Why do two people eat the same berry mix or salad and feel different effects? New research published in Nature Microbiology suggests the answer may come down to a quiet but powerful force inside the gut: the enzymes produced by our microbiome.
Many beneficial plant compounds found in foods like berries, nuts and vegetables are not active in the form we eat them. They first need to be transformed by gut bacteria. In one of the largest efforts to map this process, an international team analyzed how 775 plant nutrients interact with bacterial enzymes. The researchers found that, on average, about 70% of the enzymes in the human gut have the potential to take part in this “second digestion.”
But the most striking finding was how individual this process is. The team showed that people differ widely in which enzymes their gut microbes carry, which means they also differ in their ability to convert certain plant compounds into useful forms. These patterns varied not only among individuals but also by geography and dietary habits.
“Our results show how crucial microbiome function is for the effects of healthy nutrition,” said Gianni Panagiotou, a senior author of the study.
To understand how this process changes in disease, the researchers used artificial intelligence to compare enzyme patterns from more than 5,500 gut microbiomes around the world, including samples from people with inflammatory bowel disease, colorectal cancer and nonalcoholic fatty liver disease. They found that the microbiome’s ability to process plant compounds was significantly reduced in these groups.
The team then tested specific bacterial strains in the lab and confirmed that certain microbes are especially important for converting particular dietary compounds. These insights, the authors note, could eventually support nutrition strategies tailored to an individual’s microbiome. The goal would not be personalized diets that promise specific outcomes, but a more realistic approach: understanding why foods work differently for different people.
The study’s authors say the findings reinforce a growing theme in nutrition research. A healthy diet matters, but the biology of the gut helps determine how much benefit someone receives from certain plant foods. Future work may help identify which nutrients or probiotics support these microbial pathways, especially for people whose microbiomes have lost some of this processing capacity.
This research was supported by several European and international science agencies, including Germany’s national research foundation, the European Union and partners in China.