Diet is known to shape the gut microbiota, but scientists are still working out which microbial changes matter for health. Now, a study in mice shows that diet and eating timing can shape the quantity and behavior of gut microbes in similar ways, even when the specific bacteria present are very different.

The findings, published in Cell Reports, suggest that microbiota studies need to measure how much microbial material is present and moving through the gut to find reliable links between diet and health.

Microbiota studies often report that certain conditions or diets are linked with particular gut bacteria, but those links are inconsistent across studies. This may be because many studies focus on relative bacterial composition and miss quantitative features such as how many bacteria are present in the gut.

So, Hannah Ruple at the University of Hohenheim in Stuttgart, Germany, and her colleagues set out to study how diet and eating schedule affect the gut microbiota of mice.

Diet effect

The researchers tested different diets and used a red food dye to measure gut transit time, stool output, bacterial density, and total bacterial excretion. 

Fasting reduced stool output and total bacterial excretion, and a high-fiber diet sped up transit and lowered bacterial density, even though mice produced more stool. Both fasting and a high-fiber diet were also linked to lower expression of some inflammation-related genes. A high-fat diet slowed gut transit and increased bacterial density and total bacterial excretion.

Total bacterial excretion depended on two things: how much stool mice produced and how densely packed that stool was with bacteria. Food intake mainly affected stool amount, while gut transit time was tied to bacterial density. Slower transit gave bacteria more time to accumulate, whereas faster transit reduced bacterial load.

Quantitative traits 

The team then studied normal mice and mice lacking an immune molecule whose absence can predispose to gut inflammation. Time-restricted feeding, or allowing food only during an 8-hour window each day, shortened gut transit and reduced bacterial load and bacterial excretion in both mouse types. It also reduced some inflammation-related gene signals.

More detailed experiments, especially in humans, are needed before the findings can guide clinical use, the researchers say. However, they add, the work may help explain why studies that focus only on bacterial composition often find inconsistent results.

“Integrating quantitative gut microbiome traits thus provides a framework to improve our understanding of microbiome organization that should be explored for the identification of novel diagnostic markers and therapeutic targets for microbiome-mediated disease,” the authors say.