Gut bacteria use food signals to manage body's biological clock

Biological clocks are often associated with light. Historically, most people start their days when the sun is up, and end their days when the sun sets. But new research from Carnegie Mellon University suggests that some of the body's most important timekeepers live in the gut.

A study led by Zheng Kuang, the Eberly Family associate professor in the Department of Biological Sciences, showed that gut bacteria can detect when people eat and send signals that help intestinal cells absorb nutrients at the right time of day. The findings reveal a previously unknown link between the microbiome, circadian rhythms and metabolism.

These bacteria don't have access to light. Instead, they use food as a signal to tell time. When we eat, they produce molecules that communicate with our intestinal cells and help coordinate nutrient absorption."

Zheng Kuang, the Eberly Family associate professor, Department of Biological Sciences

The research addresses a long-standing question in microbiome science about how bacteria influence the body's daily rhythms, affecting overall health.

A microbial clock

The researchers discovered that the strain of bacteria they were working with metabolizes phytate, a naturally occurring compound found in foods such as nuts, seeds and grains. As they break down phytate, the bacteria produce molecules that activate a protein in intestinal cells, which then switches on genes responsible for nutrient absorption.

The bacteria help the body know that food is present, and that it is time to make the most of it.

"These bacteria evolved alongside humans over millions of years," Kuang said. "When food was available, it was beneficial to absorb as many nutrients as possible."

An ancient advantage meets the modern world

The study also offers a new perspective on problems people face today, like obesity.

Using mouse models, the researchers found that bacteria capable of activating this pathway promoted fat accumulation when animals consumed high-calorie diets. At first glance, that might seem harmful. But Kuang argues that the system helped humans survive when food was scarce. For most of human history, obtaining enough calories was a challenge. Bacteria that helped the body extract more energy from food provided a clear advantage.

"In the past, this relationship helped us grow and survive," Kuang said. "Today, we live in a different environment with constant access to calorie-dense foods. A system that was once beneficial may now contribute to metabolic problems."

To test that idea, the researchers also studied animals fed nutrient-poor diets to better resemble conditions faced by undernourished populations. In those animals, the bacteria and the molecules they produced improved growth, helping the animals gain more nutrients from limited food.

Potential applications

According to Kuang, bacteria involved in nutrient absorption could someday be used to address malnutrition.

The bacteria used in the study are found in humans and may appear in lower levels in undernourished children than those that are healthy, Kuang said.Future work will explore whether boosting these bacteria could help populations facing food insecurity get more nutrition and promote healthy growth. 

He also sees potential agricultural applications, including microbiome-based approaches that could improve growth in livestock.

While applications in nutrition and agriculture remain years away, the findings reveal that biological clocks are influenced by more than sunshine.

"The alignment between when we eat and when our bodies expect food appears to be very important," Kuang said. "Our work suggests that maintaining consistent eating patterns may help support a healthy relationship between the microbiome and the body."

Image caption for pic of bacteria strain if possible: Microbes are microscopic living organisms, including bacteria, fungi and viruses, while the microbiome refers to the entire community of these microbes living together in a specific environment, such as the gut or skin.