A new study shows that complex carbohydrates in foods like potatoes impact energy production in the gut microbiome. | Getty Images
Stanford Report News - July 30th, 2025
Similar to the way bacteria turn milk into yogurt or cabbage into sauerkraut, billions of microbes are busy fermenting undigested food in the human gut – and making some helpful byproducts for their hosts in the process.
A study published in the journal Cell details a more accurate method to calculate the amount of these “fermentation products,” namely short-chain fatty acids, which can affect a range of systems in humans. Researchers found that these products contribute 2%-5% of a person’s daily energy use among those eating Western diets.
While a seemingly small amount, that energy contribution rises to 10% for people eating non-Western diets, which rely more on complex carbohydrates and less on ultra-processed foods.
“It heavily depends on what we eat,” said Jonas Cremer, co-corresponding author of the study and an assistant professor of biology in Stanford’s School of Humanities and Sciences. “By quantifying variations in diet and bacterial metabolism, we were able to estimate not only a rough number but also the range as well as how this energy contribution changes with diet.”
The human body uses the vast majority of the fatty acids produced by gut microbes: More than 90%, the study found. Less than 10% is lost through human waste. In addition, the composition of gut microbial species did not affect the quantity of fatty acids produced, though the type did change, which is an area for further research.
For the quantity alone, what mattered more was the input to the system: in other words, what type of food people ate.
Since the large intestine is an environment without oxygen, microbes need to perform fermentation to break down undigested food. When they do this to complex carbohydrates – which are found in foods like oatmeal, starchy vegetables, and beans – the microbes produce the short-chain fatty acids as a byproduct: primarily acetate, propionate, and butyrate. The human body can then absorb these fermentation products from the large intestine and combine them with oxygen to use as energy.
While these fatty acids are known to influence human digestive, metabolic, and immune systems, the gut microbiome is enormously complex, and much about how this process works is still unknown. The accurate quantification of these fatty acids is a critical step to better understanding the relationship between the gut microbiome and human health, Cremer said.
To derive these numbers, the researchers first studied the efficiency of microbial fermentation in the lab. Tracking the growth and metabolism of major gut microbes over time, they determined the amount of carbohydrates they consume and fermentation products released. Building on these numbers, they analyzed the diet composition to determine the daily amount of fermentation products provided by the host’s gut microbes.
The researchers integrated data from different diet and health studies to determine diet variations, including a reference study in the United Kingdom taken in the 1970s and more recent diet composition data in the U.S. from the National Institutes of Health. The researchers compared these results to data from the Hadza, a group of hunter-gatherers in Tanzania, whose diet more closely resembles what humans ate for centuries before modern times.
In addition, the researchers analyzed the fermentation product exchange in mice, which validated their measurement system. They did find, however, that mice derive at least 20% of their energy from these fermentation products – a much higher rate than humans. Using mice in gut microbiome research is highly valuable, the authors noted, but scientists should take this difference into account.
The new quantification system described in this study should enable researchers to answer new questions, Cremer said, and his team is currently working to understand what happens when gut microbes process proteins.
“Increasingly in Western diets, protein consumption is going up,” he said. “Protein is not so important for fermentation products, but there’s a potential to affect human health because bacterial protein utilization can release a lot of toxins.”
Cremer is also a member of Bio-X.
Additional Stanford co-authors on this study are Richa Sharma and Griffin Chure, both post-doctoral scholars in biology.
This research received support from the National Institutes of Health, the National Science Foundation, the Swiss National Science Foundation, and Innosuisse.
