THE CHEMISTRY OF
MICROBIOMES
PROCEEDINGS OF A SEMINAR SERIES
Chemical Sciences Roundtable
Board on Chemical Sciences and Technology
Division on Earth and Life Studies
THE NATIONAL ACADEMIES PRESS
Washington, DC
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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.
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International Standard Book Number-13: 978-0-309-45836-8
International Standard Book Number-10: 0-309-45836-6
Digital Object Identifier: https://doi.org/10.17226/24751
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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.
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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
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
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
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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.
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Contents
Kelly C. Wrighton, Rebecca A. Daly, and Michael J. Wilkins
3 LIFE IN HIGH-TEMPERATURE ENVIRONMENTS: MODERN-DAY ANALOGS OF EARLY EARTH STILL RELEVANT TODAY
4 ADVANCING OUR UNDERSTANDING OF THE CHEMISTRY OF SOIL MICROBIOMES
Trent R. Northen, Zheyun Zhang, Jian Gao, Tami Swenson, and Yasuo Yoshikuni
Mak A. Saito, Chip Breier, Mike Jakuba, Matthew McIlvin, and Dawn Moran
6 CHEMICAL ECOLOGY: THE LANGUAGE OF MICROBIOMES
Mark E. Hay, Deanna S. Beatty, and Frank J. Stewart
7 ORGANIC NUTRIENT CHEMISTRY AND THE MARINE MICROBIOME
Daniel J. Repeta and Rene M. Boiteau
8 DIGITIZING THE CHEMISTRY ASSOCIATED WITH MICROBES: IMPORTANCE, CURRENT STATUS, AND OPPORTUNITIES
9 DECIPHERING THE CHEMISTRY OF THE HUMAN GUT MICROBIOME
10 ENGINEERING THE MICROBIOME FOR HUMAN HEALTH APPLICATIONS
Timothy K. Lu, Mark Mimee, Robert J. Citorik, and Karen Pepper
11 TALKING WITH MOLECULES: MARINE BACTERIA AND MICROALGAE
12 GENOME-SCALE METABOLIC MODELING AND ITS APPLICATION TO MICROBIAL COMMUNITIES
13 EPILOGUE AFTER THE PANEL DISCUSSIONS
B Biographic Sketches of Seminars Planning Committee and Seminars Speakers
Figures
2-1 Habitable zones for microbial life in the terrestrial subsurface
3-1 Analysis of microbial communities using integrated approaches in systems biology
3-3 In situ characterization of spatial gradients in oxygen
4-1 Soil metabolites linking microbes together
4-2 Exometabolomics can help couple soil microbiomes to soil chemistry
5-1 Schematics of the biogeochemical cycling of vitamin B12 in the tropical and polar microbiomes
6-1 Structures of the discussed molecules
7-1 Cycling of organic phosphorus by the open ocean microbiome
7-2 Phosphorous-31 NMR spectrum of HMWDOM polysaccharides following mild base hydrolysis
7-3 Microbial organic iron cycling in seawater
9-1 Metabolic functions of the human gut microbiome
10-1 Therapeutics based on alterations of the microbiota
10-2 Microbiota-based therapeutics pose certain challenges
11-1 Working model for the algal–bacterial symbiosis between P. inhibens and E. huxleyi
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 |
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 |