A team of researchers has examined how shifts in the gut environment shape the composition and activity of gut bacteria, along with the influence of diet in this context. The study was conducted as part of the PRIMA research project, led by DTU National Food Institute, in collaboration with the Department of Nutrition, Exercise and Sports at the University of Copenhagen and KU Leuven in Belgium. Published in Nature Microbiology, the research could ultimately help explain why individuals have distinct gut bacteria and why we may respond differently to the same foods.
A journey through the gut
In 2021, 50 study participants swallowed a small capsule the size of a fingertip while eating their breakfast. This capsule then embarked on its journey through the gut, collecting data on pH, temperature, and pressure as it travelled through the stomach, small intestine, and colon. Within 12 to 72 hours, the capsule exited the body with the stool. Researchers discovered that both the gut environment and transit times varied significantly between individuals.
“For instance, we observed that the capsule took two hours to pass through the small intestine in some individuals and 10 hours in others. Since we already know that most nutrients are absorbed in the small intestine, differences in transit time likely affect both how much nutrition is absorbed and how much reaches the colon, where gut bacteria come into play,” explains Associate Professor Henrik Roager from the Department of Nutrition, Exercise and Sports at the University of Copenhagen, who led the study.
Previously, gut activity was often studied using stool samples correlated with dietary intake. However, the capsule provides a far more detailed understanding of how the environment changes throughout the gut.
“The capsule allows us to gather data that helps explain individual differences in digestion, nutrient absorption, and stool patterns. It offers a much deeper insight than what dietary patterns and stool samples alone can reveal,” adds Associate Professor Henrik Roager.
The gut environment: from acidic stomach to alkaline small intestine
During its journey, the capsule first encounters the acidic stomach, where it measures a low pH due to stomach acid breaking down food. It then moves into the small intestine, where bicarbonate released by intestinal cells neutralises the stomach acid and facilitates nutrient absorption. In the colon, undigested food residues are fermented by gut bacteria, producing fatty acids that lower pH levels. However, as these fatty acids are absorbed through the colon wall and bacterial activity changes, the pH gradually rises.
“All these pH changes are recorded by the capsule, allowing us to estimate how long food stays in various parts of the gut. Since pH is a crucial factor for bacterial growth and activity, it made sense to observe that the gut environment and pH are linked to differences in the composition and activity of gut bacteria. In other words, the environmental conditions in our gut likely explain why our gut bacteria differ,” says Henrik Roager.
The Impact of Gut Transit on Health
The study also revealed that longer transit times through the colon were associated with gut bacteria producing substances derived from protein metabolism. Some of these substances are known to negatively impact kidney and cardiovascular health. Transit times vary significantly between individuals, influenced by genetic factors as well as external factors like stress, physical activity, hydration, and dietary fibre intake.
“By measuring participants’ diets and urine samples over nine consecutive days, we observed a correlation between higher daily fibre intake and lower levels of harmful substances in urine. This aligns with our earlier research, suggesting that increasing dietary fibre intake can quickly influence gut bacteria’s production of these harmful substances,” says Associate Professor Martin Frederik Laursen from the DTU National Food Institute.
“However, it’s important to note that not everyone responds to dietary fibre in the same way. We’re only beginning to understand the reasons behind these differences, with individual variations in the gut environment likely playing a key role. More research is needed to understand how the gut environment influences bacterial composition and activity,” says Martin Laursen.
Personalised Nutrition
The new findings could significantly impact future dietary guidance, according to Associate Professor Henrik Roager.
“Our results show that we are all unique – even in our gut,” he says. “We often assume that we digest food and absorb nutrients in the same way, but our study suggests otherwise. The research provides further evidence that we respond differently to food, and differences in the gut environment may play a crucial role.”
The findings highlight the importance of gut physiology and the environment in understanding individual differences in the human gut microbiome and metabolism.
