Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.
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DOI：
10.1038/s41564-022-01266-x
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发表时间：
2022-12
影响因子：
28.3
通讯作者：
Earth Microbiome Project 500 (EMP500) Consortium
中科院分区：
文献类型：
--
作者：
Shaffer JP;Nothias LF;Thompson LR;Sanders JG;Salido RA;Couvillion SP;Brejnrod AD;Lejzerowicz F;Haiminen N;Huang S;Lutz HL;Zhu Q;Martino C;Morton JT;Karthikeyan S;Nothias-Esposito M;Dührkop K;Böcker S;Kim HW;Aksenov AA;Bittremieux W;Minich JJ;Marotz C;Bryant MM;Sanders K;Schwartz T;Humphrey G;Vásquez-Baeza Y;Tripathi A;Parida L;Carrieri AP;Beck KL;Das P;González A;McDonald D;Ladau J;Karst SM;Albertsen M;Ackermann G;DeReus J;Thomas T;Petras D;Shade A;Stegen J;Song SJ;Metz TO;Swafford AD;Dorrestein PC;Jansson JK;Gilbert JA;Knight R;Earth Microbiome Project 500 (EMP500) Consortium
尽管测序取得了进展，但缺乏标准化使得研究之间的比较具有挑战性，并阻碍了对全球范围内多个栖息地微生物群落结构和功能的深入了解。在这里，我们提出了为地球微生物组计划收集的880个微生物群落样本的多组学分析。我们包括扩增子（16 S、18 S、ITS）和鸟枪宏基因组序列数据，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同出现，从而使我们能够以非凡的规模探索多样性。除了宏基因组学和代谢组学数据的参考数据库之外，我们还提供了一个框架，用于纳入其他研究，从而能够以不断发展的社区资源的形式扩展现有知识。我们证明了这个数据库的实用性，通过测试的假设，每一个微生物和代谢物无处不在，但环境选择。我们的研究结果表明，代谢物的多样性表现出营业额和嵌套相关的微生物群落和环境，而微生物相关的代谢物的相对丰度变化，并与特定的微生物财团在特定的栖息地的方式共存。我们还显示了某些化学物质，特别是萜类化合物，在区分地球的环境（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）的力量。该资源提供了对来自地球各地不同栖息地的微生物群落内的分类群和代谢产物的深入了解，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。该资源结合了扩增子测序，鸟枪宏基因组测序和非靶向代谢组学，以提供地球环境中微生物代谢物关联的全球视图。
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. This Resource combines amplicon sequencing, shotgun metagenomic sequencing and untargeted metabolomics to provide a global view of microbial–metabolite associations across Earth’s environments.
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影响因子：
6
作者：
Bikel S;Valdez-Lara A;Cornejo-Granados F;Rico K;Canizales-Quinteros S;Soberón X;Del Pozo-Yauner L;Ochoa-Leyva A
通讯作者：
Ochoa-Leyva A
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
1.4
作者：
Apprill, Amy;McNally, Sean;Weber, Laura
通讯作者：
Weber, Laura
DOI：
10.1073/pnas.1714381115
发表时间：
2017-12-26
影响因子：
11.1
作者：
Amos, Gregory C. A.;Awakawa, Takayoshi;Jensen, Paul R.
通讯作者：
Jensen, Paul R.
影响因子：
3.4
作者：
Almeida-Neto, Mario;Guimaraes, Paulo;Ulrich, Werner
通讯作者：
Ulrich, Werner