Characterisation of the British honey bee metagenome

Tim Regan, Mark W. Barnett, Dominik R. Laetsch, Stephen J. Bush, David Wragg, Giles E. Budge, Fiona Highet, Benjamin Dainat, Joachim R. De Miranda, Mick Watson, Mark Blaxter, Tom C. Freeman

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Article number4995(2018)
Number of pages13
JournalNature Communications
Issue number1
Publication statusPublished - 26 Nov 2018


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