How Diet Shapes Gut Microbes and Energy Absorption

What we eat has a big impact on the bacteria living in our gut, which in turn affects how our bodies use energy—something that plays a major role in the development and treatment of obesity. Most of what we know about this comes from animal studies or human observations, so there is still a lot to learn.

Our recent study, published in the American Journal of Clinical Nutrition, aimed to fill in some of these gaps. We looked at small molecules in the body—called metabolites—including those that are produced when food is digested by both our bodies and the microbes in our gut.

We studied healthy adults without obesity and fed them two different diets:

• A high-fiber diet (called the Microbiome Enhancer Diet or MBD), which was low in processed foods.

• A Western-style diet (WD), which was low in fiber and high in processed foods.

Both diets had the same number of calories and macronutrient percentages, and participants were carefully monitored to make sure they ate exactly what was provided.

Our study goals were:

1. To find chemical “fingerprints” of each diet that could be validated in future research.

2. To understand how diet and gut microbes work together to affect how much energy the body absorbs.

What we found:

1. The high-fiber diet changed many of the body’s metabolites compared to the processed diet. These changes could help identify diets that modulate how much energy is absorbed from the diet, in part by altering the gut microbiome.

2. Some of the changes in metabolites excreted in the stool were linked to less energy being absorbed and more growth of gut microbes—suggesting potential mechanisms by which the microbes might be using some of the energy themselves and preventing energy from being absorbed by the host.

3. Surprisingly, the high-fiber diet increased levels of a ketone body called beta-hydroxybutyrate, which usually rises during fasting or low-carb diets. This happened even though both diets had the same number of calories which were calculated to maintain participants’ starting body weight, hinting that an MBD might mimic some effects of fasting.

Why this matters:

These findings help us understand how diet and gut microbes work together to influence energy use in the body. This could lead to new ways to prevent or treat obesity by targeting the gut microbiome.