Like clockwork

Professor John Brooks II wearing a lab coat.
Focus on Molecular Biology

Like clockwork

How circadian rhythms govern the body’s defenses against disease

By Yaakov Zinberg

We like to think that our immune system protects us 24/7, but it turns out that the likelihood of contracting some infections varies based on the time of day. Like sleep, appetite, and body temperature, immunity operates on a circadian rhythm — an innate, 24-hour cycle that relies on light signals from the environment to regulate the body’s internal clock. John F. Brooks II, assistant professor of molecular biology, is trying to understand how our immune abilities fluctuate throughout the day — and how that knowledge can be used to protect people’s health.

“I’m really taken by this idea that contrary to what we thought previously, our immune systems do not function all the time at capacity, and that there are these daily rhythms in their functioning,” said Brooks, who joined Princeton in 2022. “A better understanding of how this circadian regulation of immune functions is occurring might allow us to optimize therapeutics.”

One link between circadian rhythms and immune system strength, Brooks and other researchers have found, is the gut microbiome, the community of beneficial bacteria that live within the digestive tract. These microorganisms promote the production of antimicrobial proteins in the animal host that kill invading bacteria, but the rate of production oscillates dramatically between day and night. As a postdoctoral researcher at the University of Texas-Southwestern Medical Center, Brooks led a study that showed how some of the antimicrobial proteins produced in mice are more abundant at night. Mice are nocturnal and their circadian rhythm prompts them to eat when it’s dark in their environment. These eating patterns in turn trigger the expression of proteins that confer resistance against pathogens.

The triangular relationship between the circadian rhythm, the microbiome, and immunity likely evolved to protect mice against foodborne pathogens, Brooks said. The antimicrobial proteins they produce are effective against several of these pathogens, and the mice save energy by producing them exclusively at night, when encountering these foodborne pathogens is most likely. When mice eat, the circadian rhythm essentially anticipates that they might be exposed to harmful bacteria and starts preparing the defenses.

“Our immune systems do not function all the time at capacity. There are daily rhythms.”

—John Brooks II, assistant professor of molecular biology

While it’s still unclear if this exact mechanism is present in humans, it’s certainly the case that disrupted circadian rhythms increase the risk of infection. Night-shift workers, whose internal clocks become disconnected from their environmental light cycles, are more likely than night-sleepers to contract a number of infectious diseases, including COVID-19. These workers also develop obesity and diabetes at elevated rates, likely due to dramatic changes in the composition of their microbiomes.

To investigate how the circadian rhythm-microbiome relationship might function in people, Brooks and his research team are approaching the research question from multiple directions. They use small and large intestine organoids — lab-grown versions of living tissue — to identify human-specific attributes of these interactions, while simultaneously delving into bacterial genetics and pinpointing when harmful bacteria are most potent.

“We still don’t really understand how the microbiome influences our health and fitness,” said Brooks. “And we definitely don’t understand how we can tailor the microbiome to benefit health and fitness.” Figuring out how the human microbiome is affected by circadian rhythms, however, could pave the way for new microbiome-based therapeutic approaches. People could one day take a probiotic at a specific time of the day if, say, researchers determine it’s the most opportune moment to introduce a beneficial microbe into the crowded microbiome. Likewise, antibiotics could be tailored against a single bacterial strain and administered exactly when it’s most vulnerable.

Though he’s in the process of getting his own lab off the ground, Brooks is already making numerous contributions to the broader Princeton biology community. In 2023, he was one of 22 scientists worldwide named a Pew Scholar in Biomedical Sciences and one of 15 scientists named a Searle Scholar, distinctions which provide funding that will help support his lab’s research. Brooks and his group are establishing a germ-free mouse facility, where mice are born without a microbiome. This allows scientists to study what might go wrong in the absence of a microbiome as well as the functions of individual microorganisms they can selectively introduce into the mice.

In the coming years, researchers will likely develop many microbiome-based therapeutics. For now, Brooks is focused on laying the groundwork in this new area of study. “Right now, I’m much more interested in the basic biology of how the circadian clock drives immunity,” he said.