For best experience please turn on javascript and use a modern browser!
You are using a browser that is no longer supported by Microsoft. Please upgrade your browser. The site may not present itself correctly if you continue browsing.
Microorganisms play a central role in our existence. They help to digest our food, and they are used to preserve food. Yet, they can spoil food and can poison us. They cause life-threatening infections but also produce the antibiotics that save us. They play key roles in nature as they help the global recycling of nutrients and energy. Considering their importance, it is surprising how little we know about their workings. The Microbiology theme of SILS studies the molecular mechanisms involved in these processes, works on techniques to prevent microbial pathogens, and develops novel ways to employ microbes for biotechnological applications.

Research lines in Microbiology

  • Research line Prof. Stanley Brul

    Research line Prof. Stanley Brul

    Spore forming organisms are spoilage organisms of prime-importance to the food industry due to their highly stress resistant endospores. These spores are also prominent in our gastro-intestinal tract. Their occurrence necessitates the application of harsh food preservation. The mechanistic basis of their extreme high thermal resistance (> 121˚C), as well as the molecular mechanisms of spore outgrowth are still characterized by many open questions.

    With the help of molecular biology, advanced fluorescence microscopy and proteomics, we investigate ‘Germinosome’ complex required for spore germination, using the model system Bacillus subtilis and the pathogens Bacillus cereus and Peptoclostridium difficile. Studies are currently extended with the AMC to the functional analysis of the gut microbiome.

    Studying the
    Studying the 'germinosome' in spore-forming bacteria
    Prof. dr. S. (Stanley) Brul

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Prof. Benno ter Kuile
    Use of antibiotics causes development and spreading of resistance
    The use of antibiotics causes development and spreading of resistance

    Research line Prof. Benno ter Kuile

    It is estimated that 50% to 80% of all antibiotics used are applied in agriculture. Veterinary and environmental microbes are often exposed to sublethal levels of antibiotics. Exposure to sublethal drug concentrations induces resistance, transfer of antimicrobial resistant (AMR) genes, and selection for already existing resistance. Novel approaches such as combination or alternating therapy are promising, but need to be investigated in detail before they can be implemented in daily practice.

    Prof. dr. B.H. (Benno) ter Kuile

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Dr Meike Wortel

    Research line Dr Meike Wortel

    Micro-organisms live together with each other, and in the case they for a microbiota, also together with a host. Therefore, the evolution of micro-organisms is influenced by the interactions they have. Many interactions are mediated by external compounds, for example cross-feeding of metabolites. Using metabolic and mechanistic evolutionary models as well as laboratory (evolution) experiments with micro-organisms (from the gut microbiome) and nematode-bacteria interactions, the effects of species interactions on evolution are studied.

    The main focus areas include: antibiotic resistance evolution in consortia of human gut microbes, co-evolution of C. elegans and E. coli and metabolic interactions in networks of human gut microbes and of C. elegans using bacteria as a food source.

    Dr. M.T. (Meike) Wortel

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Dr Jianbo Zhang

    Research line Dr Jianbo Zhang

    I aim to study microbiome-host interactions and harness beneficial microbial functions to fight chronic and infectious diseases, with focus on (1) the development of microbiome and tissue engineering technologies; (2) elucidation of the mechanism of microbiome-host interactions in health and diseases; (3) engineering gut commensals and microbial consortia for smart therapeutic delivery.

    Dr J. (Jianbo) Zhang

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Prof. Linda Verhoef

    Research line Prof. Linda Verhoef

    The current standard of food safety in the Netherlands is quite high. Nevertheless, production of foods is subject to societal changes which continuously challenge food safety. The Netherlands Food and Consumer product safety authority, as long established inspectorate, guards the safety of foods throughout the food chain. Their inspections and monitoring activities provide a continuous flow of data and samples, informing of the current status of food safety. By adding a combined epidemiological and microbiome approach, these samples and data may be informative of future changes as well. Research will focus on the multiple-purpose-use of samples and accompanying data enabling agile monitoring of food safety in a changing environment, and thereby implement the field of epidemiology in the supervision of food chains by the NVWA. In a creative way: by taking food (instead of humans) as a starting point.

    To this end, modern molecular epidemiological methods that are widely used for human research will be translated into methodology for food chains. This requires adjustment of existing epidemiological methods, which will be developed in research. Previous research indicated that use of genotype profiles, as based on the older techniques, was informative for transmission routes. With the recent developments in the field of microbiome, time has come to work towards the routine use of such techniques for monitoring purposes. By enriching the microbiome data with epidemiological background data, the microbiome can be examined for the added value for food safety.

    The research will build up an epidemiological tool box for ‘food epidemiology’, unraveling and identifying critical points in the food production chain.


  • Research line Prof. Sahar el Aidy

    Research line Prof. Sahar el Aidy

    Our research passion lies in unravelling the intricacies of interkingdom cross-talk. Our primary goal is to decipher the mechanisms guiding bacterial adaptation in challenging environments, with a keen focus on cell morphology, (genomic) diversity, and localization.

    To achieve this, we employ a multidisciplinary approach, integrating experimentation and bioinformatics. This synergy enables us to bridge the coordination of major physiological processes across both microscopic and macroscopic scales. Our investigations span diverse realms, encompassing (sub)-genomic diversity, metabolism, protein evolution, cell shape, and adhesion.

    Our analyses extend beyond the bacterial realm to consider dynamic changes in the surrounding environment, including host factors such as gut physiology, nutrient scarcity, and bowel movement. On the bacterial side, we delve into the intricate biogeography and ecology. This holistic approach allows us to gain comprehensive insights into the multifaceted interactions shaping bacterial adaptation.

    Prof. dr. S. (Sahar) El Aidy PhD

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Prof. Jeroen Hugenholtz

    Research line Prof. Jeroen Hugenholtz

    As a crucial part of the developing Biobased Economy, the chemical industry is looking for alternative, sustainable, production processes for all/most of their bulk and fine chemicals, fuels, pharmaceuticals and food ingredients. Microbial fermentation is one of the key technologies for biobased production of these chemicals. The work, focusses on three areas of fermentation: (i) Anaerobic fermentation, involving Clostridium, for production of various alcohols from (biological) waste streams and C1-gasses (syngas), (ii) Lipid-producing and lipid-converting microorganisms such as Cryptococcus and Pseudomonas that can produce and convert various medium- and long-chain fatty acids, and (iii) Lactic acid bacteria as producer of natural flavors, of preservatives and for nutritional enrichment of food products. The described work is an important part of the Amsterdam Green Campus

    Microbial fermentation setup
    Biobased production of chemicals
    Biobased production of various useful chemicals
    Prof. dr. J. (Jeroen) Hugenholtz

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line prof. Leendert Hamoen
    Bacterial Cytological Profiling
    Visualizing cell division proteins

    Research line Prof. Leendert Hamoen

    Cell division is a vital process, and yet, we still do not know exactly how bacterial cells divide. We use the well-known bacterial model system Bacillus subtilis to  study the dynamic interaction between cell division proteins using molecular biological and fluorescence microscopy and techniques. This latter technique is also very useful to study the mode of action of novel antimicrobial compounds, which is called bacterial cytological profiling. We this and other tools to identify and characterize new antimicrobial compounds.

    B. subtilis is used in the bioindustry to produce enzymes and vitamins. The bacterium is also used as a probiotic in animal feed, and in fact it is eaten by humans in the form of Natto. In collaboration with industrial partners we help to further optimize B. subtilis for applied purposes.

    Prof. dr. L.W. (Leendert) Hamoen

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Dr Gaurav Dugar

    Research line Dr Gaurav Dugar

    RNA molecules can act as gene regulators in bacteria, but there is a lot out there still to be discovered. We study RNA dependent microbial gene regulation by capture and analysis of global RNA-RNA and RNA-DNA interactions in bacteria. 

    Dr. G. (Gaurav) Dugar

    Faculty of Science

    Swammerdam Institute for Life Sciences

  • Research line Dr Filipe Branco dos Santos
    Schematic overview of the metabolism of Synechocystis sp. PCC6803 engineered for PHB production
    Overview of the metabolism of Synechocystis sp. PCC6803 engineered for PHB production

    Research line Dr Filipe Branco dos Santos

    We aim to integrate knowledge on the biochemical and biophysical properties of signal transduction- and metabolic networks that regulate and underlie fermentation, respiration and oxygenic photosynthesis. Ultimately, we want to understand how the environment, through evolution and natural selection, shapes microbes to be equipped with the capacity to deal with the fluctuations they encounter. For our studies, we focus on the industrially relevant lactic acid bacterium Lactococcus lactis and the model organism for studies in oxygenic photosynthesis Synechocystis PCC6803. Both organisms are highly relevant for the transition of our society towards a sustainable bio-based economy.

    Dr. F. (Filipe) Branco dos Santos

    Faculty of Science

    Swammerdam Institute for Life Sciences


The Microbiology theme is part of the UvA Research Priority Area Personal Microbiome Health and the Faculty Research Priority Area Systems Biology (Host-Microbiome Interactions). The Microbiology community in Amsterdam is further organized in the Amsterdam Microbiome Initiative. 

Amsterdam Microbiome Initiative

The Amsterdam Microbiome Initiative (AMI) is an Amsterdam wide initiative to bundle the expertise available in our area at the UvA, VU, Amsterdam UMC and ACTA. Its members meet at the Amsterdam Microbiology SeminArs (AMSA) and have as aim to study microbial consortia in biotechnological, biomedical and environmental settings using multidisciplinary approaches.

Research groups of the Research Theme Microbiology

The different PIs of the Microbiology theme are bundled in three research groups, you can find more information about the research groups on the group pages: