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

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; 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

doi:10.1038/s41564-022-01266-x

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

Journal Article · Mon Nov 28 00:00:00 UTC 2022 · Nature Microbiology

DOI: https://doi.org/10.1038/s41564-022-01266-x · OSTI ID:1915277

;

; Salido, Rodolfo A.;

; Brejnrod, Asker D.; Lejzerowicz, Franck;

; Huang, Shi;

;

; Morton, James T.; Karthikeyan, Smruthi; Nothias-Esposito, Mélissa; Dührkop, Kai;

; Kim, Hyun Woo; Aksenov, Alexander A. more »

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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: Defense Advanced Research Projects Agency (DARPA); US Department of the Navy, Office of Naval Research (ONR); USDOD; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Contributing Organization:: Earth Microbiome Project 500 (EMP500) Consortium

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1915277

Report Number(s):: PNNL-SA-174662

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Journal Issue: 12 Vol. 7; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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