Data from: Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment

The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

果蝇属（Drosophila）昆虫是研究适应性以及遗传变异与表型之间关联的经典模式生物。尽管与果蝇共生的细菌群落可能对果蝇生物学的诸多方面具有重要意义，但目前学界对其多样性、群落组成及其塑造因素的认知仍较为有限。本研究通过针对细菌16S核糖体RNA基因可变区的454测序技术，对野生及实验室培养的果蝇分离株的共生细菌群落进行了表征。为专门探究食物来源与宿主物种对细菌群落的影响，本研究分析了两类样本：一类是从多种天然基质中采集的野生黑腹果蝇（Drosophila melanogaster）和拟暗果蝇（Drosophila simulans）样本，另一类是9种实验室饲养果蝇的成虫与幼虫样本。研究结果显示，实验室饲养的果蝇中未发现宿主物种对细菌群落的影响；反之，实验室来源与随机效应的作用十分显著，这两类因素可能会干扰果蝇表型相关研究。与之相反，野生果蝇的共生微生物群主要由食物基质塑造，宿主物种身份仅存在次要的附加影响。本研究鉴定出该野生共生微生物群的一个核心类群，它隶属于葡糖杆菌属（Gluconobacter），在本研究的所有野生捕获果蝇中均有检出，但在实验室饲养的果蝇中完全缺失。该类群因此成为潜在的黑腹果蝇与拟暗果蝇天然核心微生物组的核心候选成员。此外，本研究还在野生果蝇分离株中鉴定出潜在病原菌。