Gut microbiome has become a hot topic in the recent years and conversations about foods that are “good” or “bad” for our gut health are nowadays very common. But the truth is, our understanding of the world of microbes living in our gastrointestinal tracts, and how they interact with our diets and the gut environment is still evolving.

Some years ago, my supervisor – Associate Professor Henrik Munch Roager, together with other microbiome experts, showed that gut transit time, which is essentially the time it takes for foods to pass through the gut, is strongly related to the number of different microbes that we can find in stools. Transit time is also related to microbial activity and to whether the microbes break down complex carbohydrates and fibres to produce short chain fatty acids, which we know are extremely important for us, or whether they produce compounds that may potentially harm us. Simply put, how often we visit the bathroom may hint at what our gut microbes are up to.

To learn more about the relationship between the gut environment and its gut microbes, we carried out the PRIMA study, marking the start of my PhD journey. This study included 61 dedicated healthy volunteers around the Copenhagen area, who donated biological samples, and kept thorough food and poop diaries in the name of science! A unique aspect of our study was the use of ingestible SmartPills, which the participants swallowed. These capsules recorded transit time and pH throughout the gut and transmitted the data to a receiver worn near the belly giving us a real-time look at the gut environment. This was especially exciting from a research perspective. At that time, very few studies had combined SmartPills with microbiome analysis, essential for understanding the interactions between the gut environment and the microbes. Fortunately, technological advancements now also allow researchers to directly sample from different parts of the gut.

So, what did we find in the end?

In our paper now published in Nature Microbiology, we observed substantial differences in transit time and pH across the stomach, small intestine, and large intestine among individuals, highlighting just how personal our gut environments are. These variations appeared to be major drivers of the unique microbial and metabolic profiles seen in each participant, building on previous findings.

Our work also suggests a notable connection between fiber intake and levels of certain compounds known as uremic toxins, which are linked to various health effects. Fiber intake was associated with lower levels of these toxins. We also identified a range of metabolites that varied based on transit time. For instance, metabolites from coffee were linked with faster transit, while methane measured in breath was associated with longer gut passage. Altogether, these insights highlight that the gut environment is a highly personal factor, which should be considered when developing personalized dietary recommendations.

Since our study participants provided samples daily, we also explored day-to-day variations. We found that the overall gut microbiome composition was stable over the study period (9 days), whereas the microbial metabolites showed more fluctuations, possibly reflecting differences in food intake. This tells us as that collecting multiple samples over time from the same individual can give a more complete picture of the microbiome’s metabolic activity.

Reflecting on this journey, I recall my early PhD days reading beautifully laid-out scientific articles and wondering ifmy own work would one day be shared in the same way. Four years later, this becomes true, and I hope our study contributes to advancing our knowledge of the microbiome and, perhaps, inspires others.

We would like to thank to all our colleagues at DTU and KU Leuven, the students that helped along the way and not least the participants that made the study possible.