Study Reveals TRF's Role in Reshaping Gut Microbiome and Metabolism

The gut microbiome—a diverse community of bacteria and other microorganisms in the gastrointestinal tract—plays an important role in converting food into energy.

Many of these microbes follow daily cycles of activity. However, high-fat diets and other factors can disrupt these cycles, increasing the risk of metabolic disease.

A recent study from researchers at the University of California, San Diego, and their collaborators explored whether time-restricted feeding (TRF) could restore these microbial cycles in mice fed a high-fat diet. TRF limits food intake to a specific time window each day. By analyzing daily patterns of microbial gene expression, the researchers identified a key enzyme, bile salt hydrolase (BSH), which appears to influence metabolic health.

To test its effect, they inserted the bsh gene into a harmless gut bacterium. Mice given this modified microbe showed reduced body fat, improved insulin sensitivity, and better glucose control. These outcomes were similar to those seen in mice following a time-restricted eating schedule. The findings could inform future treatments for obesity, diabetes, and other metabolic conditions. The study was published on June 18, 2025, in Cell Host and Microbe.

To study how TRF affects microbial activity, the researchers used metatranscriptomics—a method that captures real-time gene expression in gut microbes. Because TRF changes the timing of food intake, the researchers expected it to also influence the timing of microbial activity, in ways that traditional methods might miss.

They examined the microbiome activity in three groups of mice:

1. One group ate a high-fat diet under TRF (eight hours per day),

2. One group ate the same high-fat diet with unrestricted access to food,

3. A control group had a standard diet with food available at all times.

After eight weeks, they observed the following:

• TRF protected mice from metabolic dysfunction despite the high-fat diet. This supports earlier research showing TRF’s positive effects on glucose regulation and body composition.

• Metatranscriptomic analysis revealed that microbial gene activity closely followed food intake timing. This showed that TRF influences not only which microbes are present, but also what they do and when.

• TRF partially restored daily cycles in microbial gene activity. These cycles had been disrupted in mice with constant access to a high-fat diet. Although not fully restored to the level seen in healthy controls, TRF triggered notable changes in microbial behavior, especially in genes related to carbohydrate and lipid metabolism.

These functional changes were only detectable at the RNA level using metatranscriptomics. Traditional metagenomic techniques, which only identify the presence of microbial genes, did not capture these time-dependent patterns.

By looking at RNA, we are able to capture the dynamic changes of these microbes compared to metagenomics, where we do not see changes.

Stephany Flores Ramos, Ph.D., Study First Author and Postdoctoral Researcher, UC San Diego School of Medicine

While the data suggest that TRF influences microbial function in ways that benefit the host, the researchers also tested whether specific microbial activities directly contribute to those benefits.

We have long suspected that the metabolic benefits of time-restricted feeding might be driven by changes in the gut microbiome. With this study, we were finally able to test that idea directly.

Amir Zarrinpar, M.D., Ph.D., Study Senior Author, Associate Professor and, School of Medicine, University of California, San Diego

They focused on the expression of bile salt hydrolase (BSH), an enzyme involved in lipid digestion and glucose metabolism. Previous studies from Zarrinpar's group had suggested that BSH activity might help improve metabolic health. In this study, TRF increased bsh gene expression during the day in the gut bacterium Dubosiella newyorkensis, which has a similar enzyme in humans.

Based on this finding, the researchers engineered several gut bacteria to express different versions of the bsh gene. These included variants that were more active after high-fat feeding, under normal conditions, and during TRF. When tested in mice, only the variant from D. newyorkensis—which showed higher expression during TRF—led to improvements in metabolism.

Zarrinpar added, “Mice given these engineered bacteria had better blood sugar control, lower insulin levels, less body fat, and more lean mass. This demonstrates how metatranscriptomics can help identify time-dependent microbial functions that may be directly responsible for improving host metabolism. It also shows the potential for designing targeted microbial therapies based on these functional insights.”

The next step will be to test the engineered bacteria in mouse models of obesity or diabetes caused by a high-fat diet. This will help determine whether the observed benefits hold in disease conditions.

“We also plan to explore other time-sensitive microbial genes uncovered by our data to develop additional engineered bacteria that could improve metabolic health,” Zarrinpar concluded.