Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria

High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial communities’ characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in term of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artifactual sequences and contaminations, as well as noticeable differences in bacterial communities’ characteristics were observed between the extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbor different bacterial communities. Our benchmark hence suggests that cuticular microbiota of single insect individuals can be reliably retrieved provided that blank controls, appropriate data cleaning, and standardization of individual body size are considered in the experiment.针对16S核糖体RNA基因（16S rRNA gene）的高通量测序技术，已极大推动学界揭示昆虫体壁定植细菌在宿主生态生理学与行为模式中的核心功能。然而，单只昆虫体壁样本的细菌DNA含量普遍偏低，此类样本更易产生分子偏倚与外源污染，这一难题极大限制了我们对宿主-体壁微生物群反馈调控机制的认知。 本研究针对两种体型与生态位存在显著差异的新热带蚁类——切叶蚁（Atta cephalotes，体长约15 mm）与伪切叶蚁（Pseudomyrmex penetrator，体长约5 mm）的体壁细菌载量开展方法学基准测试。我们系统评估了体壁微生物群的丰富度与群落组成，同时检测了四种DNA提取方案所引入的偏倚与污染程度；此外还探究了用于DNA提取的昆虫个体数量、单只样本体型对细菌群落特征的影响。 针对体长约15 mm的切叶蚁，多数提取方案在细菌多样性与群落组成层面的检测结果趋于一致。与之形成鲜明对比的是，针对体长约5 mm的伪切叶蚁，不同提取方案间的测序伪影序列与污染水平差异显著，且细菌群落特征也呈现出明显分歧。 我们还发现，体型较大（约15 mm）与较小（约5 mm）的切叶蚁个体所携带的细菌群落存在显著差异。 综上，本基准测试结果表明：若实验中设置空白对照、开展规范的数据清洗，并统一单只昆虫的体型标准，则可可靠获取单只昆虫体壁的微生物群信息。