Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients’ skin has been shown to have an increased abundance of Staphylococcus aureus . More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus , but further studies are required to determine the effects of Staphylococcus community variation in AD. Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics. Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy). Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness. Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.

中文翻译：

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比较DADA2和OTU聚类方法研究特应性皮炎的细菌群落。

介绍。特应性皮炎（AD）的发病机理尚未完全明了，但已证明AD患者皮肤的细菌成分增加了金黄色葡萄球菌的含量。最近，凝固酶阴性葡萄球菌（CoNS）物种能够抑制金黄色葡萄球菌，但需要进一步研究以确定葡萄球菌群落变异对AD的影响。目标。在这里，我们调查了使用较新开发的DADA2方法分析元条形码数据是否比以前使用的操作分类单位（OTU）聚类方法改善了元条形码分析，并且可用于研究葡萄球菌 社区动态。方法。对来自AD患者（非病变皮肤）和非AD对照的角质层胶带样品的细菌16S rRNA区域进行了条形码分析。我们使用两种不同的生物信息学管道（OTU聚类方法和DADA2）处理了元条形码数据，在使用和不使用技术复制（采样策略）的情况下进行了分析。结果。我们发现，在社区水平的研究中，OTU聚类和DADA2表现良好，这已通过鉴定与AD相关的皮肤细菌群落的显着差异得以证明。但是，OTU聚类方法夸大了细菌的丰富度，这由于没有技术复制而恶化。用DADA2处理的数据可能会更有效地处理测序错误，从而不会增加分子丰度。结论。我们认为DADA2代表了OTU群集方法的改进，并且生物复制而不是技术复制是对资源的更有效利用。然而，OTU聚类和DADA2都未提供有关葡萄球菌的见解 社区动态，应保持谨慎，不要过分地解释较低分类级别的分类任务。