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.

西方蜜蜂（Apis mellifera）作为多种农作物的传粉媒介，在全球粮食生产中发挥着至关重要的作用。近年，美国、加拿大与欧洲的蜜蜂种群因蜂群崩溃失调症（Colony Collapse Disorder，CCD）出现了年度损失不明原因大幅攀升的情况。由于野外蜜蜂病原体研究相对匮乏，CCD的流行病学分析受到极大制约。若要明确蜂群的异常病理生理状态究竟为何，长期系统性表征健康蜂群内的外源传染性病原体谱型便尤为关键。本研究针对一家大型转地养蜂场开展前瞻性研究，采用高频采样结合定制微阵列、定量实时PCR（qPCR）及超深度测序等全面的分子检测技术。研究明确了已知病毒、微孢子虫属（Nosema sp.）、蜜蜂细滴虫（Crithidia mellificae）及细菌的季节性感染发生率与载量水平。超深度测序分析进一步鉴定出4种新型RNA病毒，其中2种为蜜蜂微生物组中已观测到的丰度最高的组分（每只蜜蜂约含10^11个病毒粒子）。研究结果显示病毒感染呈间歇性发作特征，且夏季与冬季的病原体感染模式存在显著差异。常见蜜蜂病毒与微孢子虫的感染峰值出现在夏季，而锥虫类病原体蜜蜂细滴虫及新型病毒Lake Sinai病毒2型的感染水平则在1月达到峰值。