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Bacterial Identifier: Accelerating Bacterial Genome Detection
Nejezchlebová, Julie ; Rychlík, Ivan ; Schwarzerová, Jana
Bacterial identification is crucial for effectively monitoring and controlling the spread of infectious diseases. In addressing this critical need, our study introduces an engineered application designed to expedite the analysis of bacterial sequencing data, thus providing a streamlined method for species identification. The Bacterial Identifier underwent thorough testing using a significant dataset obtained from the Veterinary Research Institute. Central to the app's functionality is the integration of three essential tools. Implemented through a cohesive bash script, these tools are seamlessly combined to ensure optimal performance and accuracy in bacterial identification. Furthermore, to enhance user experience, a userfriendly interface was developed using Python 3, facilitating intuitive navigation and efficient utilization of the application's capabilities.
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Immunomodulatory properties of microbial components
Pavličová, Anna ; Kverka, Miloslav (advisor) ; Prokešová, Ludmila (referee)
The human body is inhabited by a complex composition of microorganisms. Particularly significant is the intestinal microbiota due to its profound effect on the development and function of the immune system. The ability of the host to defend against pathogens is kept by two important, interrelated components - the mucosal barrier and immune system. The barrier is composed of several layers (gut microbiota, mucus, epithelium, and immune cells) joined into one functional unit. Through its diverse array of structural components and metabolites, the gut microbiota interacts with the epithelium and mucosal immune system, confers to its induction, and modulates immune responses. Disruption of this interplay can contribute to pathogenesis of several diseases.
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Probiotics and prebiotics in the diet of the population. Effect on disease frequency.
Cherepanova, Ekaterina ; Starnovská, Tamara (advisor) ; Horová, Eva (referee)
Over the past decade, scientific research has focused on the intricate relationship between the human microbiome and the immune system. A particular emphasis in the last three years has been on investigating the impact of the microbiome on the susceptibility and severity of COVID- 19 infections. There is substantial evidence suggesting that the consumption of fermented foods, ranging from fermented vegetables and kefir to yogurt and kimchi, has a beneficial effect on the composition of the intestinal microbiome and, consequently, on the function of the immune system. This study, part of a bachelor's thesis, explores the complex association between regular consumption of fermented foods and the frequency of infectious diseases. Through the analysis of data obtained from a questionnaire, it was found that individuals who regularly incorporated fermented products into their diet exhibited a lower frequency of infectious diseases over the past two years. These results indicate that the consumption of probiotics and prebiotics may positively influence the immune system, reducing the risk of disease. Regarding the examination of the relationship between the consumption of probiotics from food sources and the frequency of COVID-19 infections, a contrasting observation emerged. Those who were fully...
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Microbial transplantation and its effect on the course of ulcerative colitis
Březina, Jan ; Drastich, Pavel (advisor) ; Šťovíček, Jan (referee) ; Janoštiak, Radoslav (referee)
The complex etiopathogenesis of idiopathic inflammatory bowel diseases (IBD) remains unclear, with one of the main suspected causes being the dysregulation of mucosal immunity in response to specific components of the gut microbiome. This dissertation investigates the potential of faecal microbiota transplantation (FMT) as an innovative therapeutic intervention aimed at modifying the microbiome and influencing the course of IBD. FMT, involving the transfer of stool from a healthy donor to the patient, has proven highly effective in the treatment of recurrent Clostridioides difficile colitis, where it is already considered a standard therapeutic procedure. However, in relation to IBD, FMT remains an experimental method, predominantly used in clinical studies. Current systematic reviews indicate that the effect of FMT on ulcerative colitis (UC) is variable, both in terms of achieving remission and clinical response. Recent randomized controlled trials for UC, in accordance with our presented data, show a mild to moderate effect of FMT in this indication. The effectiveness of FMT is influenced by a range of factors, particularly the correct selection of donor or donors, the diversity of their microbiome, methods of application, and frequency of administration. In the case of Crohn's disease, the data...
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Tool for Visualization of Microbiome Data
Mišáková, Silvia ; Martínek, Tomáš (referee) ; Smatana, Stanislav (advisor)
Táto práca sa zameriava na vytvorenie nového nástroja pre vizualizáciu mikrobiomových dát. Vytvorený nástroj používa pre redukciu dimenzií analýzu hlavných komponent (PCA) a analýzu hlavných súradníc (PCoA). V prípade výpočtu dištančnej matice sú použité metriky Bray-Curtis odlišnosť a UniFrac. Spracované dáta sú následne ofarbené na základe užívateľom zvolených metadát. Výsledky sú prezentované pomocou dvoch typov grafov. Prvý z nich je stĺpcový a zobrazuje podiel každej hlavnej zložky. Druhý, bodový graf, vizualizuje konečný výsledok požadovanej analýzy. V rámci práce bola pridaná možnosť stiahnuť si vypočítanú maticu a taktiež tabuľku prvých N hlavných zložiek vypočítaných danou analýzou.
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Effect of TNF-α inhibitors on microbiota composition and immune response in patients with inflammatory bowel disease
Mihula, Martin ; Jirásková Zákostelská, Zuzana (advisor) ; Grobárová, Valéria (referee)
One of the most common used therapies in inflammatory bowel diseases (IBD) treatment are inhibitors of a cytokine TNF-α. Nevertheless, up to one third of IBD patients stop respond to this therapy for unknown reason. In these days, there are not any ideal biomarkers which could predict patient's long- term response to anti-TNF-α therapy. Because the gut microbiota composition changes are tightly related to the pathogenesis of IBD, my aim in this thesis was to find out if these changes in composition are happening also due the therapy by inhibitors of TNF-α as well. Moreover, I tried to find out if there are changes in production of serum biomarkers related to the gut barrier damage and to the immune response associated with microbial translocation. Also, I focused on the immune response of IBD patients against common gut commensal bacterial antigens during the anti-TNF-α therapy. In our study, we collected for these purposes stool or blood samples from 46 IBD patients before the therapy and at 38th week from the start of the therapy and 39 healthy controls. I found that IBD patients had higher bacterial diversity (α-diversity) as well as different bacterial composition across observed groups (β-diversity) at 38th week of the anti-TNF-α therapy than before the therapy. When I divided IBD patients...
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The role of gut microbiome and autoimmune mechanisms in patients with anorexia nervosa
Kovářová, Tereza ; Procházková, Petra (advisor) ; Hrdý, Jiří (referee)
In addition to gastroenterological diseases, changes in the composition and diversity of the gut microbiota have been also described in several neurological and psychiatric diseases, including eating disorders. My intention in this work is to clarify whether changes in the composition of the intestinal microbiota may be involved in the development of anorexia nervosa (AN) and whether there is a correlation between these changes and possible immunopathological reactions in patients with anorexia nervosa. The study included 30 acute patients (disease duration up to 3 years), 30 patients with a chronic course of the disease (duration longer than 7 years), and 30 healthy controls. The research included analysis of the gut microbiome using high-throughput sequencing (HTS) and determination of serum levels of autoantibodies against selected neuropeptides regulating food intake (by ELISA). Furthermore, serum levels of biomarkers of microbial translocation through the intestinal barrier, intestinal cell damage, and inflammation were detected by ELISA. The levels of pro- and anti-inflammatory cytokines were measured using Luminex instrument. We also introduced an experimental ABA (activity-based anorexia) mouse model, which may contribute significantly to further investigating mechanisms of anorexia...
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Metagenomic analysis of child gut microbioma
Zourková, Tereza ; Škutková, Helena (referee) ; Bartoň, Vojtěch (advisor)
The thesis is focused on the influence of the metagenome on child growth and the reasons for the usefulness of investigating the consequences of changes in the human intestinal microbiome. It also describes the general problematics of the microbiome and the history of its studies. The composition of the human intestinal microbiome and the connection with the immune system or, for example, hormone production, are also described here. The thesis also contains information on some methods of metagenome analysis, namely microscopic methods using previous cultivation, mass spectrometry and sequencing methods. The data analysis procedure using various bioinformatics software, with which the data were appropriately pre-processed, is also described here. Filtered data in this way are ready for the following metagenome profiling, which is also described here. At the end of the thesis, the profiling results are evaluated, based on which the course of changes in the microbiome during the aging of the child are estimated, which is the main goal of this bachelor's thesis.
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Food supporting the intestinal microbiota
JAROLÍMOVÁ, Kristýna
Diet is an important factor that affects the composition and function of the gut microbiota. The aim of this bachelor thesis was to evaluate the possible influence of food representation in the diet on gut microbiota through a questionnaire survey. A total of 753 questionnaires were obtained. It was found that the majority of respondents (89%) believe that microorganisms are important for proper digestion. Women consume more fruit than men (34%, resp. 22%; P <0,01) and are more likely to follow alternative diets such as vegetarianism. Low daily consumption of fried and fast food was found to be favorable (5% of men and no women; P <0,01). The results of this study support the importance of diet as one of the factors influencing the gut microbiota. This issue is important in view of the increasing prevalence of diseases related to gut microbiota balance.
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Microbiology of raw milk and selected dairy products
BEZÁNYIOVÁ, Michaela
Milk is an important part of the human diet due to its composition. The aim of the bachelor thesis was to create a review focused on the microbiota of raw cow's milk and dairy products. The thesis summarizes the ways of primary and secondary microbial contamination of milk and describes the intrinsic and extrinsic factors influencing the growth of microorganisms. A particular attention is focused on mastitis, which are the main source of primary contamination of milk. The great emphasis is attended to the necessity of strict following of hygiene regulations during manipulation with this raw material. In the last part, potential health risks associated with consumption of milk and dairy products is mentioned. .
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