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Mikrobiologie

Mikrobiologie

CHYBI CHARAKTERISTIKA PROGRAMU

Cílem studijního programu je vychovat odborníky s komplexním pohledem na mikrobiální populace, jejich aktivitu, fylogenetickou a metabolickou diverzitu, mechanismy řídící cílené změny jejich genetické informace či chemické principy ovlivňující vzájemné vztahy mikroorganizmů. Studijní program je založen na propojení různých forem výuky s intenzivním výzkumem, kdy je důraz kladen především na samostatnost, iniciativnost a kritický přístup studentů k řešené problematice. Ve výsledku budou absolventi studijního programu všestranní odborníci schopni získané poznatky, dovednosti i kompetence použít pro průmyslové či jiné aplikace.

Careers

Cílené spojení mikrobiologického, biochemického a inženýrského přístupu v rámci studijního programu profiluje absolventy s komplexním pohledem na mikrobiální svět. Absolventi budou disponovat hlubokými teoretickými znalostmi i praktickými dovednostmi ve všech klíčových oblastech mikrobiologie, včetně biochemie mikroorganismů, molekulární biologie, genového inženýrství i dalších blízce příbuzných oborů. Absolventi studijního programu tak naleznou uplatnění ve všech oblastech biotechnologií, potravinářského, farmaceutického či chemického průmyslu, v klinických laboratořích, v oblasti životního prostředí a zemědělství. V neposlední řadě je základem profilu absolventů studijního programu i kompetence pro práci ve výzkumu v akademické sféře.

Programme Details

Language of instruction Czech
Standard length of study 4 years
Form of study Full time + Combined
Guarantor of study programme doc. Ing. Ondřej Uhlík, Ph.D.
Programme Code D301
Place of study Praha
Capacity 15 students
Number of available PhD theses 16

List of available PhD theses

Cutibacterium acnes: virulence factors and mobile genetic elements

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: Ing. Kamila Zdeňková, Ph.D.

Annotation

The gram-positive bacterium Cutibacterium acnes (formerly Propionibacterium acnes) is a skin commensal under physiological conditions, but it can also be an opportunistic pathogen causing invasive chronic infections. The most well-known diseases associated with C. acnes include Acne vulgaris; however, the connection with a number of other diseases is also clinically significant. The pathogenicity of C. acnes is due to a number of virulence factors, one of which is the formation of a biofilm, which increases the resistance of bacteria to antibiotics and other bactericidal substances, which negatively affects the effectiveness of treatment. C. acnes phylotype IA1, associated with acne, produce virulence factors as hemolysins, CAMP factors, neuraminidase, heat shock proteins (HSP) or lipase etc. Much of genes responsible for virulence and resistance is located on mobile genetic elements (MGEs). As part of the solution of this work, virulence factors will be studied using classical microbiological and modern molecular-biological methods.

Analysis of multispecies biofilms of food-borne pathogenic bacteria

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology

Annotation

Most bacteria, due to their phenotypic adaptability, can live in a community called biofilm, which is often multi-species. Biofilm serves for their adherence, communication, protection and increases the resistance of bacteria to adverse environmental conditions. Its characteristic persistence, heterogeneity and complex dynamics are related to relatively difficult detection and problematic analyses by classical microbial methods. That is why such consortia are nowadays a challenge for many professionals. Multi-species biofilms of Listeria monocytogenes, Staphylococcus aureus and Escherichia coli, will be analysed during the course of the dissertation as selected representatives of food pathogens monitored under Commission Regulation (EC) 2073/2005. Classical microbiological and modern molecular-biological methods will be used. The multi-species biofilm study will also include analyses of gene expression levels and impact on biofilms of antibiotics or other selected antimicrobials. This will contribute to a better understanding of the spread of resistance in the environment assisted by these communities, while at the same time increasing the existing knowledge about the coexistence of the biofilms of bacteria whose eradication from undesirable sites is more complicated than single-species biofilms.

Heterogeneity of expression of effectors of Salmonella pathogenicity island 2?encoded type 3 secretion system

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Microbiology
Theses supervisor: RNDr. Ondřej Černý, Ph.D.

Impact of antibiotic resistance on the propagation of Gram-negative bacteria in the food chain

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: Ing. Sabina Purkrtová, Ph.D.

Annotation

The increasing incidence of antibiotic resistance in bacteria is one of the major problems of the 21st century, as it limits the range of suitable antibiotics for treating bacterial infections. The food chain is one of the places, where it happens the genesis of new antibiotics resistance determinants and/or their spreading (so-called hot spots). Selected groups of gram-negative bacteria (family Enterobacteriaceae, the genera Acinetobacter and Pseudomonas, etc.) form the very significant or the most numerous parts of bacteriome in many food products. At the same time, these bacterial groups are frequent carriers and spreaders of antibiotic resistance genes (e.g. by various mechanisms of horizontal gene transfer). However, the presence of antibiotic resistance genes, often linked to various mobile genetic elements, can not only bring benefits to their carriers, but in some cases can have a negative effect on their certain physiological and other properties (eg growth ability). Knowledge of the influence of the presence of antibiotic resistance genes on properties important for the spread of bacteria in the food chain (e.g. biofilm formation, growth ability, resistance to environmental stress conditions, etc.) is then important for determining the potential for their spread in the food chain and for developing methods to reduce it. The aim of the work will be to study and compare the isolates of the above groups of gram-negative bacteria isolated from food products with different antibiotic resistance profiles. The selection of important antibiotic resistance genes occurring in food isolates of the above groups of gram-negative bacteria will be performed. Furthermore, the occurrence of these antibiotic resistance genes in selected food products will be determined. It will be performed the isolation and quantification of target bacterial groups, genotypic and phenotypic characterization of the obtained isolates and comparison of the occurrence frequency of different genotypes and phenotypes. Modern methodological approaches such as next generation sequencing methods (e.g. nanopore sequencing), qPCR, MALDI-TOF MS and selected classical cultivation microbiological methods will be used for the study.

Investigation of the structure and function of Kingella kingae RtxA cytotoxin

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: Ing. Radim Osička, Ph.D.

Annotation

The secreted cytotoxin RtxA is a key virulence factor of the Gram-negative bacterium Kingella kingae, which is an important invasive pathogen causing septic arthritis, osteomyelitis, infective endocarditis and other diseases in young children. The current state of knowledge indicates that RtxA may play an important role in various steps of K. kingae infection, including colonization of the respiratory epithelium, bloodstream invasion and damage to target tissues. However, the detailed mechanism by which RtxA contributes to the pathogenesis remains largely unknown and its study is the central objective of the proposed doctoral project. Particular emphasis will be placed on the determination of membrane topology of RtxA, on the investigation of molecular mechanisms by which the toxin disturbs tight junction integrity of the respiratory epithelial barrier and on the examination of the effect of K. kingae and RtxA on the innate immune response of the respiratory epithelium. The results are expected to provide new knowledge on the RtxA toxin and on the pathogenesis of invasive K. kingae disease.

Mechanisms of bacterial antibiotic resistance and their modulation

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: Ing. Jitka Viktorová, Ph.D.

Microbial Cometabolism: Promoting Biodegradation of Pollutants

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: doc. Ing. Ondřej Uhlík, Ph.D.

Annotation

The objective of the proposed thesis is to test the hypothesis that secondary plant metabolites can promote cometabolism of persistent organic pollutants in the environment and thereby significantly influence the biodegradation potential of autochthonous microbial communities. In order to accomplish this objective, we will (i) selectively enrich soil bacterial consortia that will degrade selected pollutants (polychlorinated biphenyls, PCBs, and polyaromatic hydrocarbons, PAHs) when grown on secondary plant metabolites and (ii) test whether the consortia involved in secondary plant metabolite metabolism will increase the efficiency of biodegradation of PCBs and PAHs in soils.

Microbiota of Selected Extreme Biotopes – Diversity, Ecology and Physiology

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: doc. Ing. Ondřej Uhlík, Ph.D.

Annotation

The objective of the proposed thesis is to characterize microbial populations in extreme biotopes – chronosequence of permafrost (permafrost of differing age) and soils from salt marshes and moffettes. The characterization will be conducted by two major routes – metagenomics and modified cultivation techniques. The basic modification of the cultivation techniques will be the use of resuscitation-promoting factor and adjustment of cultivation media so that they better mimic natural conditions the bacteria are subjected to in their habitat; the goal is to increase the efficiency of the cultivation and isolate dormant or otherwise difficult-to-culture or, if possible, as-yet-uncultured bacteria.

Microorganisms and their utilisation in waste management

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: Ing. Hana Stiborová, Ph.D.

Annotation

Nowadays, more attention is paid to recycling and recovery of waste and therefore, the European Union has adopted a new Circular economy action plan. One option of reducing the environmental burden and decreasing the CO2 emissions in the (cement) building industry is the usage of recycled bio-concrete, which can be obtained using microbiologically induced calcite precipitation (MICP). This thesis's main goal will be to isolate and characterise suitable microorganisms and optimise MICP conditions concerning the yields, the structure and mechanical properties of bio-concrete.

Quorum sensing and its role in adaptation and virulence of Campylobacter jejuni

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology

Annotation

Despite its fastidious nature, Campylobacter jejuni is continuously reported as the most common cause of foodborne zoonoses. Short genome with simultanously high level of adaptability of C. jejuni suggest that it is capable of rapid change of gene expression resulting in transition from a resilient but metabolically attenuated form outside a host into a virulent and rapidly multiplying form inside a host. This adaptability could be explained by extensive use of quorum sensing systems (QS). The main aims of the thesis involve investigation of the role of QS in lifecycle of C. jejuni, with an emphasis on identification of regulatory pathways mediated by acyl homoserine lactones. Significant part of the thesis will be dedicated to establishing the role of a host-like environment in signalling and pathogenicity of C. jejuni.

Relationship between plants endophytes, and its metabolome

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: doc. Ing. Petra Lovecká, Ph.D.

Annotation

Recently, research focused on uncommon natural sources and unexplored habitats has become a subject of deep scientific interest. Exclusive relationships of endophytic bacteria and fungi with plants were shown to have a great potential to produce new and rare secondary metabolites, with unique health beneficial, technological and nutritional properties. The essence of the thesis will be studying of mutual relationships between microbial endophytes and plants by advanced tools of modern analytical chemistry – high resolution mass spectrometry-based metabolomic fingerprinting / profiling. In addition to this, potential ofendophytes to prevent pathogenic fungi growth and mycotoxins production will be assessed.

Response of microbial communities to changing climate in Arctic tundra soils

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Microbiology
Theses supervisor: RNDr. Jana Voříšková, PhD.

Annotation

Climate models predict substantial changes in temperature and precipitation patterns across the Arctic regions in future decades. Microbes are known to play key roles in determining the stability of soil carbon and its possible release into the atmosphere as greenhouse gases. Carbon-rich Arctic soil ecosystems are particularly vulnerable to carbon losses due to warming and subsequent ecosystem disturbances as wildfires. The aim of the project will be to explore the response of soil microbial communities to the conditions caused by future climate change, specifically increased winter precipitation, summer warming and wildfire disturbance. For the project, we will use the experimental sites in western and southern Greenland, maintained by University of Copenhagen, which simulate predicted changes in soil ecosystem. Microbial communities from collected soil samples will be characterized using state-of-the-art methods of molecular biology.

Structure-Function Relationships of the Bordetella Type III Secretion System Proteins

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Microbiology
Theses supervisor: prof. Ing. Peter Šebo, CSc.

Annotation

Type III secretion systems are membrane-embedded nanomachines used by many Gram-negative pathogens to inject bacterial effector proteins into the cytosol of eukaryotic cells. The aim of this thesis is to depict structure-function relationships of proteins of Bordetella III injectosome and its secreted substrates. Specifically, BopN protein that exhibits homology to the class of “gatekeepers” or “plug” proteins, Bsp22 protein that forms a unique filamentous T3SS tip complex and BteA effector protein with unknown mechanism of action. The PhD. candidate will develop reporter assays to analyze activity of Bordetella type III secretion system, perform super-resolution and cryo-electron microscopy and further carry out structural characterization and crystallization trials of the purified recombinant proteins, their domains and/or their mutated variants.

Study of the use of biocontrol agents against fungal biofilms

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology

Annotation

The subject of this doctoral project is to investigate the methods of application and effectiveness of biocontrol agents (eg Pythium oligandrum, Geotrichum candidum) against fungal biofilms (eg genera Aspergillus, Penicillium and Fusarium) and the experimental study of factors (physicochemical, nutritional, culture, hydrodynamic) that affect it. The experiments will be performed in various configurations (static, dynamic) using experimental design and evaluation by statistical methods. The project also aims to compare experimental data on the effectiveness of biofungicide with model prediction of its adhesion to fungal biofilms and model surfaces (X/DLVO theory, interfacial free energy balance) based on physicochemical surfaces properties. Using the agreement between experiments and models, the controlling force of biofungicide interaction with biofilm can be identified. In the case of interaction of biofungicide cells with model surfaces, the conditions under which they can be preventively treated with a biofungicide will be defined. All successful attempts to remove/suppress fungal biofilm with biofungicide will be accompanied by a quantitative determination of mycotoxins.

Studying speciation of arsenic in the mycosphere - from microorganisms to animals

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: prof. Ing. Pavel Kotrba, Ph.D.

Annotation

The goal of this work is to answer questions related to not so well studied biotransformations of arsenic in living organisms, with emphasis on fungi. Arsenic is rather toxic, but since it is ubiquitous, organisms have evolved various methods of As detoxification, including redox reactions, methylation and other biotransformation reactions. We suppose, that these bioprocesses are dependent on many factors, including As bioavailability and genetic background of each organism, and various compounds of the so called mycosphere, i.e. all factors related to fungi (geochemistry, microbiome, fungivores). Each factor and process of the biotransformation can thus be studied from a different perspective. The primary goal of this work will be identification, isolation and functional characterization of genes potentially playing role in As transformation in fungi and bacteria and their screening by metagenomic techniques in soil samples and fungal sporocarps. A second approach will deal with growing fungal mycelia in substrate amended with As and assessing the potential of the mycelia to transform inorganic As forms to organic by mass spectrometry. Both these approaches should answer questions such as: Can fungi methylate As? Do As forms correlate with fungal phylogeny? Can fungal As hyperaccumulators change the speciation of As in soil and thus in the surrounding bacterial community? How are As compounds transformed and translocated in the mycosphere?

Virulence Mechanisms of the genus Bordetella

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Microbiology
Theses supervisor: RNDr. Jana Kamanová, Ph.D.

Annotation

Pathogenic Bordetella species cause respiratory infections in mammals. While B. bronchiseptica is primarily an animal pathogen, B. pertussis is the causative agent of the whooping cough disease in humans. The PhD thesis aims to reveal the novel mechanisms of Bordetella virulence by genome-wide CRISPR/Cas9-mediated screen. A pool of knock-out human epithelial cells will be generated by an already validated gRNA library. Following Bordetella infection, the candidate genes that confirm the sensitivity of epithelial cells to Bordetella cytotoxicity will be determined. The hits will be further validated and their role in susceptibility to Bordetella infection confirmed.


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