Researchers have created a model that follows food beyond traditional calorie calculations, incorporating the role of gut microbes in digestion.
Food labels make calorie counts look straightforward. The number listed per serving is calculated from the food’s fat, carbohydrate, and protein content.
In reality, the digestive process is much more complex. As food moves through the body, it interacts with trillions of microbes in the gut that can affect how many calories are ultimately absorbed.
Researchers at Arizona State University have developed a mathematical model called DAMM, short for digestion, absorption, and microbial metabolism, to better capture this process. The model tracks food as it moves through the digestive system, estimating what is absorbed by the body, what reaches the colon, and how gut microbes transform the remaining material into substances that are either absorbed or eliminated.
The researchers say the model could improve understanding of obesity, diabetes, and other metabolic disorders by revealing how different diets influence both the body and the microbial communities living in the colon.
Gut Microbes Change the Calorie Equation
With further development, DAMM could help health care providers create more personalized nutrition plans.
“Digestion is not just a human process—it is a collaboration between our bodies and trillions of microbes living in the gut,” said Professor Rosa Krajmalnik-Brown. “DAMM gives us a powerful new way to quantify how those microbial partners contribute to human health and energy balance and also points at the importance of properly feeding our gut microbes.”
Krajmalnik-Brown directs the Biodesign Center for Health Through Microbiomes and is a professor in ASU’s School of Sustainable Engineering and the Built Environment.
The research team also included Professor Bruce Rittmann, director of the Biodesign Swette Center for Environmental Biotechnology and a Regents Professor of environmental engineering at ASU, along with lead author Taylor Davis, a graduate research assistant. The project was conducted in collaboration with the AdventHealth Translational Research Institute in Orlando, Florida.
Introducing DAMM: A New Digestive Modeling Tool
The findings were published in PLOS One.
For more than 100 years, scientists have used Atwater factors to estimate how much energy people obtain from food. This method calculates calories by multiplying the amounts of protein, carbohydrates, and fat by their average metabolizable energy values.
While widely used, the approach does not account for the role of gut microbes. It cannot capture how different diets influence microbial activity or how microbes convert fiber and other undigested material into compounds such as short-chain fatty acids in the colon.
The new work builds on a controlled feeding study that explored the role of the gut microbiome in human energy balance. The gut microbiome consists of the bacteria and other microorganisms that live throughout the digestive tract.
Why Fiber-Rich Diets Affect Energy Absorption
In that study, healthy adults followed one of two carefully designed diets. One was a microbiome-enhancer diet rich in fiber and resistant starch (less processed foods and foods with larger particle size). The other reflected a more typical Western diet with lower levels of those components (more processed foods and smaller particle size). Participants eating the Western diet absorbed about 116 more calories per day than those on the high-fiber diet, despite reporting no increase in hunger among the high-fiber group.
“What is truly unique about the DAMM model is that it quantitatively links human metabolism to the metabolism of the microorganisms in the colon in a way that matches the results from the clinical study and provides fundamental insight into how the microbial community works in partnership with the human host,” Rittmann said.
The model begins by breaking a diet into its protein, carbohydrate, and fat components. It then estimates how much usable energy from those nutrients is absorbed in the upper digestive tract.
DAMM next tracks the remaining material into the colon, where gut microbes break down food that escaped earlier digestion. This process generates short-chain fatty acids that can be absorbed and used as an additional energy source. The model also includes methane production by microbes known as methanogens.
How DAMM Tracks Human and Microbial Metabolism
Microbial activity contributed a meaningful share of total energy. According to the model, short-chain fatty acids absorbed from the colon provided about 140 calories per day on average, representing roughly 7.4% of total usable energy. About 85% of usable energy came from the upper gastrointestinal tract, while the remaining 15% came from the lower gastrointestinal tract, where microbes play a major role.
When the researchers compared DAMM with data from the controlled diet study, the model estimated calorie absorption more accurately than the traditional Atwater method. The standard approach tended to underestimate absorbed calories, while DAMM more closely matched the measured results.
The model also identified important differences between the high-fiber and lower-fiber diets. The microbiome-enhancer diet delivered more fermentable material to the colon, giving microbes additional fuel to produce short-chain fatty acids.
Short-Chain Fatty Acids and Calorie Absorption
DAMM projected greater short-chain fatty acid production on the microbiome-enhancer diet, matching the pattern observed in the clinical study, where higher levels of these compounds were detected in blood serum and fecal samples.
Short-chain fatty acids are not simply byproducts of digestion. They are produced when gut microbes ferment fiber and other food components that escape earlier absorption. Some of these fatty acids are then absorbed by the body and contribute to its energy supply. Even so, they represent only one part of the overall calorie equation. Although the microbiome-enhancer diet increased microbial activity and short-chain fatty acid production, it still resulted in fewer calories being absorbed overall.
DAMM allows researchers to separate these processes, distinguishing what the body absorbs directly, what gut microbes produce, and what is ultimately absorbed or excreted.
“The DAMM model is more than just a tool for characterizing diet,” Davis said. “It’s a framework designed to evolve. As we discover more on how diet, metabolism, and the microbes interact, the new insights can be incorporated into the model, allowing it to grow with us as we learn.”
Reference: “Modeling the microbial contribution to human energy balance using the Digestion, Absorption, and Microbial Metabolism (DAMM) model” by Taylor L. Davis, Blake Dirks, Elvis A. Carnero, Karen D. Corbin, Steven R. Smith, Andrew Marcus, Rosa Krajmalnik-Brown and Bruce E. Rittmann, 27 May 2026, PLOS ONE.
DOI: 10.1371/journal.pone.0347668
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