Our Approaches

Systems Biology

Understanding molecular mechanisms of host-microbial crosstalk in diseases

Novel techniques

Developing novel approaches for therapeutic manipulation of microbiome


Developing new software for microbiome data analysis

Our research

We work towards targeted modulation of human microbiota to improve human health

Microbiome Systems Biology research group investigates how our health and diseases are influenced by our gut microbiome. Our research is interdisciplinary, combining metagenomics (a technique to study gut microbiome), genomics, genetics, (meta)transcriptomics, and metabolomics to study host-microbial cross-talk.

Obesity, diabetes and several other metabolic disorders are increasing at an alarming rate across the globe. Although lifestyle changes and lack of physical activity are widely being blamed for this trend, the true cause for these diseases is more likely the interactions between human genetics, environmental factors and the human microbiome. For the past several years, researchers around the world have only been focusing on the interactions between two of these three factors, and ignoring the microbiome. The human gut microbiome plays an important role in our health, nutrition and well-being. Its imbalance may signify an unhealthy state of the host (like in Inflammatory Bowel Diseases), or worse, might be the reason for an ailment (like in Clostridium difficile infections). We aim to study the interactions between all three factors – human genetics, environmental factors and human microbiome – in order to understand the molecular mechanisms underlying metabolic disorders.

Our current externally funded studies investigate the role of gut microbiome in multiple sclerosis (Lundbeck Foundation), obesity (Novo Nordisk Foundation), alcoholic liver fibrosis (EU Horizon 2020), liver cirrhosis (EU Horizon 2020), ageing (Danish Independent Research Council) and producing antimicrobial peptides (Danish Independent Research Council). We have ongoing international collaborations studying the interaction between the gut microbiome and the host in the context of several diseases, including cardiometabolic diseases, chronic liver diseases and cancer.

Microbiome in liver diseases

We study the host-microbial cross-talk in liver fibrosis as partners in the MICROB-PREDICT, GALAXY and MicrobLiver consortia. We characterize the total gut microbiome consisting of bacteria, archaea, fungi and viruses to study it as one large community. We integrate genetics, metabolomics, proteomics and metatranscriptomics as additional layers to model the human-microbial holobiont.

Microbiome in colorectal cancer

We recently published on discovering robust biomarkers for colorectal cancer from the gut microbiome. We successfully validated them using qPCR measurements in an independent cohort. We are currently working on a meta-analysis of colorectal cancer microbiome studies.

Bioactive molecules from microbiome

We use bioinformatic approaches to discover bioactive molecules from the microbiome, for example antibiotics.

Inflammation, aging and microbiome

We investigate the gut microbiome in inflammation and aging (termed Inflammaging) as part of the Marie Curie Fellowship to post-doc Thorsten Brach.

Microbiome in multiple sclerosis

We use a spontaneous EAE mouse model to investigate the role of gut microbiome in the development of multiple sclerosis. This is a collaboration with Max-Planck Institute.