PT  - JOURNAL ARTICLE
AU  - Justin P. Shaffer
AU  - Louis-Félix Nothias
AU  - Luke R. Thompson
AU  - Jon G. Sanders
AU  - Rodolfo A. Salido
AU  - Sneha P. Couvillion
AU  - Asker D. Brejnrod
AU  - Shi Huang
AU  - Franck Lejzerowicz
AU  - Holly L. Lutz
AU  - Qiyun Zhu
AU  - Cameron Martino
AU  - James T. Morton
AU  - Smruthi Karthikeyan
AU  - Mélissa Nothias-Esposito
AU  - Kai Dührkop
AU  - Sebastian Böcker
AU  - Hyunwoo Kim
AU  - Alexander A. Aksenov
AU  - Wout Bittremieux
AU  - Jeremiah J. Minich
AU  - Clarisse Marotz
AU  - MacKenzie M. Bryant
AU  - Karenina Sanders
AU  - Tara Schwartz
AU  - Greg Humphrey
AU  - Yoshiki Vásquez-Baeza
AU  - Anupriya Tripathi
AU  - Laxmi Parida
AU  - Anna Paola Carrieri
AU  - Niina Haiminen
AU  - Kristen L. Beck
AU  - Promi Das
AU  - Antonio González
AU  - Daniel McDonald
AU  - Søren M. Karst
AU  - Mads Albertsen
AU  - Gail Ackermann
AU  - Jeff DeReus
AU  - Torsten Thomas
AU  - Daniel Petras
AU  - Ashley Shade
AU  - James Stegen
AU  - Se Jin Song
AU  - Thomas O. Metz
AU  - Austin D. Swafford
AU  - Pieter C. Dorrestein
AU  - Janet K. Jansson
AU  - Jack A. Gilbert
AU  - Rob Knight
AU  - the Earth Microbiome Project 500 (EMP500) Consortium
TI  - Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment
AID  - 10.1101/2021.06.04.446988
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.06.04.446988
4099  - http://biorxiv.org/content/early/2021/06/06/2021.06.04.446988.short
4100  - http://biorxiv.org/content/early/2021/06/06/2021.06.04.446988.full
AB  - Microbes produce an array of secondary metabolites that perform diverse functions from communication to defense1. These metabolites have been used to benefit human health and sustainability2. In their analysis of the Genomes from Earth’s Microbiomes (GEM) catalog3, Nayfach and co-authors observed that, whereas genes coding for certain classes of secondary metabolites are limited or enriched in certain microbial taxa, “specific chemistry is not limited or amplified by the environment, and that most classes of secondary metabolites can be found nearly anywhere”. Although metagenome mining is a powerful way to annotate biosynthetic gene clusters (BCGs), chemical evidence is required to confirm the presence of metabolites and comprehensively address this fundamental hypothesis, as metagenomic data only identify metabolic potential. To describe the Earth’s metabolome, we use an integrated omics approach: the direct survey of metabolites associated with microbial communities spanning diverse environments using untargeted metabolomics coupled with metagenome analysis. We show, in contrast to Nayfach and co-authors, that the presence of certain classes of secondary metabolites can be limited or amplified by the environment. Importantly, our data indicate that considering the relative abundances of secondary metabolites (i.e., rather than only presence/absence) strengthens differences in metabolite profiles across environments, and that their richness and composition in any given sample do not directly reflect those of co-occurring microbial communities, but rather vary with the environment.Competing Interest StatementS.B. and K.D. are co-founders of Bright Giant GmbH.