Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Nat Microbiol. 2022 Dec;7(12):2128-2150. doi: 10.1038/s41564-022-01266-x. Epub 2022 Nov 28.
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
尽管测序技术取得了进展，但缺乏标准化使得跨研究的比较具有挑战性，并阻碍了对行星尺度上多个生境中微生物群落的结构和功能的深入了解。在这里，我们对地球微生物组计划中收集的 880 个微生物群落样本的多种组学进行了分析。我们包括扩增子（16S、18S、ITS）和 shotgun 宏基因组测序数据，以及非靶向代谢组学数据（液相色谱-串联质谱和气相色谱质谱）。我们使用标准化的协议和分析方法来表征微生物群落，重点关注微生物相关代谢物和微生物类群在环境中的关系和共现，从而使我们能够以非凡的规模探索多样性。除了宏基因组和代谢组学数据的参考数据库外，我们还提供了一个整合其他研究的框架，从而能够以不断发展的社区资源的形式扩展现有知识。我们通过测试每个微生物和代谢物无处不在但环境选择的假设来证明该数据库的实用性。我们的结果表明，代谢物多样性与微生物群落和环境都存在周转率和嵌套性，而微生物相关代谢物的相对丰度则以特定微生物组合的特定方式变化并共同出现。我们还展示了某些化学物质的强大功能，特别是萜类化合物，能够区分地球的环境（例如，陆地植物表面和土壤、淡水和海洋动物粪便），以及某些微生物，包括 Conexibacter woesei（陆地土壤）、Haloquadratum walsbyi（海洋沉积物）和 Pantoea dispersa（陆地植物碎屑）。该资源提供了对来自地球不同生境的微生物群落中的类群和代谢物的深入了解，为微生物和化学生态学提供了信息，并为宿主和环境的多组学微生物组研究提供了基础和方法。
