Diet may affect how gut microbes evolve

Periodic variations in diet can be important to avoid the fixation of specific mutations and maintain a high genetic diversity in the microbiota.

What is already known on this topic
Switching from low-fat, high-fiber diet to a Western diet rich in fat and sugars leads to changes in the gut microbiota composition, which may result in conditions such a dysbiosis, increased body weight, and metabolic imbalances. However, the effect of dietary changes on the evolution of gut bacteria remain unknown.

What this research adds
Researchers followed the evolution of Bacteroides thetaiotaomicron, a common gut microbe that relies on fiber, in mice that were fed different diets. While bacteria in mice on a standard diet acquired mutations that promoted fiber degradation, bacteria in animals fed a Western-style diet accumulated mutations that favored the degradation of the host’s mucus.

Conclusions
The findings suggest that microbes evolve and adapt to distinct gut environments generated by changes in diet. They also indicate that B. thetaiotaomicron genetic diversity could be used as a biomarker for dietary differences among individuals.

Scientists have known that diet can influence microbiota composition and function, but whether and how dietary changes affect the evolution of gut bacteria remains unknown. Now, researchers have found that gut microbes evolve and adapt in response to diet, with potential effects on the host’s health.

The findings, published in Cell Host & Microbe, indicate that the genetic diversity of specific members of the gut microbiota could be used as a biomarker for dietary differences among individuals.

The consequences of an unbalanced diet can be much more permanent than previously recognized because diet affects not only the composition of the microbiota, but also leaves permanent genetic alterations in the gut microbes,” says study senior author Karina Xavier at the Instituto Gulbenkian de Ciencia. 

Switching from a low-fat, high-fiber diet to a Western diet rich in fat and sugars leads to changes in the gut microbiota composition, which may result in conditions such as dysbiosis, increased body weight, and metabolic imbalances. 

To investigate the effects of these changes on the evolution of gut bacteria, Xavier and her colleagues followed the evolution of a common gut microbe in mice that were fed different diets.

Diet-specific mutations

The rodents were either kept on a standard diet rich in plant fibers and low in fat and sugars, or a Western-style diet rich in fat and sugars but poor in fiber. In these two groups of mice, the researchers followed the emergence of mutations in Bacteroides thetaiotaomicron, or B. theta — a common gut microbe that relies on plant fibers for its functions.

B. theta evolved rapidly in the mouse gut, accumulating diet-specific mutations in as quickly as two weeks, the team found. And while bacteria in mice on a standard diet acquired mutations that promoted fiber degradation, bacteria in those fed a Western-style diet accumulated mutations that favored the degradation of the host’s mucus. 

This finding indicates that microbes evolve and adapt to distinct gut environments generated by dietary change, the researchers say. “Our results support the conclusion that diet can leave specific genetic signatures in B. theta and provide evidence that intraspecies mutational diversity can be a powerful biomarker of dietary differences between individuals,” they add.

Periodic changes

Next, the researchers looked at mice that shifted every week from standard to Western diet. The weekly shifts led to fluctuations in the microbe’s genetic and metabolic profile, resulting in a higher genetic diversity compared to microbes kept under constant dietary regimens. 

This suggest that periodic variations in diet can be important to avoid the fixation of specific mutations and maintain a high genetic diversity in the microbiota, the researchers say. “One can, in principle, use supplementations to manipulate intraspecies genetic diversity,” they add.

Overall, the findings highlight the importance of considering the role of microbiota evolution in shaping microbiota function. Such information could help to understand the microbiota-dependent host responses to diet and other perturbations such as the use of antibiotics, the authors say.