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.

Contents

• The National Academies of SCIENCES • ENGINEERING • MEDICINE
• PLANNING COMMITTEE FOR A WORKSHOP ON ANIMAL MODELS FOR MICROBIOME RESEARCH: ADVANCING BASIC SCIENCE AND TRANSLATIONAL RESEARCH
• ROUNDTABLE ON SCIENCE AND WELFARE IN LABORATORY ANIMAL USE
• INSTITUTE FOR LABORATORY ANIMAL RESEARCH
• Acknowledgments
• Reviewers
• Acronyms and Abbreviations
• 1. Introduction
• 2. A Trans-Kingdom Perspective on Animal Models and Microbiome Research
  • THE IMPORTANCE OF TRANS-KINGDOM INTERACTIONS
• 3. Non-Rodent Models for Microbiome Research
  • EUKARYOTIC MODELS
  • IN VITRO SYSTEMS FOR CHARACTERIZING MICROBIAL CONSORTIA
• 4. Modeling Human Microbiota in Animal Systems
  • CONNECTING MICROBES TO METABOLISM USING GNOTOBIOTIC MODELS
  • REVISITING KOCH'S POSTULATES FROM A MICROBIAL COMMUNITY PERSPECTIVE
  • THE INTERFACE BETWEEN MICROBES AND NEUROSCIENCE: TWO CASE STUDIES
• 5. Experimental Reproducibility Using Gnotobiotic Animal Models
  • CREATING STABILIZED MICROBIOMES IN LABORATORY ANIMALS
  • COMPLEX GNOTOBIOLOGY: AN EMERGING PARADIGM IN THE ERA OF NEXT-GENERATION SEQUENCING
  • THE ROLE OF HOST GENETICS
  • THE ROLE OF IMMUNOLOGICAL VARIATION
  • STANDARDIZING AND CHARACTERIZING DIETS
  • THE ROLE OF BIOLOGICAL SEX
• 6. Establishing and Evolving Gnotobiotic Facilities
  • BUILDING AND MAINTAINING A GNOTOBIOTIC FACILITY
  • ALTERNATIVES TO GNOTOBIOTICS: NORMALIZING THE ENVIRONMENT
• 7. Reflections on the Workshop
• References
• APPENDIXES
  • Appendix A. Workshop Agenda
  • Appendix B. Biographical Sketches of Planning Committee
  • Appendix C. Biographical Sketches of Workshop Speakers and Moderators
  • Appendix D. Glossary

Rapporteurs: Jenna Ogilvie, Lida Anestidou, and Joe Alper.

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.