BACKGROUND The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. METHODS In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. CONCLUSION While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

中文翻译：

---

扩增子和宏基因组测序方法的比较分析揭示了动物代谢生物体进化的关键特征。

背景技术宿主与其相关微生物组之间的相互作用现在被认为是两个参与者的生态、进化和发展的基本基础。这些相互依赖性激发了一种将多细胞生物称为“元生物”的新观点。“元生物体的起源和功能”合作研究中心的目标是了解微生物群落为何以及如何与不同分类群的宿主形成长期关联，这些宿主包括从海绵到人类以及植物。方法 为了优化分析程序的选择（根据宿主生物体和当前问题的不同，分析程序可能有所不同），我们在十个小组中系统地比较了分析微生物群落的两种主要技术方法，16S rRNA 基因扩增子和宏基因组鸟枪测序。宿主类群。这包括两个常用的 16S rRNA 基因区域和两个扩增程序，因此每个宿主样本总共有五种不同的微生物特征。结论 虽然基于 16S rRNA 基因的分析受到很多怀疑，但我们证明细菌群落表征的许多方面在不同方法中是一致的。由此产生的见解有助于在广泛的宿主分类单元中选择适当的方法。总体而言，我们建议采用单步多步扩增程序，尽管存在例外和权衡，但 16S rRNA 基因的 V3 V4 优于 V1 V2 区域。最后，通过对比分类学和功能特征并进行系统发育分析，我们为代谢生物之间广泛的进化模式提供了重要而新颖的见解，其中动物从水生栖息地到陆地栖息地的转变标志着宿主相关微生物进化的重大事件。作品。