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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Animal Models for
Microbiome Research

Advancing Basic and Translational Science

PROCEEDINGS OF A WORKSHOP

Joe Alper, Lida Anestidou, and Jenna Ogilvie, Rapporteurs

Roundtable on Science and Welfare in Laboratory Animal Use

Institute for Laboratory Animal Research

Division on Earth and Life Studies

images

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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001

This project was supported by the American Veterinary Medical Association; Covance Laboratories, Inc.; Genentech; GlaxoSmithKline; Massachusetts General Hospital; Merck; National Primate Research Centers; National Science Foundation; Novartis; University of California, Davis; University of Michigan; University of Pittsburgh; University of Washington; U.S. Food and Drug Administration; and Yale University. Funding for this conference was made possible, in part, by the U.S. Food and Drug Administration through grant 5 R13 FD 005298-02. The views expressed in written conference materials or publications and by speakers or moderators do not necessarily reflect the official policies of the U.S. Department of Health and Human Services; nor does any mention of trade names, commercial practices, or organization imply endorsement by the U.S. government. This material is based on work supported by the National Science Foundation under Grant No. IOS-1639899. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. 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: 978-0-309-46388-1
International Standard Book Number-10: 0-309-46388-2
Digital Object Identifier: https://doi.org/10.17226/24858

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Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. https://doi.org/10.17226/24858.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

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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.

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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

PLANNING COMMITTEE FOR A WORKSHOP ON ANIMAL MODELS FOR MICROBIOME RESEARCH: ADVANCING BASIC SCIENCE AND TRANSLATIONAL RESEARCH

JAMES G. FOX (Co-Chair), Professor and Director, Division of Comparative Medicine, and Professor of Biomedical Engineering, Massachusetts Institute of Technology

JOSEPH T. NEWSOME (Co-Chair), Clinical Director, Division of Laboratory Animal Resources and Associate Professor, Pathology, University of Pittsburgh

WENDY S. GARRETT, Melvin J. and Geraldine L. Glimcher Associate Professor of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health

JEFFREY I. GORDON, Dr. Robert J. Glaser Distinguished University Professor and Director, Center for Genome Sciences and Systems Biology, Washington University in St. Louis

VINCENT B. YOUNG, Associate Professor, Department of Internal Medicine/Division of Infectious Diseases and Department of Microbiology and Immunology, University of Michigan

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

ROUNDTABLE ON SCIENCE AND WELFARE IN LABORATORY ANIMAL USE1

Co-Chairs

LYNN C. ANDERSON, Vice President, Global Animal Welfare and Comparative Medicine, Covance Laboratories, Inc.

ROBERT C. DYSKO, Professor and Director, Unit for Laboratory Animal Medicine, University of Michigan Medical School

Liaison to ILAR Council

PAUL A. LOCKE, Associate Professor, Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health

Members

DAVID M. ANDERSON, Executive Director, Health Sciences Administration, University of Washington

JILL ASCHER, Deputy Director, Division of Veterinary Services, U.S. Food and Drug Administration

BONNIE V. BEAVER, Professor, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Texas A&M University

SAVERIO “BUDDY” CAPUANO III, Attending Veterinarian and Associate Director, Animal Services, Wisconsin National Primate Research Center, University of Wisconsin–Madison

CAROL CLARKE, Research Specialist Staff Officer, U.S. Department of Agriculture, Animal and Plant Health Inspection Service Animal Care

GAIL C. GOLAB, Director, Animal Welfare Division, American Veterinary Medical Association

DONNA MATHEWS JARRELL, Attending Veterinarian, Director, Center for Comparative Medicine, Massachusetts General Hospital

ESTELLA Z. JONES, Senior Regulatory Veterinarian and Acting Institutional Official, White Oak Animal Program, Office of Counterterrorism and Emerging Threats, Office of the Chief Scientist/Office of the Commissioner, U.S. Food and Drug Administration

BRUCE W. KENNEDY, Compliance Associate, Office of Research, California State Polytechnic University

DAVID M. KURTZ, Veterinary Staff Scientist, National Institute of Environmental Health Sciences, National Institutes of Health

___________________

1 Membership of the Roundtable and member affiliations current as of December 2016.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

MARGARET S. LANDI, Chief of Animal Welfare, Ethics and Strategy, GlaxoSmithKline

K. C. KENT LLOYD, Professor and Director, Mouse Biology Program, University of California, Davis

JOSEPH T. NEWSOME, Clinical Director, Division of Laboratory Animal Resources and Associate Professor, Pathology, University of Pittsburgh

STEVEN NIEMI, Director, Office of Animal Resources, Harvard University Faculty of Arts and Sciences

PATRICIA PREISIG, Professor of Internal Medicine (Nephrology) and Cellular and Molecular Biology, Yale University

SUSAN BRUST SILK, Director, Division of Policy and Education, Office of Laboratory Animal Welfare, National Institutes of Health

EDDA (FLOH) THIELS, Program Director, Integrative Organismal Systems Division, Biological Sciences Directorate, National Science Foundation

RHONDA J. WILER, Senior Director, Transgenic Technology, Genentech

GINA P. WILKERSON, Global Animal Welfare Officer, Scientific Operations, Novartis Institute for Biomedical Research, Inc.

ROBERT H. WURTZ, NIH Distinguished Investigator, Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health

National Academies of Sciences, Engineering, and Medicine Staff

LIDA ANESTIDOU, Director, Roundtable on Science and Welfare in Laboratory Animal Use

JENNA OGILVIE, Research Associate, Board on Life Sciences

ANGELA KOLESNIKOVA, Senior Program Assistant, Board on Life Sciences

Page viii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

INSTITUTE FOR LABORATORY ANIMAL RESEARCH1

Members

MARGARET S. LANDI (Chair), Chief of Animal Welfare, Ethics and Strategy, GlaxoSmithKline

KARIN BLUMER, Scientific Affairs, Novartis International AG

CORY BRAYTON, Associate Professor of Molecular and Comparative Pathobiology, Johns Hopkins University

JOSEPH J. DEGEORGE, Global Head of Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories

MICHAEL DUVALL, Scientific Director, Head of Toxicology and Laboratory Animal Medicine, Johnson & Johnson, Janssen Pharmaceuticals

LEWIS B. KINTER, Independent Consultant

MALAK KOTB, Chair, Department of Basic Sciences, University of North Dakota

PAUL A. LOCKE, Associate Professor, Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health

DANIEL S. MARSMAN, Head, Safety and Regulatory Affairs, Procter & Gamble Health Care

MELINDA A. NOVAK, Professor of Psychology, Department of Psychology, University of Massachusetts

JAMES A. ROTH, Clarence Hartley Covault Distinguished Professor, Director, Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University

LAWRENCE B. SCHOOK, Vice President for Research, Edward William and Jane Marr Gutgsell Professor, University of Illinois

ROBERT S. SIKES, Professor of Biology, University of Arkansas at Little Rock

Staff

DOROTHY ZOLANDZ, Acting Director

LIDA ANESTIDOU, Senior Program Officer

___________________

1 Membership of the Roundtable and member affiliations current as of December 2016.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Acknowledgments

The support of the Roundtable on Science and Welfare in Laboratory Animal Use was vital to the planning and conduct of the workshop on Animal Models for Microbiome Research: Advancing Basic and Translational Science. Federal sponsors are the National Science Foundation and the U.S. Food and Drug Administration. Nonfederal sponsorship was provided by the American Veterinary Medical Association; Covance Laboratories, Inc.; Genentech; GlaxoSmithKline; Massachusetts General Hospital; Merck; National Primate Research Centers; Novartis; University of California, Davis; University of Michigan; University of Pittsburgh; University of Washington; and Yale University.

The Roundtable on Science and Welfare in Laboratory Animal Use wishes to express gratitude to the members of the planning committee for their work in developing a far-reaching workshop agenda and the expert speakers who took part in the workshop’s discussions.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Reviewers

This Proceedings of a Workshop 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:

Angela Douglas, Cornell University

Robert Dysko, University of Michigan Medical School

Alton G. Swennes, Baylor College of Medicine

Tamara Tal, U.S. Environmental Protection Agency

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. The review of this proceedings was overseen by Jeffrey Everitt, Duke University School of Medicine. He was responsible for making certain that an independent examination of this proceedings was carried out in accordance with standards of the National Academies and that all review comments were carefully considered. Responsibility for the final content rests entirely with the rapporteurs and the National Academies.

Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Acronyms and Abbreviations

BSL-2 biosafety level 2
CCFA Crohn’s & Colitis Foundation of America
DGRP Drosophila Genetic Resource Panel
EEN exclusive enteral nutrition
IACUC Institutional Animal Care and Use Committee
IBD inflammatory bowel disease
LPS lipopolysaccharide
NAPE-PLD N-acyl phosphatidylethanolamine phospholipase D
NIH National Institutes of Health
NKT natural killer T cells
NOD non-obese diabetic
sDMDMm2 Stable Defined Moderately Diverse Mouse Microbiota 2
SOP standard operating procedure
SPF specific pathogen-free
TMAO trimethylamine-N-oxide
USDA U.S. Department of Agriculture
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Page xiii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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The surface of the human body and its mucous membranes are heavily colonized by microorganisms. Our understanding of the contributions that complex microbial communities make to health and disease is advancing rapidly. Most microbiome research to date has focused on the mouse as a model organism for delineating the mechanisms that shape the assembly and dynamic operations of microbial communities. However, the mouse is not a perfect surrogate for studying different aspects of the microbiome and how it responds to various environmental and host stimuli, and as a result, researchers have been conducting microbiome studies in other animals.

To examine the different animal models researchers employ in microbiome studies and to better understand the strengths and weaknesses of each of these model organisms as they relate to human and nonhuman health and disease, the Roundtable on Science and Welfare in Laboratory Animal Use of the National Academies of Sciences, Engineering, and Medicine convened a workshop in December 2016. The workshop participants explored how to improve the depth and breadth of analysis of microbial communities using various model organisms, the challenges of standardization and biological variability that are inherent in gnotobiotic animal-based research, the predictability and translatability of preclinical studies to humans, and strategies for expanding the infrastructure and tools for conducting studies in these types of models. This publication summarizes the presentations and discussions from the workshop.

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