# The Circadian Clock Coordinates Animal and Microbial Metabolism

> **NIH NIH DP2** · PRINCETON UNIVERSITY · 2024 · $1,457,999

## Abstract

Project Summary
Our circadian clocks synchronize physiological processes and behaviors like eating and sleeping to
environmental light cycles. The central clock located in the brain attunes peripheral clocks located throughout
the body to daily rhythms in environmental light. This systems level coordination of biological processes extends
across all cell types and tissues and drives synchronization of whole-body metabolism. Recent work indicates
that these biological timers also synchronize functions of our gut microbiome to daily rhythms in our feeding
behavior. Given the essential role that the gut microbiome plays in nutrient acquisition, tuning the metabolic
functions of the microbiome with the rhythms of the animal host is logical. However, the underlying mechanisms
by which animal and microbial metabolism are synchronized, and the extent to which this synchronization
impacts animal physiology is not well understood. I propose to address this evidence gap by investigating how
circadian clocks and feeding rhythms promote oscillations in microbiome composition and function and how
these oscillations in microbial function impact host physiology. We have discovered a key mechanism whereby
the circadian clock may coordinate host and microbial metabolism through the regulation of multiple antimicrobial
proteins (AMPs). These proteins produced by the epithelial cells in the intestine, have previously been shown to
tailor the composition of the microbiome. This discovery has prompted two questions. First, how do rhythms in
distinct AMPs shape the composition and metabolic functions of the microbiome across the day-night cycle.
Second, how does the arrhythmic production of AMPs impact host physiology. To address these questions, my
lab will employ an interdisciplinary approach that incorporates emerging technologies with metabolomics,
gnotobiotic mouse models, and bacterial genetics.

## Key facts

- **NIH application ID:** 10908838
- **Project number:** 1DP2DK143367-01
- **Recipient organization:** PRINCETON UNIVERSITY
- **Principal Investigator:** John Francis Brooks
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $1,457,999
- **Award type:** 1
- **Project period:** 2024-09-15 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10908838

## Citation

> US National Institutes of Health, RePORTER application 10908838, The Circadian Clock Coordinates Animal and Microbial Metabolism (1DP2DK143367-01). Retrieved via AI Analytics 2026-06-08 from https://api.ai-analytics.org/grant/nih/10908838. Licensed CC0.

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