biostudies-literatureShaffer JPNCCIH NIH HHSNIA NIH HHSNIDDK NIH HHSNIAID NIH HHSNHLBI NIH HHSNIGMS NIH HHS2128-2150https://www.ebi.ac.uk/biostudies/studies/S-EPMC9712116biostudies-literatureUnknown7(12)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 exploreNature microbiologyStandardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.PMC9712116R01 HL134887U01 AI124316R01 HL140976R01 DK102932R01 GM107550DP1 AT010885U19 AG063744K12 GM068524RF1 AG058942McDonald DMetcalf JLHumphrey GMousseau TAMarzinelli EMSeedorf HJansson JKSandin SAMartino CZhang SLavrinienko ACouvillion SPSanders JGCowan DAHaiminen NBowen JLThompson LRGirguis PRDuhrkop KAksenov AADeReus JShipway JRBittleston LSEarth Microbiome Project 500 (EMP500) ConsortiumHuerta-Cepas JAckermann GMetz TOPetras DShaffer JPCarrieri APAngenant LTKing GMMacRae-Crerar AZaneveld JRSanders KRamond JBMurillo-Cruz CGonzalez AKarthikeyan SLadau JJiang LBryant MMRoyChowdhury TVasquez-Baeza YLejzerowicz FMyrold DPalenik BMayer GPorazinska DLMarotz CDas PChavarria MShade ALutz HLBeck KLSmith JEBocker SKim HWSwafford ADMorton JTSalido RAThomas TTripathi ADistel DNothias-Esposito MBittremieux WNothias LFSchwartz TStewart FJWatts PCParida LMinich JJDorrestein PCWebster NSMakhalanyane TPAlbertsen MRowher FSong SJGilbert JAKnight RTucker YHuang SJensen PRBrejnrod ADMcMahon KDMappes TKarst SMTait KU'Ren JMZhu QMiyake SPinto-Tomas AAStegen JBerry AMSchmidt SKfalseStandardized 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 explore2022-01-01T00:00:00Z2022 Dec2026-05-28T21:28:55.339Z2025-04-19T22:48:56.667ZS-EPMC97121163644345810.1038/s41564-022-01266-x