Evidence map›Paper›PMID 36443458›Full record

ArticleNature microbiology2022

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

Justin P Shaffer, Louis-Félix Nothias, Luke R Thompson, Jon G Sanders, Rodolfo A Salido, Sneha P Couvillion, Asker D Brejnrod, Franck Lejzerowicz, Niina Haiminen, Shi Huang and 42 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.

0numbers the graph read from it
0cells of the map it votes in
90citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

90 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Impacts of pollution on the soil microbiome.Nature reviews. Microbiology · 2026
    Review
  5. Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Review
  11. Article
  12. Review
  13. Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026
    Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Article
  19. Review
  20. Metagenomic Data Preprocessing and Quality Control.Methods in molecular biology (Clifton, N.J.) · 2026
    Article

30 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

52 authors.

Justin P Shaffer *Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9371-6336
Louis-Félix Nothias *Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6711-6719
Luke R Thompson *Northern Gulf Institute, Mississippi State University, Starkville, MS, USA.ORCID http://orcid.org/0000-0002-3911-1280
Jon G SandersDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.ORCID http://orcid.org/0000-0001-6077-4014
Rodolfo A SalidoDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Sneha P CouvillionEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0003-0307-9343
Asker D BrejnrodSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Franck LejzerowiczDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Niina HaiminenIBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA.ORCID http://orcid.org/0000-0002-8663-1019
Shi HuangDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Holly L LutzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6454-809X
Qiyun ZhuSchool of Life Sciences, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-3568-6271
Cameron MartinoCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9334-1258
James T MortonCenter for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
Smruthi KarthikeyanDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Mélissa Nothias-EspositoCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Kai DührkopChair for Bioinformatics, Friedrich Schiller University, Jena, Germany.
Sebastian BöckerChair for Bioinformatics, Friedrich Schiller University, Jena, Germany.ORCID http://orcid.org/0000-0002-9304-8091
Hyun Woo KimCollege of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do, Korea.
Alexander A AksenovCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Wout BittremieuxCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3105-1359
Jeremiah J MinichScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Clarisse MarotzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
MacKenzie M BryantDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Karenina SandersDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Tara SchwartzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Greg HumphreyDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Yoshiki Vásquez-BaezaCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Anupriya TripathiDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Laxmi ParidaIBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA.ORCID http://orcid.org/0000-0002-7872-5074
Anna Paola CarrieriIBM Research Europe, Daresbury, UK.
Kristen L BeckIBM Research, Almaden Research Center, San Jose, CA, USA.ORCID http://orcid.org/0000-0002-4603-0235
Promi DasDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Antonio GonzálezDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Daniel McDonaldDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0876-9060
Joshua LadauEnvironmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Søren M KarstDepartment of Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark.
Mads AlbertsenDepartment of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.ORCID http://orcid.org/0000-0002-6151-190X
Gail AckermannDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Jeff DeReusDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Torsten ThomasCentre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, The University of New South Wales, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0001-9557-3001
Daniel PetrasCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-6561-3022
Ashley ShadeDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.ORCID http://orcid.org/0000-0002-7189-3067
James StegenEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
Se Jin SongCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Thomas O MetzEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0001-6049-3968
Austin D SwaffordCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5655-8300
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3003-1030
Janet K JanssonEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0002-5487-4315
Jack A GilbertDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7920-7001
Rob KnightDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.ORCID http://orcid.org/0000-0002-0975-9019
Earth Microbiome Project 500 (EMP500) Consortium

Funding

Project 4 - Mechanistic studies on the role of the gut microbiome in models for Alzheimer's diseaseU19AG063744 · NIA · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Rima F Kaddurah-Daouk · 2019 to 2026
$54.1M
UCSD/SDSU IRACDAK12GM068524 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TREJO, JOANN · 2003 to 2025
$24.4M
Systems Biology Approach to Redefine Susceptibility Testing and Treatment of MDR Pathogens in the Context of Host ImmunityU01AI124316 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PALSSON, BERNHARD O · 2016 to 2020
$10.2M
Unified Computation Tools for Natural Products ResearchR01GM107550 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI COTTRELL, GARRISON W, GERWICK, WILLIAM HENRY · 2013 to 2025
$8.2M
Mapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5M
Gut Liver Brain Biochemical Axis in Alzheimer's DiseaseRF1AG058942 · NIA · DUKE UNIVERSITY · PI KADDURAH-DAOUK, RIMA F, VAN DUIJN, CORNELIA MARJA · 2018 to 2018
$3.4M
Integrated analysis of CVD risk in HIV: gut microbiota, immune function and metabolitesR01HL140976 · NHLBI · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI KAPLAN, ROBERT C, KNIGHT, ROB · 2018 to 2021
$3.3M
Translational Studies of Age-Associated Arterial Dysfunction, Western Diet and Aerobic Exercise: Role of the Gut MicrobiomeR01HL134887 · NHLBI · UNIVERSITY OF COLORADO · PI SEALS, DOUGLAS R · 2017 to 2020
$3.1M
The Subgingival Microbiome and Impaired Glucose RegulationR01DK102932 · NIDDK · UNIVERSITY OF MINNESOTA · PI DEMMER, RYAN T. · 2015 to 2019
$3.1M
NCCIH NIH HHS DP1 AT010885NHLBI NIH HHS R01 HL134887NHLBI NIH HHS R01 HL140976NIAID NIH HHS U01 AI124316NIA NIH HHS RF1 AG058942NIA NIH HHS U19 AG063744NIDDK NIH HHS R01 DK102932NIGMS NIH HHS K12 GM068524NIGMS NIH HHS R01 GM107550
6 · The paper itself

Abstract

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.

Indexed as

MicrobiotaAnimalsEarth, PlanetMetagenomeMetagenomicsSoilSoil

Identifiers

PMID36443458
PMCPMC9712116

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.