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首页> 外文期刊>Journal of Medical Microbiology: An Official Journal of the Pathological Society of Great Britain and Ireland >Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis
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Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

机译：比较DADA2和OTU聚类方法研究特征性皮炎的细菌群体

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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.
机译：引言尚未完全理解特应性皮炎（AD）的发病机制，但已显示AD患者皮肤的细菌组成具有增加的葡萄球菌丰富。最近，显示凝结酶阴性葡萄球菌（CIS）物种被证明能够抑制金黄色葡萄球菌，但需要进一步的研究来确定葡萄球菌群落变异在AD中的影响。目的在这里我们调查了与最近开发的DADA2方法的分析数据是否改善了与先前使用的运营分类单位（OTU）聚类相比的成立分析，并且可用于研究葡萄球菌群落动态。方法采用AD患者的角质层（非损害皮肤）和非AD对照的磁带条样品中的细菌16S rRNA区域进行组成。我们用两种不同的生物信息管道（OTU聚类方法和DADA2）处理了沟通数据，并在没有技术复制（采样策略）的情况下分析。结果我们发现OTU聚类和DADA2对社区级研究表现良好，如鉴定与广告相关的皮肤细菌社区的显着差异。然而，OTU聚类方法膨胀了细菌性丰富，这通过没有技术复制恶化。使用DADA2处理的数据可能更有效地处理测序误差，从而不会膨胀分子丰富性。结论我们认为，DADA2代表了对OTU聚类方法的改进，并且生物复制而不是技术复制是更有效的资源利用。然而，OTU聚类和DADA2都没有对葡萄球菌的洞察力进行了解，并且谨慎应留在较低的分类法中的分类学队伍过度解释。

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