DOI: 10.5061/dryad.9n8rh
title: Data from: Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

description: 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.
description: Bee microbiome
 paired-end, part AThe paired-end
 deep-sequence data from this paper was generated as a single lane of
 Illumina data, but was split up into 6 parts (A-F) for Dryad submission.
 This is part A. The file will unzip into two files containing the
 paired-end reads for the first 5.5M sequenced clusters. Phred+64 quality
 score encoding. Library prep details can be found in the Methods of the
 linked manuscript.s_4_partA.tar.gzBee microbiome paired-end, part BThe paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission. This is part B. The file will unzip into two files containing the paired-end reads for the second 5.5M sequenced clusters. Phred+64 quality score encoding. Library prep details can be found in the Methods of the linked manuscript.s_4_partB.tar.gzBee microbiome paired-end, part CThe paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission. This is part C. The file will unzip into two files containing the paired-end reads for the third 5.5M sequenced clusters. Phred+64 quality score encoding. Library prep details can be found in the Methods of the linked manuscript.s_4_partC.tar.gzBee microbiome paired-end, part DThe paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission. This is part D. The file will unzip into two files containing the paired-end reads for the fourth 5.5M sequenced clusters. Phred+64 quality score encoding. Library prep details can be found in the Methods of the linked manuscript.s_4_partD.tar.gzBee microbiome paired-end, part EThe paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission. This is part E. The file will unzip into two files containing the paired-end reads for the fifth 5.5M sequenced clusters. Phred+64 quality score encoding. Library prep details can be found in the Methods of the linked manuscript.s_4_partE.tar.gzBee microbiome paired-end, part FThe paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission. This is part F. The file will unzip into two files containing the paired-end reads for the last less-than-5.5M sequenced clusters. Phred+64 quality score encoding. Library prep details can be found in the Methods of the linked manuscript.s_4_partF.tar.gz