Identifying non-human primate models for specific human microbiome traits

Abstract: The gut microbiota is increasingly recognized as an important contributor to a range of human
physiological processes and is attracting increasing attention as a dynamic area for the development of
therapeutics. To realize the potential of the gut microbiome in a therapeutic context, animal models are
necessary to generate causal, mechanistic data describing host-microbe interactions. While mice and fish have
been critical in generating foundational microbiome data toward this goal, they have key genetic, physiological,
and behavioral differences from humans that can interfere with the translation of findings. Non-human primates
share many genetic, physiological, and behavioral traits with humans, increasing their translational potential.
Although non-human primates are used for research across the NIH, they are currently underutilized in
microbiome research and have not been systematically validated as models in this context. Given the
significant investment required for non-human primate studies, it is especially important to characterize which
models are best suited for particular questions as we seek to examine how microbiomes impact human health
and disease. Here we propose to develop non-human primates as valuable model organisms for functional
studies of the human microbiota. Specifically, we aim to identify the best uses for different non-human primate
species in microbiome research. We will generate baseline microbiome (shotgun metagenomics, analysis of
SCFA concentrations, untargeted metabolomics) and physiological data (metabolic panels, immune cell
populations, serum metabolomics) from humans and five non-human primate species commonly used as
biomedical models (marmosets, owl monkeys, squirrel monkeys, baboons, and macaques). These data will
allow us to determine which non-human primate species model different taxonomic and functional features of
the human gut microbiome and to measure the consistency of host-microbiome interactions across human and
non-human primate species. Our efforts hold potential to unlock critical insight about the utility of longstanding
non-human primate biomedical models for different aspects of microbiome research and will ultimately help
researchers accelerate the translation of microbiome discoveries into clinical settings. By identifying how well
different non-human primate species model humans in a subclinical context, the proposed project will lay the
groundwork for future R01 proposals that use non-human primate models to interrogate host-microbe
interactions in a disease context. Overall, this line of inquiry will facilitate future studies targeting key questions
about host-microbe interactions with a high potential for translational science and medical benefit.

Grant Number: 5R21OD033659-02
NIH Institute/Center: NIH
Principal Investigator: Katherine Amato