Microbiomes associated iwth European Foul Brood disease and idiopathic brood disease syndrome in honey bees.

Critical for pollination in agricultural and ecosystems, modern commercial honey bees (Apis mellifera) are faced with a variety of pathogenic and environmental stressors that often result in colony or crop loss. One highly prevalent pathogen is the larval disease European foulbrood (EFB) attributed to the bacterium Mellisococcus plutonius. However, many disease phenotypes classified morphologically as EFB do not contain M. plutonius based on microscopy and molecular markers, and are referred to as idiopathic. Here we improve the informational context of the larval disease microbiome with the end goal of developing diagnoses and management strategies for EFB and EFB-like disease. We used next generation sequencing and qPCR to detail the microbiomes of phenotypically healthy and diseased larvae from six different apiaries in the state of Illinois, USA. A state apiary inspector diagnosed the disease at all six apiaries as EFB according to a gestalt morphological phenotype. At five of the six apiaries, Mellisococcus plutonius dominated the larval disease microbiome, showing associations with three different firmicutes dependent on apiary. At the sixth site, diseased larvae were uniquely described as melty, sunken and deflated, and the resulting microbiota indicates a novel disease state that corresponds to idiopathic brood disease syndrome. Our results contribute to the diagnosis of brood disease, a growing problem for agriculture worldwide.