The gut microbiome, a vast assortment of bacteria and other microorganisms that inhabit our digestive system, plays a critical role in converting food into energy. Many of these microbes follow rhythmic cycles of activity throughout the day. However, high-fat diets and other factors can disrupt these rhythms and contribute to metabolic disease.
A new study by researchers at University of California San Diego and their colleagues used time-restricted feeding (TRF), an intervention that limits dietary intake to a short time window each day, to restore microbial rhythms in mice fed a high-fat diet. By analyzing daily fluctuations in microbial gene expression, they identified a specific enzyme — a bile salt hydrolase (BSH) — that appears to play a role in protecting metabolic health.
They then engineered the bsh gene into a harmless gut bacterium and found that mice given this modified microbe had less body fat, better insulin sensitivity and improved glucose control, thereby mimicking the effects of time-restricted feeding. The findings could contribute to the development of targeted therapies for obesity, diabetes and other metabolic conditions in humans. The study was published in Cell Host & Microbe on June 18, 2025.
To explore how TRF affects microbial function, the researchers used a technique called metatranscriptomics, which measures real-time gene expression in gut bacteria. Because TRF changes the timing of food intake, the team hypothesized that it would drive time-sensitive shifts in microbial activity that conventional methods can't capture. To test this, they studied gut microbiome function in three groups of mice: one fed a high-fat diet under TRF (eight hours per day), one fed the same diet with food available all day long, and a control group fed a standard diet with unrestricted access.
They researchers found that after eight weeks:
- TRF protected mice from metabolic dysfunction, even when they consumed a high-fat diet. This replicates earlier findings and confirms the beneficial effects of TRF on glucose regulation and body composition.
- Metatranscriptomics detected fluctuations in microbial gene activity that tracked closely with the timing of food intake, helping explain how TRF influences metabolism — not just by changing which microbes are present, but by altering what they do and when they do it.
- TRF partially restored daily rhythms in microbial gene activity that were absent in mice that had access to a high-fat diet all day long. While TRF did not fully re-establish the functional cycling seen in healthy control mice, it did induce distinct shifts in microbial activity, preserving the time-dependent expression of microbial genes involved in carbohydrate and lipid metabolism.
These functional changes were only apparent at the RNA level through the use of metatranscriptomics. Metagenomics, a more traditional method, only identified which genes were present in the microbial community.
"By looking at RNA, we are able to capture the dynamic changes of these microbes compared to metagenomics where we don't see changes," said Stephany Flores Ramos, Ph.D., a postdoctoral researcher at UC San Diego School of Medicine and first author of the study.
While these findings suggest that TRF alters microbial function in ways that benefit the host, the researchers also conducted an experiment to establish whether specific microbial activities were directly responsible for the metabolic improvements.
"We've long suspected that the metabolic benefits of time-restricted feeding might be driven by changes in the gut microbiome," said Amir Zarrinpar, M.D., Ph.D., associate professor of medicine at UC San Diego School of Medicine and senior author of the study. "With this study, we were finally able to test that idea directly."
The team focused on the transcription of BSH, an enzyme known to break down fats during digestion and to influence glucose metabolism. Previous research in Zarrinpar's lab suggested that BSH activity may contribute to metabolic improvements. In the current study, TRF resulted in the expression of the bsh gene during the daytime in the gut bacteria Dubosiella newyorkensis, which has a functional equivalent in humans.
With this knowledge in hand, the researchers engineered a set of gut bacteria to express different versions of the bsh gene. These included variants from bacteria that were more active under high-fat feeding, under normal conditions, and under TRF. When tested in mice, only the version from D. newyorkensis — which was more highly expressed during TRF — led to metabolic improvements.
"Mice given these engineered bacteria had better blood sugar control, lower insulin levels, less body fat, and more lean mass," said Zarrinpar. "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 is to test the engineered bacteria in mice with obesity or diabetes caused by a high-fat diet to see if the observed benefits hold up in disease models. "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 added.
Additional co-authors on the study include: Nicole Siguenza, Wuling Zhong, Amulya Lingaraju, R. Alexander Richter, Smruthi Karthikeyan, April L. Lukowski, Ipsita Mohanty, Wilhan D.G. Nunes, Jasmine Zemlin, Zhenjiang Zech Xu, Jeff Hasty, Pieter C. Dorrestein and Rob Knight at UC San Diego; Satchidananda Panda at the Salk Institute for Biological Studies; and Qiyun Zhu at Arizona State University.
