Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Authors: Shaffer Justin P. , Nothias Louis-Félix , Thompson Luke R. , Sanders Jon G. , Salido Rodolfo A. , Couvillion Sneha P. , Brejnrod Asker D. , Lejzerowicz Franck , Haiminen Niina , Huang Shi , Lutz Holly L. , Zhu Qiyun , Martino Cameron , Morton James T. , Karthikeyan Smruthi , Nothias-Esposito Mélissa , Dührkop Kai , Böcker Sebastian , Kim Hyun Woo , Aksenov Alexander A. , Bittremieux Wout , Minich Jeremiah J. , Marotz Clarisse , Bryant MacKenzie M. , Sanders Karenina , Schwartz Tara , Humphrey Greg , Vásquez-Baeza Yoshiki , Tripathi Anupriya , Parida Laxmi , Carrieri Anna Paola , Beck Kristen L. , Das Promi , González Antonio , McDonald Daniel , Ladau Joshua , Karst Søren M. , Albertsen Mads , Ackermann Gail , DeReus Jeff , Thomas Torsten , Petras Daniel , Shade Ashley , Stegen James , Song Se Jin , Metz Thomas O. , Swafford Austin D. , Dorrestein Pieter C. , Jansson Janet K. , Gilbert Jack A. , Knight Rob ,   the Earth Microbiome Project 500 (EMP500) Consortium, Angenant Lars T. , Berry Alison M. , Bittleston Leonora S. , Bowen Jennifer L. , Chavarría Max , Cowan Don A. , Distel Dan , Girguis Peter R. , Huerta-Cepas Jaime , Jensen Paul R. , Jiang Lingjing , King Gary M. , Lavrinienko Anton , MacRae-Crerar Aurora , Makhalanyane Thulani P. , Mappes Tapio , Marzinelli Ezequiel M. , Mayer Gregory , McMahon Katherine D. , Metcalf Jessica L. , Miyake Sou , Mousseau Timothy A. , Murillo-Cruz Catalina , Myrold David , Palenik Brian , Pinto-Tomás Adrián A. , Porazinska Dorota L. , Ramond Jean-Baptiste , Rowher Forest , RoyChowdhury Taniya , Sandin Stuart A. , Schmidt Steven K. , Seedorf Henning , Shade Ashley , Shipway J. Reuben , Smith Jennifer E. , Stegen James , Stewart Frank J. , Tait Karen , Thomas Torsten , Tucker Yael , U’Ren Jana M. , Watts Phillip C. , Webster Nicole S. , Zaneveld Jesse R. , Zhang Shan 
Published: November 2022

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.