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The human microbiome

The billions of microbes that colonize the human body are collectively referred to as the microbiome. Most microorganisms inhabit our gastrointestinal tract, but also the skin, urogenital tract, and the respiratory tract are colonized by a wide variety of microbes.

The human microbiome plays a key role in human health by providing a natural barrier against pathogen colonization, supporting the provision of nutrients and exerting a critical role in shaping the mucosal immune system. Moreover, metabolites and innate immune stimuli produced by enteric microbes have numerous effects beyond the site of microbial colonization. Understanding what defines a healthy microbiome is fundamental to maintain healthy living and prevent disease development. 

Our department has a long track record on microbiome research that goes back to the early 1990’s, long before microbiome research became such a booming field of science. At present, microbiome research at our department is at the international forefront with on-site automated sample processing, next-generation sequencing facilities and extensive bioinformatic expertise. The microbiome research group has strong links with clinical departments within our MUMC+ and is involved in many national and international research consortia, including the ambitious Million Microbiomes of Humans Project. 

To further strengthen our Euregional collaboration on microbiome research and cross borders between research disciplines, we recently initiated the Euregional Microbiome Center ( together with research groups at Maastricht University Campus Venlo, Uniklink RWTH Aachen and the University of Liège.

There are three main themes within the microbiome research group.

  1. Development of a healthy microbiome
    In order to understand which dietary, environmental and host factors contribute to the development of a healthy microbiome, we study the microbiome establishment from birth onwards within the context of many population-based birth cohorts. By profiling the microbiome of thousands of babies, toddlers, children and adults, we aim to understand what drives the inter-individual variation in microbiota composition and function and how this relates to a healthy life. Next to these observational studies in humans, mechanistic in vivo and in vitro studies are conducted to understand the interactions between the microbiota, diet and the host. 
    This research line is embedded within large national and international consortia such as the NWO Carbohydrate Competence Center, the JPI Healthy Diet for a Healthy Life and the World Universities Network inVivo Planetary Health. Contract research with (international) companies as well collaboration with microbiome related institutions are part of our research program.
  2. The microbiome in health, disease and routine patient care
    Next to maintaining a healthy microbiome for a healthy life, the microbiome is a target for treatment of already manifested diseases by the application of functional food ingredients, viable bacteria (probiotics), fecal transplant strategies or novel drugs and constitutes of a pool of innovative non-invasive diagnostic and prognostic biomarkers. In close collaboration with many clinical departments within our MUMC+ as well as across the world, we examine the role of the microbiome and microbial components, such as membrane vesicles, in a wide variety of diseases, including chronic intestinal diseases (Inflammatory Bowel Disease, Irritable Bowel Syndrome), metabolic diseases (overweight and obesity, type 2 diabetes), chronic respiratory diseases (COPD, asthma) and several types of cancer. Automated rapid technologies and Artificial Intelligence algorithms are studied for clinical purpose and improvement of patient care, e.g. to predict and/or prevent exacerbations and optimize treatment in an early phase based on defined changes in the microbiome composition.
    In recent years, it has become apparent that the microbiome also has a significant influence on treatment drugs as specific microbes can convert drugs into active, inactive or even toxic components. We therefore also study the impact of the microbiome on treatment response.
  3. The microbiome as a reservoir of antimicrobial resistance
    Although the extensive overuse and misuse of antibiotics in both humans and animals is mainly fueling AMR, it is the increased globalization that subsequently results in rapid dissemination of (novel) AMR bacteria or bacterial mobile genetic elements from AMR hot zones, such as South and Southeast Asia, to other parts of the world. 
    The intestinal microbiome is the most important reservoir through which these travelers to AMR hot zones may acquire and import AMR. The gastrointestinal tract is an open system, which every day encounters a myriad of bacterial acquisitions originating from the environment (e.g. from food, water, soil, and other humans or animals. These incoming bacteria acquired in countries with a high prevalence of AMR often harbor antibiotic resistance genes. Consequently, local emergence of AMR can rapidly become a worldwide health problem.
    Within our department, we study the impact of migration (including tourists, business travelers, students and refugees) on the import and spread of AMR. We are amongst others coordinating the worldwide largest study on the Carriage Of Multidrug resistant Bacteria After Travel (COMBAT-study). Using a combination of metagenomic approaches, we mine the gut microbiome to reveal potential novel AMR genes. This is not only done in travelers, but also in local populations, the environment and livestock in countries with a high prevalence of AMR (e.g. India and Vietnam).
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