribution of viruses to ARG dissemination across different environments. Notably, virus-encoded ARGs were distributed across 43 Resfams families (RFs), with 32 detected in earthworm gut and only 23 in soil. Crucially, 1,568 potential HGT events between vOTUs and MAGs were identified, with a significantly higher frequency observed in the earthworm gut (1,110 events) compared to soil (458 events). Interestingly, the potential HGT regions against the Resfams database revealed that 32 gut-associated HGT events involved 11 RFs, whereas only 12 events associated with 5 RFs were detected in soil. These findings reveal the earthworm gut’s role in accelerating antibiotic resistance proliferation within agricultural ecosystems, highlighting the interconnected health risks emphasized by the One Health framework.