How we got captivated by colonic transit time

The story about being at the right place at the right time, grasping the idea, having access to the right data and collaborate with a great multidisciplinary team
How we got captivated by colonic transit time

We recently showed that the time it takes for ingested food to travel through the human gut – also called transit time – is a key factor for the composition and activity of the intestinal bacteria.

But how did we get there? Well, it all started back in June 2015 when I was attending the EMBL conference on ‘The Human Microbiome’ in Heidelberg, Germany. Prof. Jeroen Raes gave a talk presenting recent data from his lab showing how the Bristol stool scale, a stool consistency scale which reflects colonic transit time, strongly associates with the gut microbiota composition.

EMBL conference

It all started at the EMBL conference on ‘The Human Microbiome’ in Heidelberg, Germany in June 2015 (Photo: Henrik M. Roager).

As a PhD student, eager to learn, I was taking notes as it struck me that I maybe had a chance to validate, elaborate and extent their findings by also looking at microbial activity in relation to transit time. So I noted down that I had to check their publication in the journal Gut (Vandeputte et al., 2015), which was published online the exact same day.

From my notebook with a reminder to check the publication in the journal Gut (Photo: Henrik M. Roager).

When I read their paper I was puzzled by their finding that a slow colonic transit associates with high gut microbial richness, which is generally thought to reflect a healthy gut microbial ecosystem. Did that mean that it is healthy to be constipated?

I needed to figure this out. So after a great conference, I returned to my office and started approaching people with my ideas. At that time I was involved in two ongoing dietary human intervention studies, through a large research collaboration headed by my supervisor, Prof. Tine Rask Licht ( I had already performed metabolomics on baseline urine samples obtained from participants of these interventions and I knew that their transit time and gut microbiome profiles had been determined as well. Therefore, I decided to suggest to my supervisor that we should contact our collaborators to combine the measurements of the colonic transit time of these adults together with their gut microbiome profile and urine metabolite profile. My preliminary results convinced her and we were fortunate that all collaborators agreed on the plan.


Thus, in the summer of 2015, I started investigating the importance of colonic transit time on the gut microbial composition, diversity and metabolism, and already in October the main findings of our work were emerging.

First of all we confirmed the finding of Jeroen Raes’ lab, since we found a very strong positive association between colonic transit time and gut microbial richness. But even more striking, we were amazed that more than 10% of the molecular features measured in urine by liquid chromatography mass spectrometry were associated with transit time, suggesting that colonic transit time is an important variable to consider in both gut microbiota and metabolomics studies.

Importantly we found that although a long transit time associates with high microbial richness, it also gives rise to higher levels of potential deleterious protein degradation products, suggesting that a rich bacterial composition in the gut is not necessarily synonymous with a healthy digestive system, if it is an indication that food takes a long time to travel through the colon.

These findings were condensed in the manuscript, which was written in November/December and submitted just before I handed in my PhD thesis, right before Christmas.

Looking back, it only took one year (!) from idea to publication. I think it was a result of being the right place at the right time, grasping the idea, having access to the right data and collaborate with a great multidisciplinary team, which may be today’s recipe for doing great research.

Henrik M. Roager, Lea B. S. Hansen, Martin I. Bahl, Henrik L. Frandsen, Vera Carvalho, Rikke J. Gøbel, Marlene D. Dalgaard, Damian R. Plichta, Morten H. Sparholt, Henrik Vestergaard, Torben Hansen, Thomas Sicheritz-Pontén, H. Bjørn Nielsen, Oluf Pedersen, Lotte Lauritzen, Mette Kristensen, Ramneek Gupta and Tine R. Licht (2016). Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nature Microbiology, doi: 10.1038/nmicrobiol.2016.93

Poster Image Photo credit:

Please sign in or register for FREE

If you are a registered user on Nature Portfolio Microbiology Community, please sign in