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The Overlooked Fact: the Critical Role of Bioinformatics Pipeline in Microbiome Analysis
Polakovičová, Petra
The research on the human microbiome has gained significant popularity over the past couple of years across both scientific and public communities. This area has revealed considerable knowledge, mainly thanks to next-generation sequencing. Even though technology possibilities evolve faster than ever, and there is an enormous amount of publicly available data, there are not yet precise procedures, methods, and bioinformatics tools to work accurately enough with microbiome data, and there are no standardized recommendations for bioinformatics pipelines to assess the most accurate results. Here, we demonstrate the potential inaccuracies that can arise from various bioinformatics processing of amplicon 16S RNA sequencing data by performing a comparative analysis of diverse pipeline configurations using mock community samples and biological material originating from biopsy samples obtained during regular colonoscopy from patients with primary sclerosing cholangitis.
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Dietary measures in irritable bowel syndrome
Leschinger, Alena ; Maruna, Pavel (advisor) ; Živný, Jan (referee)
The bachelor thesis focuses on dietary measures for irritable bowel syndrome. The aim of the work was to find out the eating habits of patients with this disease and to evaluate whether they follow the dietary measures recommended for this disease, to find out what the nature of the difficulties are and when the symptoms appear, and whether the patients are sufficiently educated about dietary measures. This work is based on the hypothesis that patients do not eat according to the dietary measures that are recommended for this disease, and therefore the symptoms occur more often. The research was conducted using a questionnaire survey. Patients were asked about the most common manifestations of this disease, the frequency of symptoms, their eating habits, experiences with diets, and also about the level of awareness regarding dietary measures. A total of 32 questionnaires were evaluated. The results of the research show that the majority of patients do not eat according to dietary measures. The consequence is their low awareness of dietary procedures. For most patients, symptoms occur every day or several times a week. Although patients have purposefully reduced certain foods known to cause symptoms, the frequency of symptoms is still high. Key words: irritable bowel syndrome, microbiome, dietary...
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Mechanisms responsible for sex bias in the prevalence of autoimmune diseases
Ráček, Vojtěch ; Daňková, Pavlína (advisor) ; Ciferská, Hana (referee)
Studies have shown that women typically have stronger immune responses than men. This can also make them more susceptible to autoimmune diseases, with females comprising 80% of autoimmune patients. In women, one X chromosome is epigenetically silenced through a process called X chromosome inactivation. However, some immune-related genes located on the X chromosome, such as TLR7 and CD40L, may escape this silencing process in certain cells or tissues. This can result in a sex-biased expression that contributes to the development and susceptibility of autoimmune diseases like lupus, rheumatoid arthritis, and Sjögren's syndrome. Another interesting factor that explains this sex bias is lncRNA XIST, which is a primary regulator of the inactivation process. It plays a crucial role in lupus development and creates an XIST ribonucleoprotein complex with proteins that help establish a repressed chromatin state on the inactivated chromosome. Importantly, many of these proteins are autoantigens in various autoimmune diseases and may serve as clinical markers for the diagnosis of these conditions. While microbiome and sexual hormones also play important roles, the focus remains primarily on XIST RNA and escape genes. Keywords: autoimmune disease, sex bias, X chromosome, escape genes, lncRNA XIST, sexual...
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The influence of roots on the chemical properties of the apoplast and the rhizosphere
Puldová, Kristýna ; Fendrych, Matyáš (advisor) ; Šámalová, Markéta (referee)
Chemical properties of the apoplast and rhizosphere are crucial for plant development and its overall well-being. Apoplast includes space outside the plasma membrane and its content, such as gas, water, and solutes. Changes in apoplast properties significantly influence various processes. One of them is cellular growth - the pH-dependent extension of cell walls. The rhizosphere is the soil environment near and under the influence of roots. It is characterised by abiotic factors like the availability of nutrients and toxic compounds. It is also a space with a high representation of microbiome communities. Plants can significantly influence the chemical properties of both apoplast and rhizosphere to improve their growth conditions. This thesis summarises the most important mechanisms of plants' roots that change these chemical properties, focusing on the model plant Arabidopsis thaliana. It shows how and where these mechanisms intersect and in which way they influence each other. Emphasis is placed on the process of growth regulation and mechanisms of increasing nutrient availability. Keywords: apoplast, rhizosphere, H+ ATPase, root growth, rhizodeposition, root exudates, nutrients, microbiome
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Fleas as hosts and vectors of bacteria
Hovorková, Jana ; Hammerbauerová, Iva (advisor) ; Myslivcová Fučíková, Alena (referee)
Fleas (Siphonaptera) are worldwide significant ectoparasites and vectors of several human pathogens. The most serious flea-born infections include plague, rickettsiosis and bartonellosis caused by Yersinia pestis, Rickettsia spp. and Bartonella spp. I have focused on the microbiome of fleas with an emphasis on bacteria which are transmitted by fleas or are pathogenic, mutualistic or commensal in relation to their flea host, from the point of view of their mutual interactions. The composition of the flea microbiome can be influenced both by mutual interactions between individual bacteria and by many different factors, which include, for example, the species or gender of flea or its host, humidity and temperature of the environment or geographic location.
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Microbial Forensics
Stejskalová, Pavlína ; Vaněk, Daniel (advisor) ; Šneberger, Jiří (referee)
Microbial forensics is a young field that emerged in response to the Anthrax attacks in September and October 2001, later known as Amerithrax. At this time, forensic microbiology aimed to analyze microbial evidence associated with bioterrorism and biocrime. With the onset of metabarcoding and the advent of new generation sequencing, it has been possible to extend the scope of forensic microbiology. Nowadays microbial forensics can be applied in environmental monitoring, forensic identification based on personalized microbiomes, study of the influence of microorganisms on corpse decomposition, investigation of sexually motivated crime, archaeological and anthropological investigations, interpretation of forensic toxicology results and in the clarification in cases of sudden death. Keywords: bioterrorism, B-agens, environmental monitoring, microbiome, identification, PMI, stability of forensic samples, sexome, SIDS
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Metatranscriptomic evaluation dashboard using BiBakery.
Hýl, Jan ; Jurečková, Kateřina (referee) ; Bartoň, Vojtěch (advisor)
Metatranscriptomic analysis provides information about the currently expressed genes of an organism at the time the sample is collected. The boom in the study of genes came with the development of sequencing technologies and other technological advances. This thesis discusses nucleic acids and their importance in genetics. It explores the concepts of metatranscriptome, metagenome and microbiome. It describes the Illumina sequencing method and introduces software suitable for metatranscriptomic analysis. Subsequently, the work includes the creation of a test dataset, the creation of a dashboard for data visualization, and the testing of this dashboard using the test dataset.
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Microbiome of smear ripened cheese and its changes in dependence on the stages of production
Jandová, Karolína ; Mikešová,, Martina (referee) ; Trachtová, Štěpánka (advisor)
The theoretical part describes soft smeared cheeses, then deals with the technology of manufacturing said cheese with importance on the development of microbiome and describes the most commonly wanted microorganisms and contaminants. Shortly also deals with legislation requirements on the microbial quality of these chesses. The experimental part studies the development of microbiome and contamination by fungi of soft smeared cheese. Firstly, samples were collected in manufacture from each step of manufacturing. In the first part, microbial and microscopical assessment was done. In the second part, DNA was isolated from samples by a commercial kit and phenol-chloroform extraction. The concentration and purity of isolates were determined by spectrophotometry. By qPCR of the DNA isolates the main microbiome and contamination by fungi were examined. As part of the microbial and microscopical assessment, the expected bacteria were determined, and several species of yeast were found, instead of the expected one. Mold contamination was also found. Using molecular diagnostic techniques, the presence of bacteria, yeasts, fungi and the genera Brevibacterium and Candida was proved.
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Metagenomic analysis of animal gut microbioma based on diet
Spanakis, Martin Nikolaos ; Čejková, Darina (referee) ; Bartoň, Vojtěch (advisor)
This bachelor’s thesis deals with the sequencing of the microbiome and its composi- tion. It focuses on the gut microbiome of animals, which differs among animals with different diets. The work describes theoretical knowledge about metagenomic analysis of the microbiome, such as sampling procedures, various sequencing methods and data processing. The practical part of the work includes the preparation of the dataset, which includes the collection of data and their preparation for the following metagenomic anal- ysis. The result of the work is the taxonomic classification of bacterial species in the samples and the analysis of their diversity according to the type of diet of individual animals.
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Gut microbiome and its changes related to therapy of chronic diseases
Hurych, Jakub ; Cinek, Ondřej (advisor) ; Kolář, Milan (referee) ; Falt, Přemysl (referee)
This work examines the response of the gut microbiome to therapeutic interventions in three longitudinal studies of chronic gastrointestinal diseases: Crohn's disease, celiac autoimmunity and irritable bowel syndrome. Multiple methods of stool microbiome analysis (especially massively parallel 16S rDNA or 18S rDNA sequencing and metagenomic sequencing) followed by bioinformatic and statistical analysis were used. In Crohn's disease, we detected a previously undescribed secondary nature of changes in the gut bacteriome after anti-TNF treatment. In celiac disease autoimmunity, where previous works described an effect of probiotic intervention on serological markers of the disease, the gut bacteriome and metabolome, we described the absence of significant changes in beneficial gut protozoa. In irritable bowel syndrome, we observed a significant response of the bacteriome after administering four doses of mixed microbiota transplantation but no response in the reduction of clinical symptoms. The results of these studies could contribute to a better understanding of the gut microbiome's role in the pathogenesis of these serious diseases. Keywords: microbiome, Crohn's disease, celiac disease, irritable bowel syndrome
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