skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Earth Microbiome Project and Global Systems Biology

Abstract

Here, we published the first large-scale analysis of data from the Earth Microbiome Project (EMP) (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with more than 100,000 amplicon data sets and more than 500 paired metagenomic and metabolomic data sets. Importantly, the techniques, data, and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale of integration that just 7 years ago seemed impossible.

Authors:
 [1];  [2];  [3]
  1. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  3. Univ. of California San Diego, La Jolla, CA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1490091
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 3; Journal Issue: 3; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; amplicon; global; meta-analysis; metadata; microbiome; systems biology

Citation Formats

Gilbert, Jack A., Jansson, Janet K., and Knight, Rob. Earth Microbiome Project and Global Systems Biology. United States: N. p., 2018. Web. doi:10.1128/mSystems.00217-17.
Gilbert, Jack A., Jansson, Janet K., & Knight, Rob. Earth Microbiome Project and Global Systems Biology. United States. doi:10.1128/mSystems.00217-17.
Gilbert, Jack A., Jansson, Janet K., and Knight, Rob. Tue . "Earth Microbiome Project and Global Systems Biology". United States. doi:10.1128/mSystems.00217-17. https://www.osti.gov/servlets/purl/1490091.
@article{osti_1490091,
title = {Earth Microbiome Project and Global Systems Biology},
author = {Gilbert, Jack A. and Jansson, Janet K. and Knight, Rob},
abstractNote = {Here, we published the first large-scale analysis of data from the Earth Microbiome Project (EMP) (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with more than 100,000 amplicon data sets and more than 500 paired metagenomic and metabolomic data sets. Importantly, the techniques, data, and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale of integration that just 7 years ago seemed impossible.},
doi = {10.1128/mSystems.00217-17},
journal = {mSystems},
issn = {2379-5077},
number = 3,
volume = 3,
place = {United States},
year = {2018},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science

Figures / Tables:

FIG 1 FIG 1: The Earth Microbiome Project was a result of collaborations with hundreds of scientists around the planet; each with their own research interests.

Save / Share:

Works referenced in this record:

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
journal, January 2014


Microbial seed banks: the ecological and evolutionary implications of dormancy
journal, January 2011

  • Lennon, Jay T.; Jones, Stuart E.
  • Nature Reviews Microbiology, Vol. 9, Issue 2
  • DOI: 10.1038/nrmicro2504

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
journal, October 2017


Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest
journal, April 2014

  • Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W.
  • The ISME Journal, Vol. 8, Issue 9
  • DOI: 10.1038/ismej.2014.36

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
journal, June 2012

  • Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon
  • The ISME Journal, Vol. 6, Issue 9
  • DOI: 10.1038/ismej.2012.59

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill
journal, August 2017


The Earth Microbiome project: successes and aspirations
journal, August 2014


A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA
journal, October 2012


Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

  • Gibbons, S. M.; Caporaso, J. G.; Pirrung, M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 12
  • DOI: 10.1073/pnas.1217767110

Diversity, structure and convergent evolution of the global sponge microbiome
journal, June 2016

  • Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11870

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
journal, March 2015

  • Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel
  • Nature, Vol. 521, Issue 7551
  • DOI: 10.1038/nature14238

Scaling laws predict global microbial diversity
journal, May 2016

  • Locey, Kenneth J.; Lennon, Jay T.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 21
  • DOI: 10.1073/pnas.1521291113

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

  • Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion
  • Standards in Genomic Sciences, Vol. 3, Issue 3
  • DOI: 10.4056/sigs.1433550

A communal catalogue reveals Earth’s multiscale microbial diversity
journal, November 2017

  • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
  • Nature, Vol. 551, Issue 7681
  • DOI: 10.1038/nature24621

Structure, fluctuation and magnitude of a natural grassland soil metagenome
journal, February 2012

  • Delmont, Tom O.; Prestat, Emmanuel; Keegan, Kevin P.
  • The ISME Journal, Vol. 6, Issue 9
  • DOI: 10.1038/ismej.2011.197

    Figures / Tables found in this record:

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.