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.Table of ContentsFront Matter1 Introduction2 A Trans-Kingdom Perspective on Animal Models and Microbiome Research3 Non-Rodent Models for Microbiome Research4 Modeling Human Microbiota in Animal Systems5 Experimental Reproducibility Using Gnotobiotic Animal Models6 Establishing and Evolving Gnotobiotic Facilities7 Reflections on the WorkshopReferencesAppendix A: Workshop AgendaAppendix B: Biographical Sketches of Planning CommitteeAppendix C: Biographical Sketches of Workshop Speakers and ModeratorsAppendix D: Glossary