Hi-C-resolved metagenomics reveals host range variation among mobile genetic elements within the European honey bee

ABSTRACT Mobile genetic elements (MGEs), such as plasmids and bacteriophages, are major contributors to the ecology and evolution of host-associated microbes due to symbiotic interactions and gene flow via horizontal gene transmission. Antibiotic resistance genes (ARGs), which are frequently trafficked via MGEs, are known to be enriched within North American honey bee microbiomes due to decades of antibiotic exposure. While previous studies have identified nearly identical MGE-associated ARGs across geographically disparate honey bee colonies, our understanding of how ARGs are distributed and mobilized within and between individual microbiomes is limited. To address this limitation, we leverage Hi-C-resolved metagenomics with the honey bee worker gut microbiome and show that the worker gut contains dense, nested, and highly distinct MGE communities. We show that phage-microbe networks exhibit high variation among individual metagenomes and that phages show broad host range with respect to both the number and phylogenetic distance of their hosts. Comparisons of individual microbiomes reveal highly individualized plasmid communities that exhibit broad host range variation within microbiomes. Finally, we provide specific evidence that antibiotic resistance cassettes are being actively shuttled between honey bee microbes via plasmids and that these broad host range plasmids frequently recombine to share gene content. Our work corroborates early observations of ARG dispersal in honey bee colonies and provides evidence for how these genes are mobilized within and across honey bee-associated microbial communities. IMPORTANCE Mobile genetic elements (MGEs) are found in every microbial community and often encode genes conferring antibiotic resistance (ARGs). Within the honey bee worker gut microbiome, ARGs are particularly frequent due to decades of antibiotic exposure. Previous studies have identified nearly identical ARGs in geographically disparate honey bee colonies, which suggests recent mobilization by MGEs into these colonies, but identifying how these ARGs are mobilized and distributed within honey bee colonies remains a challenging task, as most techniques rely on microbial culture. Applying metagenomic Hi-C, we describe how these ARGs are distributed among individual plasmid backbones and how those plasmids are distributed among host microbial populations. Remarkably, we find plasmids exhibit broad host range variation, although they encode nearly identical ARGs. Our work corroborates earlier observations of ARG dispersal in honey bee colonies and provides further evidence for how these ARGs are mobilized across vast geographic distance.