Research projects

Ongoing research projects

Ongoing research projects

The laboratory staff is engaged in three projects of the Jan Amos Komenský Operational Programme (Inter-micro, Photomachines, Micro-biotech), the MSCA-CZ project (Marie Skłodowska-Curie Actions, Molecular basis for determining the competence of ticks in the transmission of pathogens), and other projects. The Ministry of Education, Youth and Sports is engaged in research on the secondary metabolism of intracellular pathogens and the development and evaluation of a web-based screening tool for assessing diet quality in vegans. The Health Research Grant Agency is investigating invasive aspergillosis in a prospective study, while the Czech Grant Agency is examining the spatial metabolomics of central nervous system infections.

Secondary metabolism of intracellular pathogens

Vladimír Havlíček

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. LUAUS24214 (2024-2028)

We will explore the metabolism of clinically relevant intracellular pathogens within host cells in collaboration with Stanford University. The research will thoroughly investigate the secondary metabolism of the endemic fungus Coccidioides immitis, as well as study mycoviruses and bacterial endosymbionts in fungi, bacteriophages in bacteria, and Mycobacterium tuberculosis in mammalian cells.

A prospective study on invasive pulmonary aspergilosis

Vladimír Havlíček

Supported by Czech Health Research Council, grant No. NU23-05-00095 (2023-2026)

The aims of the project are: 1. In a prospective format, to generate critical diagnostic parameters (sensitivity, specificity, negative and positive predictive values) in a larger cohort of patients with invasive pulmonary aspergilosis. 2. To provide a fair kinetic comparison between standard PCR, routine mycological serology, microscopy, microbiology, imaging data, and our next-generation PTX3/siderophore panel. 3. To develop an affinity-based TafC preconcentration workflow for the enrichment of siderophores in human bodily fluids.
INTER-MICRO: Talking microbes - understanding microbial interactions within One Health framework

Jan Jansa/Andrea Palyzová

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/22_008/0004597 (2024-2028)
INTER-MICRO advances the understanding of communication within microbial communities and between microbes and their hosts. The project will utilize knowledge from biology and chemistry, as well as different research areas within each discipline. These areas include general microbiology, microbial physiology and ecology, immunology, biochemistry, molecular biology, organic chemistry, and chemical engineering. The project will be supported by advanced biochemical, microscopic, molecular biological, and bioinformatics expertise and infrastructures. Our MS and microbiology groups contribute to this project using mass spectrometry and our Infection metallomics strategies.
Molecular fundamentals driving tick competence in pathogen transmission

Lenka Minichová

Supported by the Ministry of Education, Youth and Sports of the Czech Republic (Marie Sklodowska-Curie Action-CZ, 2024-2026)
Climate change is already affecting vector-borne disease transmission and spreading to new areas. Whereas they are responsible for more than 17% of all infectious diseases (causing more than 700 000 deaths annually) vector control and preventing the outbreaks become one of the WHO’s priorities. This project will elucidate the vector competence for pathogen transfer and describe the molecular and functional interface between the pathogenic bacteria (Rickettsia spp. and Coxiella burnetii) and their common tick vectors in Europe (Dermacentor marginatus and Ixodes ricinus). Both pathogens can cause severe illnesses in humans or economic losses in ruminants (goats, sheep, cows), respectively. Pathogenic and immune pathways together with mechanisms of pathogen survival within the vector and host were characterized, but only a few studies were focused on the complex pathogen-vector interactions during feeding. To expand the borders of our knowledge, I will apply an interdisciplinary approach and state-of-the-art imaging techniques to describe how the tick immune system may control the preservation of pathogens and their transmission. My objective is (i) to develop new strategies for visualization and quantitation of tick-borne pathogens using state-of-art imaging techniques. This will lead me to (ii) identification of biomarkers (specific metabolites and proteins) important for pathogen transmission, which will be annotated or determined de novo. Finally, I will (iii) use identified tick-specific compounds modulated by bacterial factors as targets for defining effective antimicrobial therapy and development of protective antigens capable of blocking pathogens’ transmission.
Microorganisms in ecological restoration - bacteria as cell factories for controlled bioremediation of ecosystems

Marek Kuzma

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/23_020/0008502 (2025-2028)
A large Jan Amos Komensky project on new bioremediation strategies involves the Institute of Microbiology (IMIC), Charles University, Envisan, and Deconta. The project will fund the upgrade of NMR spectrometers installed at IMIC.
Photomachines: Photosynthetic cell redesign for high yields of therapeutic peptides

Roman Sobotka/Marek Kuzma

Supported by the Ministry of Education, Youth and Sports of the Czech Republic, grant No. CZ.02.01.01/00/22_008/0004624 (2024-2028)
The project will successfully design and develop photomachines, a new type of photosynthetic production cells that will achieve high productivity. The project is divided into two Research Objectives and 13 specific tasks that synergistically convert a cyanobacterial cell into a ‘bio-factory’, called Syn2Cell. A key feature of this system is the strict separation of the growth and production phases. Our NMR group contributes to this project through the use of NMR spectroscopy.
Aspergillus-Pseudomonas Interaction Modulated by Human Neutrophils

Rutuja Patil

Supported by the European Society of Clinical Microbiology and Infectious Diseases (2025)

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