Gut microbes, diet and health

The research group's vision is to understand the mechanisms by which the gut microbiota contributes to food digestion and health, and to accelerate this knowledge toward personalised nutrition strategies and novel food products for improvement of health and wellbeing.


The focus of the research group is to understand how diet shapes the gut microbiome, how gut microbes digest our food, and how the resulting small diet-derived molecules (metabolites) interact with our physiology in health and disease. Our work involves multiple disciplines including nutrition, chemistry, microbiology and bioinformatics.

We conduct human dietary intervention studies and cohort studies and profile the metabolome (collection of all small molecules) in stool, blood and urine using targeted and untargeted liquid chromatography mass spectrometry (UPLC-MS) based metabolomics.

Furthermore, we collaborate with leading microbiome researchers around Europe and experts in immunology and intestinal host receptors to elucidate host-microbial cross-talk.


Research projects


Diet-derived microbial metabolites to modulate gut motility in infants

MotilityThe Sapere Aude project will generate new knowledge about how gut microbes via production of small molecules can impact gut motility in infants.

Infantile colic, functional constipation and diarrhoea are stressful conditions in early life associated with transient dysregulation of intestinal motility, which may depend on the interplay between nutrition and the gut microbiota.

Infantile colic, functional constipation and diarrhoea are stressful conditions in early life associated with transient dysregulation of intestinal motility, which may depend on the interplay between nutrition and the gut microbiota.

The purpose of the project is to conduct an infant cohort study following 125 infants’ progression from milk to solid foods, concurrent with their progression in gut microbiota diversity, with the aim of identifying diet-dependent gut microbial metabolites, which affect intestinal motility. If successful, this knowledge may lay the foundation for innovative strategies to prevent and alleviate stomach ache in infants.

Involved in the project


Associate professor Henrik Munch Roager

PhD Fellow Gladys Thingstrup Mathieu


Lindsay Hall, TU München

Catherine Stanton, APC Microbiome Ireland, University College Cork

Thue W. Schwartz, Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen

Funded by

Independent Research Fund Denmark – Sapere Aude: DFF Starting Grant.

Period:  1 June 2021 - 31 May 2025.


Associate professor Henrik Munch Roager



Towards Personalized dietary Recommendations based on the Interaction between diet, Microbiome and Abiotic conditions in the gut

PRIMAThe project will generate more knowledge of the role the gut microbiota plays when people react differently to the same diet.

Focus areas

To investigate how the gut microbiota and environmental (abiotic) factors in the gut shape personal responses to food.

To investigate how and why digestion of food by the gut microbiota into small molecules (metabolites) varies from individual to individual.

About the project

You are what you eat, but why don’t we all react to foods in the same way?

Our guts contain a large community of microbes, and when we eat something and our microbes digest the food, they create products called microbial metabolites. These metabolites affect our immune system, our hormone balance, our health and possibly even our mood. When looking at dietary advice, there is no good ‘one-size fits-all’ solution.

In PRIMA, we want to explore the effect of diet from a different perspective, namely from your gut. We believe we can predict an individual’s response to a given diet based on fundamental factors such as pH and transit time in the gut, which govern the microbial responses. This way, we will develop better dietary advice tailored to a given person.

Involved in the project


Associate Professor Henrik Munch Roager

Professor Lars Ove Dragsted

PhD Fellow Nicola Procházková


Tine Rask Licht, DTU Fødevareinstituttet

Thue Schwartz, Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen

Jeroen Raes, Katholieke Universiteit Leuven

Abigail Johnson, BioTechnology Institute, University of Minnesota

Funded by

Novo Nordisk Fonden

Period: February 2020 – January 2026.



Telephone: +45 2917 6795







Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes
Published in Microbiome in 2022: we found that one group of Danish overweight individuals (dominated by Bacteroides bacteria), which had higher body weight, also had less energy in stool (per gram dried faeces), suggesting that this group of individuals have a gut microbiome that is more efficient in extracting energy from the diet. 

Advancing human gut microbiota research by considering gut transit time
Published in Gut in 2022: we argue that by taking gut transit time into account, we can advance our understanding of diet–microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time.

Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut
Published in Nature Microbiology in 2021; we demonstrated that Bifidobacterium species promoted by breastmilk produce aromatic lactic acids via a previously unrecognized aromatic lactate dehydrogenase in the infant gut. These metabolites can impact immune function via two different host receptors, suggesting that they may be important for immune development in early life. 

Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake
Published in Gut in 2020; we demonstrated that when switching to a Mediterranean diet, subjects reduced their blood cholesterol depiste unaltered energy intake and changed their gut microbiome and metabolome, which may be relevant in future strategies for the improvement of metabolic health.

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial
Published in Gut in 2019, we demonstrated in Danish overweight adults that a wholegrain-rich diet compared with a refined grain diet, did not alter insulin sensitivity and the gut microbiome, but reduced body weight and systemic low-grade inflammation.




Members of research group

Name Title Phone E-mail
Gladys Thingstrup Mathieu PhD Fellow +4535334217 E-mail
Henrik Munch Roager Associate Professor +4535324928 E-mail
Malte Studnitz Jørgensen PhD Fellow +4535328985 E-mail
Nicola Procházková PhD Fellow +4535320472 E-mail