Data from: Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing PhyloH as a novel phylogenetic diversity analysis tool

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.

生物群落多样性研究是极具吸引力的研究方向之一。如今依托创新性DNA测序技术可获取海量实验数据，但对这些数据开展管理、分析与结果可视化工作并非易事。本研究首次提出将系统发育熵（phylogenetic entropy）作为微生物群落结构研究中细菌多样性的衡量指标。随后，本研究将自身用于划分系统发育多样性的新方法——即网页工具phyloh——与传统细菌群落多样性分析方法进行了对比。本研究利用phyloh工具对西方蜜蜂（Apis mellifera，昆虫纲：膜翅目）及其寄生螨瓦螨（Varroa destructor，蛛形纲：寄螨目）的微生物组（microbiome）进行了特征分析。本研究的理论依据在于，对蜜蜂与瓦螨微生物组的比较分析，可为解析寄生生物对蜂群健康的作用机制提供全新研究视角。研究结果显示，当瓦螨寄生时，西方蜜蜂的微生物组会发生显著改变，表明该寄生生物能够调控宿主的微生物组组成。在所采用的多种分析方法中，唯有结合phyloh中所实现的系统发育约束的熵方法，能够有效区分瓦螨微生物组与被寄生蜜蜂的微生物组。综上，我们预计系统发育熵的应用将成为群落结构分析领域的新范式，尤其可用于量化各生物实体对整体群落多样性的贡献程度。