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. Miranda, Mick Watson, Mark Blaxter () and Tom C. Freeman ()
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Tim Regan: University of Edinburgh
Mark W. Barnett: University of Edinburgh
Dominik R. Laetsch: The University of Edinburgh
Stephen J. Bush: University of Edinburgh
David Wragg: University of Edinburgh
Giles E. Budge: Fera, The National Agrifood Innovation Campus
Fiona Highet: Science and Advice for Scottish Agriculture
Benjamin Dainat: Agroscope, Swiss Bee Research Centre
Joachim R. Miranda: Swedish University of Agricultural Sciences
Mick Watson: University of Edinburgh
Mark Blaxter: The University of Edinburgh
Tom C. Freeman: University of Edinburgh

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract 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.

Date: 2018
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DOI: 10.1038/s41467-018-07426-0

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