The power of gut enzymes: why healthy eating affects everyone differently

The Microbiome: Our Second, Invisible Chemical Factory

Many healthful plant compounds, such as those found in berries, nuts, or vegetables, are not immediately active in the form we consume them. They first need to be chemically transformed by the countless microorganisms in our gut, via a kind of »second digestion.« The international research team systematically mapped 775 different phytonutrients and their conversion by gut bacterial enzymes. On average, 70 percent of all enzymes in our microbiome are potentially involved in this process—far more than previously known.

However, the study also revealed a crucial challenge: the »chemical cookbook« of gut bacteria is highly individual. Whether a person can optimally convert a plant compound into its active form depends on which specific enzymes are present in their gut flora. The enzymes, and this capability, vary not only from person to person but also according to geographic origin and dietary habits.

Prof. Dr. Gianni Panagiotou, Professor for »Microbiome Dynamics« at the University of Jena and the Leibniz-HKI, emphasizes the importance of multidisciplinary collaboration: »Our results show how crucial microbiome function is for the effects of healthy nutrition. Only through cooperation between bioinformaticians, chemists, disease model specialists and microbiologists were we able to capture the full diversity and dynamics of gut bacteria.«

When the »Cookbook« Malfunctions in Disease

The researchers used artificial intelligence to compare enzyme profiles of healthy individuals and patients, including those with inflammatory bowel disease, colorectal cancer, or non-alcoholic fatty liver disease. The results were clear: in patients with these chronic conditions, the microbiome’s potential to process healthy foods was significantly reduced.

The AI models could predict with high accuracy whether an individual was healthy or diseased based on the presence of certain bacterial enzymes. For example, colorectal cancer patients lacked a key enzyme needed to process a certain plant compound, which was abundant in healthy individuals. This reduced conversion capacity may explain why general dietary recommendations often fail to have the expected effect in chronically ill patients.

The Path to Tailored Nutrition

To unravel these complex interactions, the team combined bioinformatics with the analysis of over 5,500 human gut microbiomes from around the world. Promising bacterial strains were then tested in the lab to experimentally confirm the predicted conversion reactions.

These groundbreaking insights lay the foundation for the nutrition medicine of the future. Instead of universal recommendations, analyzing an individual’s microbiome could soon enable precise, personalized nutrition plans. The goal is either to supply the microbiome with the right nutrients or to »seed« it with probiotics that carry the precise enzymes needed for optimal conversion of beneficial plant compounds.

Excellence in Collaborative Research

The study directly aligns with the core research topics of the Cluster of Excellence »Balance of the Microverse« in Jena: the systematic study of microorganisms and their interactions with the host. The research highlights that a balanced microbiome is crucial not only in its composition but also and especially in its function, in this case, its ability to chemically process food. The scientists provide a key building block for promoting this balance through targeted, individualized interventions.