地球微生物组的标准化多组学揭示了微生物和代谢物的多样性,Nature Microbiology

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地球微生物组的标准化多组学揭示了微生物和代谢物的多样性
Nature Microbiology ( IF 20.5 ) Pub Date : 2022-11-28 , DOI: 10.1038/s41564-022-01266-x
Justin P Shaffer ₁ , Louis-Félix Nothias _{2,

3} , Luke R Thompson _{4,

5} , Jon G Sanders ₆ , Rodolfo A Salido ₇ , Sneha P Couvillion ₈ , Asker D Brejnrod ₃ , Franck Lejzerowicz _{1,

9} , Niina Haiminen ₁₀ , Shi Huang _{1,

9} , Holly L Lutz _{1,

11} , Qiyun Zhu _{12,

13} , Cameron Martino _{9,

14} , James T Morton ₁₅ , Smruthi Karthikeyan ₁ , Mélissa Nothias-Esposito _{2,

3} , Kai Dührkop ₁₆ , Sebastian Böcker ₁₆ , Hyun Woo Kim ₁₇ , Alexander A Aksenov _{2,

3,

18} , Wout Bittremieux _{2,

3,

19} , Jeremiah J Minich ₁₁ , Clarisse Marotz ₁ , MacKenzie M Bryant ₁ , Karenina Sanders ₁ , Tara Schwartz ₁ , Greg Humphrey ₁ , Yoshiki Vásquez-Baeza ₉ , Anupriya Tripathi _{1,

3} , Laxmi Parida ₁₀ , Anna Paola Carrieri ₂₀ , Kristen L Beck ₂₁ , Promi Das _{1,

11} , Antonio González ₁ , Daniel McDonald ₁ , Joshua Ladau ₂₂ , Søren M Karst ₂₃ , Mads Albertsen ₂₄ , Gail Ackermann ₁ , Jeff DeReus ₁ , Torsten Thomas ₂₅ , Daniel Petras _{2,

11,

26} , Ashley Shade ₂₇ , James Stegen ₈ , Se Jin Song ₉ , Thomas O Metz ₈ , Austin D Swafford ₉ , Pieter C Dorrestein _{2,

3} , Janet K Jansson ₈ , Jack A Gilbert _{1,

11} , Rob Knight _{1,

7,

9,

28} ,

Affiliation

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.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Northern Gulf Institute, Mississippi State University, Starkville, MS, USA.
Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA.
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany.
College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do, Korea.
Department of Chemistry, University of Connecticut, Storrs, CT, USA.
Department of Computer Science, University of Antwerp, Antwerp, Belgium.
IBM Research Europe, Daresbury, UK.
IBM Research, Almaden Research Center, San Jose, CA, USA.
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark.
Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, The University of New South Wales, Sydney, New South Wales, Australia.
Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Baden-Württemberg, Germany.
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.

尽管测序取得了进步，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，我们对为地球微生物组计划收集的 880 个微生物群落样本进行了多组学分析。我们包括扩增子（16S、18S、ITS）和鸟枪法宏基因组序列数据，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）。我们使用标准化方案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不同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。除了宏基因组学和代谢组学数据的参考数据库外，我们还提供了一个框架来整合其他研究，以不断发展的社区资源的形式扩展现有知识。我们通过检验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。我们的研究结果表明，代谢物多样性表现出与微生物群落和环境相关的周转率和嵌套性，而微生物相关代谢物的相对丰度各不相同，并以特定于栖息地的方式与特定微生物群同时发生。我们还展示了某些化学物质，特别是萜类化合物，在区分地球环境（例如，陆地植物表面和土壤，Conexibacter woesei（陆生土壤）、Haloquadratum walsbyi（海洋沉积物）和Pantoea dispersa（陆生植物碎屑）。该资源提供了对地球上不同栖息地微生物群落中的分类群和代谢物的洞察，为微生物和化学生态学提供信息，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。

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Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

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.

更新日期：2022-11-29

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