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/Vladimír Havlíček

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.
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.
Fermented Foods and Bone Health: Investigating the Gut-Bone Axis in Premenopausal Vegan Women

Marek Kuzma

Supported by the Czech Science foundation, grant No. 25-19309L (2025-2028)

Recent epidemiological studies suggest that individuals following vegan diets may be at higher
risk of lower bone mineral density (BMD) and fractures, particularly among women. Evidence
suggests that the gut microbiota plays a key role in regulating bone metabolism through the “gutbone
axis.” Fermented foods, such as yogurts and fermented vegetables, have been shown to
positively influence gut microbiota, supporting bone health by supplying essential nutrients,
enhancing nutrient absorption, and reducing bone resorption.
This project aims to test the hypothesis that consuming plant-based fermented foods can
improve bone turnover markers (BMTs) in vegan premenopausal women over a 12-week
period. We will further focus on the broader impact of vegan diets and fermentation processes
on nutrient bioavailability and gut microbiota. Additionally, the project will leverage existing data
on vegans to conduct a comprehensive analysis of BMD and BTMs, metabolomic profiles, and
dietary patterns in vegan and omnivore populations across multiple European countries.
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.
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