Microbial Ecology in States of Health and Disease: Workshop Summary
2014

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Individually and collectively, resident microbes play important roles in host health and survival. Shaping and shaped by their host environments, these microorganisms form intricate communities that are in a state of dynamic equilibrium. This ecologic and dynamic view of host-microbe interactions is rapidly redefining our view of health and disease. It is now accepted that the vast majority of microbes are, for the most part, not intrinsically harmful, but rather become established as persistent, co-adapted colonists in equilibrium with their environment, providing useful goods and services to their hosts while deriving benefits from these host associations. Disruption of such alliances may have consequences for host health, and investigations in a wide variety of organisms have begun to illuminate the complex and dynamic network of interaction - across the spectrum of hosts, microbes, and environmental niches - that influence the formation, function, and stability of host-associated microbial communities.

Microbial Ecology in States of Health and Disease is the summary of a workshop convened by the Institute of Medicine's Forum on Microbial Threats in March 2013 to explore the scientific and therapeutic implications of microbial ecology in states of health and disease. Participants explored host-microbe interactions in humans, animals, and plants; emerging insights into how microbes may influence the development and maintenance of states of health and disease; the effects of environmental change(s) on the formation, function, and stability of microbial communities; and research challenges and opportunities for this emerging field of inquiry.

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548 pages · 6 x 9 · paperback
ISBN Paperback: 0-309-29062-7
ISBN Ebook: 0-309-29063-5
DOI: https://doi.org/10.17226/18433

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Institute of Medicine. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.

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Front Matter i-xxvi
Workshop Overview 1-92
A1 Effector and memory T cell responses to commensal bacteria--Yasmine Belkaid, Nicolas Bouladoux, and Timothy W. Hand 93-109
A2 What are the consequences of the disappearing human microbiota?--Martin J. Blaser and Stanley Falkow 110-130
A3 Pathways in microbe-induced obesity--Laura M. Cox and Martin J. Blaser 131-152
A4 Microbial exposure during early life has persistent effects on natural killer T Cell function--Torsten Olszak, Dingding An, Sebastian Zeissig, Miguel Penilla Vera, Julia Richter, Andre Franke, Jonathan N. Glickman, Reiner Siebert, Rebecca M. Barron, Dennis L. Kasper, and Richard S. Blumberg 153-163
A5 The application of ecological theory toward an understanding of the human microbiome--Elizabeth K. Costello, Keaton Stagaman, Les Dethlefsen, Brendan J. M. Bohannan, and David A. Relman 164-183
A6 Seasonal restructuring of the ground squirrel gutmicrobiota over the annual hibernation cycle--Hannah V. Carey, William A. Walters, and Rob Knight 184-206
A7 Lessons from studying insect symbioses--Angela E. Douglas 207-223
A8 A new vision of immunity: homeostasis of the superorganism--Grard Eberl 224-248
A9 Host defense and immunomodulation of mucosal candidiasis--Paul L. Fidel, Jr., and Mairi C. Noverr 249-272
A10 Microbiota-targeted therapies: An ecological perspective--Katherine P. Lemon, Gary C. Armitage, David A. Relman, and Michael Fischbach 273-291
A11 Community ecology and the vaginal microbiome--Larry J. Forney and Jacques Ravel 292-322
A12 Investigating bacterial-animal symbioses with light sheet microscopy--Michael J. Taormina, Matthew Jemielita, W. Zac Stephens, Adam R. Burns, Joshua V. Troll, Raghuveer Parthasarathy, and Karen Guillemin 323-346
A13 Clinical application of fecal microbiota transplantation in Clostridium difficile infection and beyond--Josbert J. Keller and Els van Nood 347-355
A14 Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications--Daniel Garrido, David C. Dallas, and David A. Mills 356-382
A15 Bacteriophage adhering to mucus providea nonhost-derived immunity--Jeremy J. Barr, Rita Auro, Mike Furlan, Katrine L. Whiteson, Marcella L. Erb, Joe Pogliano, Aleksandr Stotland, Roland Wolkowicz, Andrew S. Cutting, Kelly S. Doran, Peter Salamon, Merry Youle, and Forest Rohwer 383-400
A16 Topographic diversity of fungal and bacterial communities in human skin--Keisha Findley, Julia Oh, Joy Yang, Sean Conlan, Clayton Deming, Jennifer A. Meyer, Deborah Schoenfeld, Effie Nomicos, Morgan Park, NIH Intramural Sequencing Center Comparative Sequencing Program, Heidi H. Kong, and Julia A. Segre 401-411
A17 Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types--Neil R. Gottel, Hector F. Castro, Marilyn Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz, and Christopher W. Schadt 412-434
A18 Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis--Iliyan D. Iliev, Vincent A. Funari, Kent D. Taylor, Quoclinh Nguyen, Christopher N. Reyes, Samuel P. Strom, Jordan Brown, Courtney A. Becker, Phillip R. Fleshner, Marla Dubinsky, Jerome I. Rotter, Hanlin L. Wang, Dermot P. B. McGovern, Gordon D. Brown, and David M. Underhill 435-444
A19 Metagenomics and personalized medicine--Herbert W. Virgin and John A. Todd 445-470
A20 From genetics of inflammatory bowel disease towards mechanistic insights--Daniel B. Graham and Ramnik J. Xavier 471-488
A21 Antimicrobial peptides and the microbiome--Michael Zasloff 489-496
Appendix B: Agenda 497-500
Appendix C: Acronyms 501-502
Appendix D: Glossary 503-512
Appendix E: Speaker Biographies 513-522

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AIDS	acquired immune deficiency syndrome
AMD	acid mine drainage
AMP	antimicrobial peptide
ATP	adenosine triphosphate

BAM	bacteriophage adherence to mucus

CA-MRSA	community-acquired methicillin-resistant S. aureus
CBER	Center for Biologics Evaluation and Research
CD	Crohn’s disease
CDC	U.S. Centers for Disease Control and Prevention

DOE	U.S. Department of Energy
DIO	diet-induced obesity
DNA	deoxyribonucleic acid

FDA	U.S. Food and Drug Administration
FMT	fecal microbiota transplantation

GE	gastroesophageal
GEJ	gastroesophageal junction
GI	gastrointestinal
GIO	gene-induced obesity

HIV	human immunodeficiency virus

HMO	human milk oligosaccharides
HMP	Human Microbiome Project

IBD	inflammatory bowel disease
iNKT	invariant natural killer T
IOM	Institute of Medicine

MAMP	microbe-associated molecular pattern
MIO	microbe-induced obesity
mRNA	messenger ribonucleic acid
MRSA	methicillin-resistant S. aureus

NASH	nonalcoholic steatohepatitis
NIAID	National Institute of Allergy and Infectious Diseases
NIH	National Institutes of Health
NO	nitric oxide
NSF	National Science Foundation

OPC	oropharyngeal candidiasis
OTU	operational taxonomic unit

PAMP	pathogen-associated molecular pattern
PAT	pulsed antibiotic treatment
PCoA	principal coordinate analysis
PCR	polymerase chain reaction
POP	pattern of pathogenesis
PRR	pattern-recognition receptor

rDNA	ribosomal deoxyribonucleic acid
RNA	ribonucleic acid
rRNA	ribosomal ribonucleic acid
RYGB	Roux-en-Y gastric bypass

SCFA	short-chain fatty acid
SIV	simian immunodeficiency virus
STAT	subtherapeutic antibiotic treatment

TMAO	trimethylamine N-oxide

VVC	vulvovaginal candidiasis

Microbial Ecology in States of Health and Disease: Workshop Summary (2014)

Chapter: Appendix C: Acronyms

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Microbial Ecology in States of Health and Disease: Workshop Summary (2014)

Chapter: Appendix C: Acronyms