Food labels present calorie counts as fixed values, but new research suggests that the amount of energy people actually absorb from food depends partly on the microbes living in their gut. Scientists at Arizona State University have developed a mathematical model showing how gut bacteria can influence the number of calories the body extracts from meals.
The model, called DAMM, which stands for digestion, absorption and microbial metabolism, follows food from consumption through digestion to the energy ultimately absorbed or excreted. By accounting for both human digestive processes and the activity of trillions of gut microorganisms, it provides a more detailed understanding of energy absorption than conventional calorie calculations.
Why calorie labels fall short
For more than a century, nutritional science has relied on Atwater factors, which assign average calorie values to fats, carbohydrates and proteins. However, this approach does not fully account for how food structure, processing and fiber content influence digestion. It also largely overlooks the contribution of microorganisms in the lower digestive tract.
One important limitation involves the fermentation of fiber and resistant starch that pass through the small intestine without being digested. In the colon, gut bacteria convert these substances into short-chain fatty acids, some of which are absorbed into the bloodstream and provide additional energy that traditional calorie calculations may not adequately reflect.
To address this limitation, the Arizona State University researchers used DAMM to reanalyze a controlled feeding study conducted with the AdventHealth Translational Research Institute. Their goal was to connect dietary composition, microbial metabolism and the actual amount of energy absorbed by healthy adults under carefully monitored conditions.
Fiber-rich diet cut absorbed calories
Participants followed one of two carefully controlled dietary plans. The first was a microbiome-enhancer diet rich in fiber and resistant starch, featuring less-processed foods with larger particle sizes. The second resembled a typical Western diet, containing less fiber and more highly processed foods.
Although both diets were designed to provide the same total number of calories, participants following the Western-style diet absorbed approximately 116 more calories per day than those eating the fiber-rich meals. Importantly, participants on the high-fiber diet did not report greater hunger, suggesting that feelings of fullness do not necessarily correspond to calorie values printed on food labels.
Professor Bruce Rittmann explained that DAMM is distinctive because it quantitatively connects human metabolism with the metabolic activity of microorganisms in the colon. When researchers compared the model’s predictions with measured energy absorption, DAMM performed better than the traditional Atwater approach, which tended to underestimate the number of calories absorbed.
Microbes supply about 140 calories daily
The DAMM model divides energy extraction into two principal stages. First, it estimates how much protein, fat and carbohydrate the body absorbs in the upper gastrointestinal tract. It then tracks undigested material entering the colon, where microorganisms ferment it into substances including short-chain fatty acids and gases.
According to the analysis, short-chain fatty acids absorbed from the colon contributed approximately 140 calories per day on average, representing about 7.4% of total usable energy. Overall, the model estimated that roughly 85% of calories were obtained from the upper digestive tract and about 15% from the lower gut, where microbial activity plays a major role.
The researchers also incorporated methane production by methanogenic microorganisms, which can affect the availability of hydrogen and carbon for other metabolic processes. By accounting for these interactions, DAMM provides a more comprehensive picture of how food is converted into usable energy throughout the digestive system.
How fiber reshapes the energy balance
One particularly important finding concerns how fiber-rich diets alter the body’s energy balance. The microbiome-enhancer diet supplied more fermentable material to the colon, increasing microbial activity and short-chain fatty acid production compared with the Western-style diet.
Blood and stool samples from participants consuming the fiber-rich diet contained higher levels of these microbial byproducts. Nevertheless, their total net calorie absorption remained lower than that of participants following the lower-fiber Western diet. This demonstrates that increased microbial fermentation does not necessarily mean the human body receives more usable energy overall.
The model helps explain this apparent contradiction by distinguishing energy absorption in different regions of the digestive tract. Although gut microorganisms can extract additional energy from undigested food, digestion and absorption in the small intestine remain the dominant contributors. Food processing, texture and fiber content can influence how quickly and completely this earlier absorption occurs.
Toward personalized nutrition strategies
By integrating human digestion and microbial metabolism into a single quantitative framework, DAMM may help explain why individuals respond differently to diets containing the same labeled calorie amounts. It could also help researchers investigate how changes in fiber intake, food processing and meal timing influence the amount of energy the body absorbs.
Although the model is not yet ready to guide individualized dietary prescriptions, the researchers believe it could support more personalized nutritional approaches. In the future, dietitians may be able to consider not only calories and macronutrients but also an individual’s gut microbiome and the way their microorganisms process particular foods.
Future research will focus on validating DAMM in more diverse populations, age groups and dietary patterns while incorporating new findings from large-scale microbiome studies. As understanding of interactions between gut microbes and their human hosts improves, the model could be refined to better predict individual risks of obesity, diabetes and other metabolic conditions.
Lead investigator Rosa Krajmalnik-Brown emphasized that digestion involves cooperation between human cells and the microorganisms living within the digestive system. By measuring this relationship, DAMM challenges the assumption that identical calorie counts always translate into identical energy absorption and suggests that nourishing gut bacteria may be as important as considering the nutritional content of food itself.
