Sbardellati, D. L. | bioRxiv Science

bioRxiv2025

Bee Microbiomes Harbor Diverse Antimicrobial Resistance Genes on Plasmids

Antimicrobial resistance (AMR) is an emerging public health threat. In North America, tetracycline and macrolide antibiotics are often used to prevent or treat bacterial infections in honey bees. Previous research has shown that this practice has led to widespread drug resistance in honey bee gut microbiomes. However, where bee-associated bacteria encode AMR, genomically or on mobile genetic elements, is less well understood. Moreover, how the abundance, diversity, and mechanism of AMR differs between managed honey bees and other bees remains largely unexplored. Here we use existing metagenomic data from two previous studies to profile the AMR genes associated with managed honey bees, commercially produced bumble bees, and wild bumble bees. Our results suggest that honey bee associated bacteria house a greater diversity of AMR genes, specifically on plasmids, compared to bumble bees. In addition, we show that honey and bumble bee bacteria likely develop resistance to tetracyclines via different mechanisms. Overall, this study showcases how agricultural management has shaped the AMR genes associated with bees, and offers insights into the ecological context of differential AMR evolution within host-associated systems.

microbiology↗

bioRxiv2024

Targeted Viromes and Total Metagenomes Capture Distinct Components of Bee Gut Phage Communities

Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low abundance and low occupancy phage, while total metagenomes were biased towards sampling temperate phage and the most prominent phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage.

microbiology↗