ABSTRACT: Marine invertebrates are surrounded by and interact with an array of microbes, yet their microbiomes remain largely unexplored. With a seemingly endless choice of nucleic acid extraction kits, there is a need to assess the compatibility across approaches to determine whether microbiome results are comparable across studies employing different extraction methods. In this study, 5 kits were compared for extracting DNA from dermal swabs from 2 sea star species: Pisaster ochraceus and Dermasterias imbricata. DNA yield varied by kit, as did the ease of PCR amplification. Using 16S rRNA amplicon sequencing, differences in microbial richness and diversity were observed between sea star species, but not among extraction kits. Relative abundances of the most abundant prokaryotic phyla were largely attributed to sea star species rather than kit: the D. imbricata microbiome was dominated by Proteobacteria, whereas P. ochraceous had more even representation of Proteobacteria, Spirochaetota and Bacteroidota. Our results suggest that, despite some differences in ease of amplification, all 5 extraction kits examined here provide comparable and suitable results for characterizing sea star dermal microbiomes.

中文翻译：

---

用于检查海星真皮微生物组的拭子 DNA 提取方法的比较

摘要：海洋无脊椎动物被一系列微生物包围并与之相互作用，但它们的微生物组在很大程度上仍未被探索。由于核酸提取试剂盒的选择似乎无穷无尽，因此需要评估各种方法的兼容性，以确定采用不同提取方法的研究中微生物组结果是否具有可比性。在这项研究中，比较了从 2 个海星物种（Pisaster ochraceus和Dermasterias imbricata）的皮拭子中提取 DNA 的 5 个试剂盒。DNA 产量因试剂盒的不同而不同，PCR 扩增的难易程度也不同。使用 16S rRNA 扩增子测序，观察到海星物种之间微生物丰富度和多样性的差异，但提取试剂盒之间没有差异。最丰富的原核生物门的相对丰度主要归因于海星物种而不是套件：D. imbricata微生物群以变形菌门为主，而P. ochraceous则更均匀地代表变形菌门、螺旋毛菌门和拟杆菌门。我们的结果表明，尽管扩增的难易程度存在一些差异，但此处检查的所有 5 个提取试剂盒都为表征海星真皮微生物组提供了可比且合适的结果。