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

Animals Microbiota / genetics Metagenome Metagenomics Earth, Planet Soil

Journal

Nature microbiology

ISSN: 2058-5276

Titre abrégé: Nat Microbiol

Pays: England

ID NLM: 101674869

Informations de publication

Date de publication:
12 2022

Historique:

received: 03 11 2021

accepted: 10 10 2022

pubmed: 29 11 2022

medline: 3 12 2022

entrez: 28 11 2022

Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1038/s41564-022-01266-x PMID: 36443458 PMC: PMC9712116

pubmed: 36443458

doi: 10.1038/s41564-022-01266-x

pii: 10.1038/s41564-022-01266-x

pmc: PMC9712116

doi:

Substances chimiques

Soil 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

Pagination

2128-2150

Subventions

Organisme : NCCIH NIH HHS

ID : DP1 AT010885

Pays : United States

Organisme : NIGMS NIH HHS

ID : K12 GM068524

Pays : United States

Investigateurs

Lars T Angenant (LT)

Alison M Berry (AM)

Leonora S Bittleston (LS)

Jennifer L Bowen (JL)

Max Chavarría (M)

Don A Cowan (DA)

Dan Distel (D)

Peter R Girguis (PR)

Jaime Huerta-Cepas (J)

Paul R Jensen (PR)

Lingjing Jiang (L)

Gary M King (GM)

Anton Lavrinienko (A)

Aurora MacRae-Crerar (A)

Thulani P Makhalanyane (TP)

Tapio Mappes (T)

Ezequiel M Marzinelli (EM)

Gregory Mayer (G)

Katherine D McMahon (KD)

Jessica L Metcalf (JL)

Sou Miyake (S)

Timothy A Mousseau (TA)

Catalina Murillo-Cruz (C)

David Myrold (D)

Brian Palenik (B)

Adrián A Pinto-Tomás (AA)

Dorota L Porazinska (DL)

Jean-Baptiste Ramond (JB)

Forest Rowher (F)

Taniya RoyChowdhury (T)

Stuart A Sandin (SA)

Steven K Schmidt (SK)

Henning Seedorf (H)

Ashley Shade (A)

J Reuben Shipway (JR)

Jennifer E Smith (JE)

James Stegen (J)

Frank J Stewart (FJ)

Karen Tait (K)

Torsten Thomas (T)

Yael Tucker (Y)

Jana M U'Ren (JM)

Phillip C Watts (PC)

Nicole S Webster (NS)

Jesse R Zaneveld (JR)

Shan Zhang (S)

Informations de copyright

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