Data from: The effect of gut microbiota elimination in Drosophila melanogaster: a how-to guide for host-microbiota studies

In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behaviour, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low-dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analysed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low-dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioural research. Our study raises the important issue that the efficacy of and impacts on the host of these methods, requires investigation in a case by case manner, rather than assuming homogeneity across species and laboratories.

近年来，宿主微生物群（microbiota）对宿主的影响受到了广泛关注。我们逐渐认识到肠道微生物群（gut microbiota）在调控宿主生理、生态、行为与演化过程中的重要意义。评估微生物群影响的常用方法之一是抑制或清除宿主微生物群，并将处理组与未处理个体的宿主表型进行对比。本研究以模式生物黑腹果蝇（Drosophila melanogaster）为研究对象，对这些常用方法进行了评估。我们采用完全析因设计（fully factorial design），检测了低剂量链霉素（streptomycin）饲喂法、卵脱绒膜处理（egg dechorionation）法以及无菌饲料（axenic diet）饲喂法对该物种肠道细菌的清除效果。我们还通过一系列标准生理学测定（physiological assays），探究了这些方法对宿主生理的潜在副作用。结果显示，与正常饲养的果蝇相比，所有处理组果蝇的发育时长均显著延长，体重亦更低。经历卵脱绒膜处理的雌雄果蝇体重均显著低于经链霉素饲喂的个体。同样，无菌饲养的雌性果蝇（而非雄性）在运动能力测定（locomotion assay）中表现出显著更低的活动水平。所有处理方式均降低了卵至成虫的存活率，其中卵脱绒膜处理诱导的死亡率显著更高。我们认为，饲料中添加低剂量链霉素的方法在清除肠道细菌方面比卵脱绒膜处理更为有效，且对宿主生理的不利影响相对更小。更重要的是，该方法在行为学研究中是最具实用性与可靠性的手段。本研究提出了一个重要议题：这些方法的有效性及其对宿主的影响需针对具体案例开展研究，而非默认不同物种与实验室间的方法效果具有一致性。