Methane Producing Gut Microbes Unlock Extra Energy From High-Fiber Diets

In the jungle of microbes living in your gut, there’s one oddball that makes methane. 

This little-known methane-maker might play a role in how many calories you absorb from your food, according to a new study from Arizona State University.

The entire ecosystem of microbes is called the microbiome. Some people’s gut microbiomes produce a lot of methane, while others produce hardly any.

The study found that people whose gut microbiomes produce a lot of methane are especially good at unlocking extra energy from a high-fiber diet. This may help explain why different individuals get different amounts of calories from food that makes it to the colon.

The researchers note that high-fiber diets are not the villain here. People absorb more calories overall from a Western diet of processed foods, regardless of methane production. On a high-fiber diet, people absorb fewer calories overall — but the amount varies according to methane production.

Insights from this study could be a foundation for personalized nutrition.

“That difference has important implications for diet interventions. It shows people on the same diet can respond differently. Part of that is due to the composition of their gut microbiome,” says Blake Dirks, lead author of the study and graduate researcher at the Biodesign Center for Health Through Microbiomes. Dirks is also a PhD student in ASU’s School of Life Sciences.

The study, published today in The ISME Journal, found that methane-producing microbes called methanogens are associated with a more efficient microbiome and higher energy absorption from food.

One of the microbiome’s main jobs is helping to digest food. Microbes ferment fiber into short-chain fatty acids, which the body can use for energy. In the process, they produce hydrogen. Too much hydrogen pauses their activity, but other microbes can help keep this process going by using up the hydrogen.

Methanogens are hydrogen-eaters. As they consume hydrogen, they create methane. They are the only microbes to make this chemical compound.

“The human body itself doesn’t make methane, only the microbes do. So we suggested it can be a biomarker that signals efficient microbial production of short-chain fatty acids,” says Rosy Krajmalnik-Brown, corresponding author of the study and director of the Biodesign Center for Health Through Microbiomes.

The research suggests that these microbe interactions affect the body’s metabolism. The team found that higher methane production was associated with more short-chain fatty acids being made and absorbed in the gut.

In the experiment, researchers provided each study participant with two different diets. One diet had more processed foods and low fiber. The other diet was high in whole foods and fiber. Both diets contained the same proportion of carbs, proteins and fats.

ASU researchers collaborated with the AdventHealth Translational Research Institute to use a unique facility for their experiment. For six days, each participant lived inside a sealed, hotel-like room called a whole-room calorimeter that measured their body’s metabolism and methane output. 

Other experiments rely on a single-breath test to measure methane. The team’s method can gather more comprehensive data. It captures methane that the body emits as breath and gas (ahem), rather than just breath, and over a continuous period, rather than a single moment.

“This work highlights the importance of the collaboration between clinical-translational scientists and microbial ecologists. The combination of precise measures of energy balance through whole-room calorimetry with ASU’s microbial ecology expertise made key innovations possible,” says Karen D. Corbin, a co-author and associate investigator at the institute.

Data from blood and stool samples measured how much energy participants’ bodies absorbed from food and tracked their microbes’ activity. The team compared data from people whose gut microbiomes produced high versus low methane levels.

On the high-fiber diet, almost everyone absorbed fewer calories than they did on the processed-food diet. But those whose guts produced more methane absorbed more calories from the high-fiber diet than those whose guts produced less methane.

This research creates a foundation for future studies and medical treatments.

“The participants in our study were relatively healthy. One thing that I think would be worthy to look at is how other populations respond to these types of diets — people with obesity, diabetes or other kinds of health states,” Dirks says.

Study participants weren’t intended to lose weight during the experiment, though some lost a little while on the high-fiber diet. The team is interested to see how methanogens in the microbiome impact a diet that is intentionally aimed at helping participants lose weight.

“You can see how important it is that the microbiome is personalized,” Krajmalnik-Brown says. “Specifically, the diet that we designed so carefully to enhance the microbiome for this experiment had different effects on each person, in part because some people’s microbiomes produced more methane than others.”

Reference: Dirks B, Davis TL, Carnero EA, et al. Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy. ISME J. 2025;19(1):wraf103. doi: 10.1093/ismejo/wraf103

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