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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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THE CHEMISTRY OF
MICROBIOMES

PROCEEDINGS OF A SEMINAR SERIES

Chemical Sciences Roundtable

Board on Chemical Sciences and Technology

Division on Earth and Life Studies

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THE NATIONAL ACADEMIES PRESS
Washington, DC
www.nap.edu

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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THE NATIONAL ACADEMIES PRESS500 Fifth Street, NWWashington, DC 20001

This activity was supported by the National Institutes of Health under Contract No. HHSN26300024, the National Science Foundation under Grant No. CHE-1546732, and the U.S. Department of Energy under Grant No. DE-FG02-07ER15872.

This publication was prepared as an account of work sponsored in part by agencies of the U.S. government. Neither the U.S. government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to a specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the U.S. government or any agency thereof. Any opinions, findings, conclusions, or recommendations expressed in this publication do not necessarily reflect the views of any organization or agency that provided support for the project.

International Standard Book Number-13: 978-0-309-45836-8
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Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: https://doi.org/10.17226/24751.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
×

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The National Academy of Sciences was established in 1863 by an Act of Congress, signed by President Lincoln, as a private, nongovernmental institution to advise the nation on issues related to science and technology. Members are elected by their peers for outstanding contributions to research. Dr. Marcia McNutt is president.

The National Academy of Engineering was established in 1964 under the charter of the National Academy of Sciences to bring the practices of engineering to advising the nation. Members are elected by their peers for extraordinary contributions to engineering. Dr. C. D. Mote, Jr., is president.

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Learn more about the National Academies of Sciences, Engineering, and Medicine at www.nationalacademies.org.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
×

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Consensus Study Reports published by the National Academies of Sciences, Engineering, and Medicine document the evidence-based consensus on the study’s statement of task by an authoring committee of experts. Reports typically include findings, conclusions, and recommendations based on information gathered by the committee and the committee’s deliberations. Each report has been subjected to a rigorous and independent peer-review process and it represents the position of the National Academies on the statement of task.

Proceedings published by the National Academies of Sciences, Engineering, and Medicine chronicle the presentations and discussions at a workshop, symposium, or other event convened by the National Academies. The statements and opinions contained in proceedings are those of the participants and are not endorsed by other participants, the planning committee, or the National Academies.

For information about other products and activities of the National Academies, please visit www.nationalacademies.org/about/whatwedo.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
×

SEMINARS PLANNING COMMITTEE

TINA BAHADORI, U.S. Environmental Protection Agency

CAROLE BEWLEY, National Institutes of Health

EDWARD DELONG, University of Hawai‘i

JIM FREDRICKSON, Pacific Northwest National Laboratory

BARBARA GERRATANA, National Institutes of Health

DAVID ROCKCLIFFE, National Science Foundation

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
×

CHEMICAL SCIENCES ROUNDTABLE

Co-Chairs

JENNIFER SINCLAIR CURTIS, University of California, Davis

MARK E. JONES, The Dow Chemical Company

Members

TINA BAHADORI, U.S. Environmental Protection Agency

MICHAEL R. BERMAN, Air Force Office of Scientific Research

DONNA G. BLACKMOND, The Scripps Research Institute

EMILIO BUNEL, Argonne National Laboratory

ALLISON CAMPBELL, Pacific Northwest National Laboratory

RICHARD R. CAVANAGH, National Institute of Standards and Technology

MICHELLE CHANG, University of California, Berkeley

MILES FABIAN, National Institute of General Medical Sciences

MICHAEL J. FULLER, Chevron Energy Technology Company

MIGUEL GARCIA-GARIBAY, University of California, Los Angeles

BRUCE GARRETT, U.S. Department of Energy

MALIKA JEFFRIES-EL, Boston University

JACK KAYE, National Aeronautics and Space Administration

MARY KIRCHOFF, American Chemical Society

JOANN SLAMA LIGHTY, National Science Foundation

LAURIE LOCASCIO, National Institute of Standards and Technology

DAVID MYERS, GCP Applied Technologies

ASHUTOSH RAO, U.S. Food and Drug Administration

ANGELA WILSON, National Science Foundation

National Academies of Sciences, Engineering, and Medicine Staff

TERESA FRYBERGER, Board Director

MARILEE SHELTON-DAVENPORT, Senior Program Officer

CAMLY TRAN, Program Officer

ANNA SBEREGAEVA, Associate Program Officer

SAMUEL M. GOODMAN, Postdoctoral Fellow

JARRETT NGUYEN, Program Assistant

SHUBHA BANSKOTA, Financial Associate

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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BOARD ON CHEMICAL SCIENCES AND TECHNOLOGY

Co-Chairs

DAVID BEM, PPG Industries

DAVID R. WALT, Tufts University

Members

HÉCTOR D. ABRUÑA, Cornell University

JOEL C. BARRISH, Achillion Pharmaceuticals, Inc.

MARK A. BARTEAU, NAE, University of Michigan

JOAN BRENNECKE, NAE, University of Notre Dame

MICHELLE V. BUCHANAN, Oak Ridge National Laboratory

DAVID W. CHRISTIANSON, University of Pennsylvania

JENNIFER SINCLAIR CURTIS, University of California, Davis

RICHARD EISENBERG, NAS, University of Rochester

SAMUEL H. GELLMAN, NAS, University of Wisconsin–Madison

SHARON C. GLOTZER, NAS, University of Michigan

MIRIAM E. JOHN, Sandia National Laboratories (retired)

FRANCES S. LIGLER, NAE, University of North Carolina at Chapel Hill and North Carolina State University

SANDER G. MILLS, Merck Research Laboratories (retired)

JOSEPH B. POWELL, Shell

PETER J. ROSSKY, NAS, Rice University

TIMOTHY SWAGER, NAS, Massachusetts Institute of Technology

National Academies of Sciences, Engineering, and Medicine Staff

TERESA FRYBERGER, Board Director

MARILEE SHELTON-DAVENPORT, Senior Program Officer

CAMLY TRAN, Program Officer

ANNA SBEREGAEVA, Associate Program Officer

SAMUEL M. GOODMAN, Postdoctoral Fellow

JARRETT NGUYEN, Program Assistant

SHUBHA BANSKOTA, Financial Associate

Page viii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
×

Acknowledgments

This Proceedings of a Seminar Series was reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise. The purpose of this independent review is to provide candid and critical comments that will assist the National Academies of Sciences, Engineering, and Medicine in making each published proceedings as sound as possible and to ensure that it meets the institutional standards for quality, objectivity, evidence, and responsiveness to the charge. The review comments and draft manuscript remain confidential to protect the integrity of the process.

We thank the following individuals for their review of this proceedings:

KRISTEN DEANGELIS, University of Massachusetts Amherst

TIMOTHY MIYASHIRO, The Pennsylvania State University

THOMAS SCHMIDT, University of Michigan

James M. TIEDJE, Michigan State University

SETH WALK, Montana State University

Although the reviewers listed above provided many constructive comments and suggestions, they were not asked to endorse the content of the proceedings nor did they see the final draft before its release. Responsibility for the final content rests entirely with the speakers and the National Academies.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Page xiii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Figures

2-1 Habitable zones for microbial life in the terrestrial subsurface

2-2 Uncultivated candidate phyla contain a wide variety of carbohydrate active enzymes that drive respiratory metabolisms linked to the cycling of hydrogen, metals, and sulfur

2-3 Quantification of metabolites identified by 1H NMR in fluids from hydraulically fractured shales indicated metabolic processes to investigate in metagenomics data

2-4 Linking metabolite chemical data to microbial metagenomics provides the first metabolic predictions in hydraulically fractured shales

3-1 Analysis of microbial communities using integrated approaches in systems biology

3-2 Acidic geothermal channels provide unique opportunities for studying the aerobic oxidation and subsequent biomineralization of Fe(III) oxides by thermophilic microorganisms (Norris Geyser Basin, Yellowstone National Park, Wyoming, United States)

3-3 In situ characterization of spatial gradients in oxygen

3-4 Hypothetical model of Fe(II) oxidation in M. yellowstonensis strain MK1, based on annotation of the draft genome sequence, expression results, and functional modeling of putative proteins encoded by the Fox supercomplex

4-1 Soil metabolites linking microbes together

4-2 Exometabolomics can help couple soil microbiomes to soil chemistry

4-3 Workflow for using field studies, fabricated laboratory ecosystems with systems, and synthetic biology tools to discover causal mechanisms for building and testing predictive models

5-1 Schematics of the biogeochemical cycling of vitamin B12 in the tropical and polar microbiomes

5-2 Distributions of the NiSOD metalloenzyme measured by targeted metaproteomics and particulate nickel across the central Pacific Ocean

5-3 An example of several thousand proteins that can be measured simultaneously on a vertical profile through the Equatorial Pacific Ocean and the design of autonomous underwater vehicle Clio

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Acronyms and Abbreviations

AHL N-acyl homoserine lactone
APase alkaline phosphatase
AUV autonomous underwater vehicle
BBD black band disease
C–N carbon–nitrogen
C–P carbon–phosphorous
CCA crustose coralline algae
CP candidate phyla
CPR candidate phyla radiation
cut choline utilization
CutC choline TMA-lyase
DMSO dimethyl sulfoxide
DMSP dimethylsulfoniopropionate
DOC dissolved organic carbon
DOE U.S. Department of Energy
DOM dissolved organic matter
DON dissolved organic nitrogen
DOP dissolved organic phosphorous
ESIMS electrospray ionization mass spectrometry
GNPS Global Natural Product Social Molecular Networking
GT gigaton
HF hydraulically fractured
HMP Human Microbiome Project
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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HMWDOM high molecular weight dissolved organic matter
HPLC high-performance liquid chromatography
IBD inflammatory bowel disease
ICPMS inductively coupled plasma mass spectrometry
IGERT Integrative Graduate Education and Research Traineeship
JGI–EMSL Joint Genome Institute and Environmental Molecular Sciences Laboratory
MMA monomethylamine
MSI mass spectrometry imaging
NiSOD nickel superoxide dismutase
NRPS nonribosomal protein synthesis
NSF National Science Foundation
PAA phenylacetic acid
pCA p-coumaric acid
PepM phosphoenolpyruvate mutase
QS quorum sensing
RSB roseobacticide
SHIV simian/human immunodeficiency virus
TDA tropodithietic acid
TMA trimethylamine
TMAO trimethylamine-N-oxide
YNP Yellowstone National Park
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Page viii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Page xiii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2017. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington, DC: The National Academies Press. doi: 10.17226/24751.
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The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication.

The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystems—earth, marine, and human—and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

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