Characterisation of the UK honey bee metagenome

The European honey bee (Apis mellifera) plays a major role in pollination and food production.
Honey bee health is a complex product of the environment, host genetics and
associated microbes (commensal, opportunistic and pathogenic). Improved understanding of
these factors will help manage modern challenges to bee health. Here we used DNA
sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from
across Britain. Low heterozygosity was observed in many Scottish colonies which had high
similarity to the native dark bee. Colonies exhibited high diversity in composition and relative
abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs.
Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.