Our intestines are home to trillions of bacteria and other microorganisms. Collectively known as the microbiome, these organisms, and the metabolites they produce, are mostly harmless or even beneficial to their human hosts. For example, interactions between gut bacteria and the immune system can help prepare the body to fight off pathogenic bacteria that enter the gastrointestinal tract. Long-term changes in the composition of the gut microbiome are associated with a wide variety of illnesses, from various types of cancer to Alzheimer’s disease. But researchers are now beginning to realize that the composition of the microbiome also varies over the course of the day. John Brooks is interested in what causes these fluctuations and the implications this has for human health and disease.

“We’re finding that the body’s circadian clock, which determines our sleep/wake and feed/fasting cycles, has a really large impact on the innate immune functions that govern the microbiome, and this, in turn, drives daily rhythms in the microbiome’s composition and function,” Brooks explains.

Brooks first became interested in the interactions between bacteria and their hosts as a graduate student with Mark Mandel at Northwestern University, studying the unique symbiosis between a luminous bacterium, Vibrio fischeri, and the Hawaiian bobtail squid Euprymna scolopes. Brooks identified hundreds of factors produced by the bacterium that allow it—and none of the other trillions of bacterial species living in the ocean—to colonize the squid’s light organ and provide the luminescence the squid needs to hunt at night.

As a postdoctoral researcher in Lora Hooper’s lab at UT Southwestern Medical School, Brooks turned his attention to the more complex microbiome of mice, studying its effects on the innate immune system and the epithelial cells that line the intestinal wall. Brooks discovered that, by controlling the rodents’ feeding behavior, the circadian clock promotes daily rhythms in the attachment of a specific type of gut bacterium to the intestinal lining. This, in turn, induces daily rhythms in the production of an antimicrobial factor by intestinal epithelial cells, providing maximal protection from Salmonella and other foodborne pathogens at night, when mice do most of their eating.

“So, there are daily rhythms in our resistance to gastrointestinal pathogens, and animals can be more or less susceptible to infection, depending on the time that they’re exposed,” Brooks says. “A lot of this is due to the circadian clock and specific innate immune factors that are regulated by it.”

Attracted by Princeton’s broad range of expertise and its collaborative culture, Brooks is now building on this research in his own lab, which has rapidly grown in size since he joined the department in January 2022. He is currently a Hanna Gray Fellow with the Howard Hughes Medical Institute, and was recently named a Pew Scholar in the Biomedical Sciences by the Pew Charitable Trusts.

Much of his group’s work focuses on mice missing various components of the circadian clock or lacking gut bacteria, and examining how these changes affect the innate immune system. But Brooks’s team are also beginning to use miniature intestinal “organoids” grown in the lab, where the effects of specific bacteria on innate immune functions can be easily visualized.

“The key question for us right now is to determine the extent to which the circadian clock dictates daily rhythms in our resistance to pathogens both bacterial and viral. We are currently focused on the cell intrinsic clocks  within the epithelial and immune cells themselves,” Brooks says. “How do these cells coordinate immune functions with environmental light cycles, in essence how do these cells know what time of day it is, and how do they communicate with both the central clock in the brain and the microbiome? We’re discovering that there are multiple mechanisms by which the circadian clock regulates rhythms in innate immune functions that drive both beneficial and pathogenic host-microbe associations.”