Colonic transit—the time it takes food to move through the gut—can be evaluated clinically but experts disagree on what these measures mean for health. A recent study, published in Nature Microbiology, has found associations between colonic transit time and aspects of patients’ gut microbiota in terms of composition, diversity, and also metabolic products. Researchers found that a longer colonic transit time correlated with high microbial richness, but also with higher urinary levels of potentially harmful metabolites. A shorter transit time, on the other hand, correlated with higher levels of metabolites that might signal renewal of the colonic mucosa. The study’s first author, Dr. Henrik M. Roager, answered questions for GMFH editors by email.

What motivated this study?

I attended a European Molecular Biology Laboratory (EMBL) conference on the human microbiome in 2015 where 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. While I was sitting there, it struck me that I maybe could access data that would enable me to validate, elaborate and extend their findings.

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 contacting our collaborators to combine the measurements of the colonic transit time of these adults together with their gut microbiome profile and urine metabolite profile. We were fortunate that all collaborators agreed on the plan.

 What did you find out about colonic transit time, gut microbiota diversity, and bacterial metabolites?

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. This suggests that a rich bacterial composition in the gut is not necessarily synonymous with a healthy digestive system in cases where it indicates that food takes a long time to travel through the colon.

In these associations, which one do you think was causal?

Although we did not prove causality, we do think colonic transit time is the driving force behind the increased gut microbial diversity and systemic circulation of protein degradation products.

How might diet have affected your measures?

We checked that our findings were not confounded by the participants’ habitual diet. However, having said that it is known that transit time is related fiber intake, water intake and physical activity, which may explain some of the inter-individual differences.

How does this modify the concept that diversity is a general indicator of a healthy gut microbiota?

Our findings expand the current understanding of microbial richness as a measure of a healthy ecosystem, as we found that high richness can be confounded by a long colonic transit time. Thus a high gut microbial richness does not per se imply a healthy gut microbial ecosystem if it is associated with (or possibly even results from) a prolonged colonic transit time.

What is the take-home message about colonic transit time?

The take-home message is that colonic transit time is strongly related to the gut microbial composition, diversity and metabolism. Therefore future studies should consider this very important factor. Including this measure may also improve the identification and reproducibility of microbial biomarkers.

What are the limits of your findings?

As our study is limited to statistical associations in humans, we cannot make a final conclusion on causality. We only know transit time, microbial diversity, and metabolites are strongly interrelated. Furthermore, additional studies are needed to understand how the metabolites accompanying a long transit time are related to health.


Roager HM, Hansen LBS, Bahl MI, et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nature Microbiology. 2016; 1. doi:10.1038/nmicrobiol.2016.93