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In his presentation, “Microbiome Modulation Through a Non-Industrialized Diet,” at the 132nd Congress of the German Society for Internal Medicine (DGIM) 2026 in Wiesbaden, Germany, Stephan C. Bischoff, MD, professor and director of the Department of Nutritional Medicine and Prevention, University of Hohenheim in Stuttgart, Germany, said, “Microbiome research hasn’t really made its way into clinical practice yet.” Although research in this field has continued for more than 10 years, the practical knowledge available to clinicians is still limited.

“And what we had pinned our hopes on — probiotics — is increasingly being called into question,” Bischoff said. According to him, this is partly because, while the numerous publications in top-tier journals contain vast datasets on the complex gut microbiome, hardly anyone understands them.

“It would be more transparent if we didn’t try to mimic every single bacterium or sequence but instead focused on the function,” Bischoff said. He noted that this would make it possible to evaluate natural or therapeutic factors without having to delve into every detail of microbiome research.

Gut Function

Citing a recent paper from the International Scientific Association for Probiotics and Prebiotics, Bischoff proposed a definition of gut health as “a state of normal gastrointestinal (GI) function without active GI disease and gut-related symptoms that affect quality of life.”

He explained that the contribution of gut microbiota to host energy production varies, but it is typically estimated to provide up to 10% of a human’s daily energy requirement, depending largely on dietary patterns. For example, individuals consuming non-Western dietary patterns show significantly higher proportions than those consuming Western diets, in some cases reaching 10%. This likely depends on dietary habits, that is, “how much we rely on this bacterial support for digestion,” said Bischoff.

Over the past several years, researchers have associated an increasing number of chronic diseases with dysbiosis or disruptions in the gut microbiome.

“Nearly all chronic diseases are associated with dysbiosis…. When we are sick, this is reflected at the microbiome level,” Bischoff said.

Possible causes of dysbiosis include the following:

• Unhealthy Western-style dietary patterns
• Repeated use of antibiotics
• Severe or recurrent GI infections, including postinfectious irritable bowel syndrome
• Medications beyond antibiotics alone

Dietary Interventions

Bischoff emphasized that dietary interventions are among the most promising strategies to restore a healthier gut microbiome, while acknowledging that environmental factors, lifestyle, probiotics, prebiotics, postbiotics, and fermented foods also influence microbiome composition.

He highlighted that recent guidelines increasingly support low-FODMAP diets, where FODMAP is an acronym for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. Bischoff described the approach as an extension of low-sugar dietary strategies that have become an important component in the management of irritable bowel syndrome.

He then reviewed three dietary approaches that he considered particularly promising for improving gut microbiome health.

Mediterranean Diet (MD)

Regarding the MD, Bischoff said, “It doesn’t really matter which version you choose or whether you opt for a combination. They’re all effective.”

Bischoff attributed these effects largely to lower sugar intake, lower FODMAP content, higher fiber intake, and reduced consumption of highly processed foods.

He cited findings from a 2018 study published in the New England Journal of Medicine showing that participants who followed MD for a median of 5 years showed reductions in cardiovascular risk. He noted that the extent of the benefit exceeded what is typically achieved with medication alone.

The reported findings included the following:

• Olive-oil-based MD: hazard ratio (HR), 0.70 (95% CI, 0.53-0.91; P = .009)
• Nut-based MD: HR, 0.70 (95% CI, 0.53-0.94; P = .02)

The primary endpoints included acute myocardial infarction, stroke, and death from cardiovascular events. 

One proposed mechanism underlying these effects is the production of short-chain fatty acids (SCFAs) and the resulting improvement in intestinal barrier function. However, Bischoff noted that this mechanism depends on the composition of the gut microbiome, meaning that individuals may respond differently to an MD. According to him, beneficial effects require the presence of bacteria capable of generating SCFAs from available nutrients. The gut microbiome therefore influences how effectively dietary fiber is metabolized into SCFAs and, consequently, the extent of the benefit. 

Restore Diet

Bischoff also discussed the Restore Diet, a primal style evaluating the diet based on an approach derived from eating patterns similar to the Paleo diet. A crossover study in which researchers investigated the effects of the Restore Diet was based on the high-fiber diet of people living in the jungles of Papua New Guinea. Participants who had previously followed a Western diet switched to the Restore Diet for 3 weeks. Researchers found that individuals consuming less healthy diets before the study had gut microbiome profiles that differed from those of people following healthier diets. After switching to the Restore Diet, the composition of the gut microbiome was changed.

To determine whether these microbiome changes affect health, researchers examined metabolic markers that are relatively easy to measure. Levels of SCFAs increased, which Bischoff said suggested that the high-fiber diet was being metabolized effectively. At the same time, inflammatory markers, including C-reactive protein and calprotectin, as well as cholesterol levels, decreased, while established metabolic parameters improved.

African Heritage Diet (AHD)

A similar study was published in 2025 in Nature Medicine. Researchers examined a dietary pattern derived from the traditional diet of people living in Tanzania, referred to as AHD. Compared with the Restore Diet, this approach emphasized not only high fiber intake but also a large number of fermented foods. Typical foods included:

• A traditional breakfast of millet porridge with sour (fermented) milk or taro
• Ugali, a thick porridge made from cornmeal or cassava flour, served with okra and green vegetables known as mchicha
• Kiburu, a dish of boiled green plantains with kidney beans and avocado
• Mbege, a traditional fermented banana beer of Tanzania’s Chagga people, hand-brewed using specific “cow bananas” and sprouted finger millet flour

The intervention lasted 1-2 weeks and included participants who were relatively healthy but had some metabolic abnormalities. Researchers found that switching from AHD to a Western-style diet negatively affected several metabolic pathways associated with noncommunicable diseases and promoted a proinflammatory state. In contrast, switching from a Western-style diet to AHD or consuming fermented beverages produced anti-inflammatory effects. Some immune and metabolic changes persisted at follow-up, suggesting lasting effects despite the short duration of the intervention.

“These dietary interventions have potential that we do not yet fully understand, and this warrants further research,” Bischoff said.

Conclusion

Bischoff concluded that fermented foods and foods high in fiber could play a valuable role in counteracting the reduced diversity of and increased inflammation commonly observed in industrialized societies. He also emphasized limiting sugar and highly processed foods. According to Bischoff, these resource-conserving dietary patterns may benefit not only human health but also environmental sustainability.

This story was translated from Coliquio, part of the Medscape Professional Network.