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Title: Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

Abstract

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [5];  [6];  [7];  [8];  [8];  [9]; ORCiD logo [10]
  1. New York Univ. School of Medicine, New York, NY (United States)
  2. Marine Biological Laboratory, Woods Hole, MA (United States)
  3. Stanford Univ., Palo Alto, CA (United States)
  4. Univ. of North Carolina, Chapel Hill, NC (United States)
  5. Univ. of Wisconsin-Madison, Madison, WI (United States)
  6. Univ. of Oregon, Eugene, OR (United States)
  7. Univ. of California San Diego, La Jolla, CA (United States)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Univ. of California, San Francisco, CA (United States)
  10. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1580015
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 7; Journal Issue: 3; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Blaser, Martin J., Cardon, Zoe G., Cho, Mildred K., Dangl, Jeffrey L., Donohue, Timothy J., Green, Jessica L., Knight, Rob, Maxon, Mary E., Northen, Trent R., Pollard, Katherine S., and Brodie, Eoin L. Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. United States: N. p., 2016. Web. doi:10.1128/mBio.00714-16.
Blaser, Martin J., Cardon, Zoe G., Cho, Mildred K., Dangl, Jeffrey L., Donohue, Timothy J., Green, Jessica L., Knight, Rob, Maxon, Mary E., Northen, Trent R., Pollard, Katherine S., & Brodie, Eoin L. Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. United States. doi:10.1128/mBio.00714-16.
Blaser, Martin J., Cardon, Zoe G., Cho, Mildred K., Dangl, Jeffrey L., Donohue, Timothy J., Green, Jessica L., Knight, Rob, Maxon, Mary E., Northen, Trent R., Pollard, Katherine S., and Brodie, Eoin L. Fri . "Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges". United States. doi:10.1128/mBio.00714-16. https://www.osti.gov/servlets/purl/1580015.
@article{osti_1580015,
title = {Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges},
author = {Blaser, Martin J. and Cardon, Zoe G. and Cho, Mildred K. and Dangl, Jeffrey L. and Donohue, Timothy J. and Green, Jessica L. and Knight, Rob and Maxon, Mary E. and Northen, Trent R. and Pollard, Katherine S. and Brodie, Eoin L.},
abstractNote = {Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.},
doi = {10.1128/mBio.00714-16},
journal = {mBio (Online)},
number = 3,
volume = 7,
place = {United States},
year = {2016},
month = {5}
}

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  • Todd-Brown, Katherine E. O.; Hopkins, Francesca M.; Kivlin, Stephanie N.
  • Biogeochemistry, Vol. 109, Issue 1-3
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Rapid evolutionary innovation during an Archaean genetic expansion
journal, December 2010


Structure, mechanism and regulation of an artificial microbial ecosystem for vitamin C production
journal, July 2012


Climate change, plant diseases and food security: an overview: Climate change and food security
journal, January 2011


General and condition-specific essential functions of Pseudomonas aeruginosa
journal, April 2015

  • Lee, Samuel A.; Gallagher, Larry A.; Thongdee, Metawee
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 16
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Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
journal, June 2014

  • Shi, Weibing; Moon, Christina D.; Leahy, Sinead C.
  • Genome Research, Vol. 24, Issue 9
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Human Occupancy as a Source of Indoor Airborne Bacteria
journal, April 2012


Synthetic Ecology of Microbes: Mathematical Models and Applications
journal, February 2016


Detonator of the population explosion
journal, July 1999


Humans differ in their personal microbial cloud
journal, January 2015

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  • PeerJ, Vol. 3
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Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee
journal, February 2012

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  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 11
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A prudent path forward for genomic engineering and germline gene modification
journal, March 2015


Asthma: Undoing millions of years of coevolution in early life?
journal, September 2015


DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.
journal, November 2013

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  • Nucleic Acids Research, Vol. 42, Issue D1
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National Bioeconomy Blueprint, April 2012
journal, June 2012


Intestinal Microbiota of Termites and other Xylophagous Insects
journal, October 1982


Investigating microbial micro-habitat structure using X-ray computed tomography
journal, August 2006


A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis
journal, January 2013

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  • Journal of Allergy and Clinical Immunology, Vol. 131, Issue 1
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Evidence for oxygenic photosynthesis half a billion years before the Great Oxidation Event
journal, March 2014

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  • Nature Geoscience, Vol. 7, Issue 4
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Evolution of the indoor biome
journal, April 2015

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  • Trends in Ecology & Evolution, Vol. 30, Issue 4
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The plant microbiome
journal, June 2013


Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
journal, November 2007

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  • Nature, Vol. 450, Issue 7169
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Permafrost carbon-climate feedbacks accelerate global warming
journal, August 2011

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Thermodynamic limitations on microbially catalyzed reaction rates
journal, August 2012


Prospects for systems biology and modeling of the gut microbiome
journal, June 2011


Cell factories for insulin production
journal, October 2014

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  • Microbial Cell Factories, Vol. 13, Issue 1
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Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans
journal, January 2016


The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production
journal, September 2011


Arsenic Mobility and Groundwater Extraction in Bangladesh
journal, November 2002


Design and synthesis of a minimal bacterial genome
journal, March 2016


Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
journal, September 2009

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  • Nature Methods, Vol. 6, Issue 10
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Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems
journal, July 2013

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An integrated catalog of reference genes in the human gut microbiome
journal, July 2014

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A unified initiative to harness Earth's microbiomes
journal, October 2015


Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
journal, July 2007

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Early life events influence whole-of-life metabolic health via gut microflora and gut permeability
journal, October 2013


Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray
journal, April 2005

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Gene-centric approach to integrating environmental genomics and biogeochemical models
journal, January 2014

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  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
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The Microbial Engines That Drive Earth's Biogeochemical Cycles
journal, May 2008


Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
journal, September 2013


Life cycle evaluation of emerging lignocellulosic ethanol conversion technologies
journal, January 2010


Integrating microbial ecology into ecosystem models: challenges and priorities
journal, September 2011

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Towards an evolutionary ecology of life in soil
journal, February 2005


Human gut microbes associated with obesity
journal, December 2006

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