Data from: Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

Honey bees (Apis mellifera) play a critical role in global food production
as pollinators of numerous crops. Recently, honey bee populations in the
United States, Canada, and Europe have suffered an unexplained increase in
annual losses due to a phenomenon known as Colony Collapse Disorder (CCD).
Epidemiological analysis of CCD is confounded by a relative dearth of bee
pathogen field studies. To identify what constitutes an abnormal
pathophysiological condition in a honey bee colony, it is critical to have
characterized the spectrum of exogenous infectious agents in healthy hives
over time. We conducted a prospective study of a large scale migratory bee
keeping operation using high-frequency sampling paired with comprehensive
molecular detection methods, including a custom microarray, qPCR, and
ultra deep sequencing. We established seasonal incidence and abundance of
known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep
sequence analysis further identified four novel RNA viruses, two of which
were the most abundant observed components of the honey bee microbiome
(∼10(11) viruses per honey bee). Our results demonstrate episodic viral
incidence and distinct pathogen patterns between summer and winter
time-points. Peak infection of common honey bee viruses and Nosema
occurred in the summer, whereas levels of the trypanosomatid Crithidia
mellificae and Lake Sinai virus 2, a novel virus, peaked in January.