|
|
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
|
|
|
Biofilm formation in probiotic cultures and its application in pharmacy
Ryšávka, Petr ; Obruča, Stanislav (referee) ; Vorlová, Lenka (referee) ; Márová, Ivana (advisor)
The work was comprehensively focused on the development of adhesive forms of probiotics in the form of a biofilm on combined carriers with a prebiotic component. The second part dealed with the influence of food on the multiplication and survival of selected types of probiotic bacteria. Subsequently, the effect of individualized probiotic supplements on changes in the human intestinal microbiome was monitored. Suitable adherent probiotic strains for biofilm formation were selected and tested. Methods have been introduced and different variants of carriers for culturing and binding bacteria have been tested. In vitro experiments verified the stability of biofilm stucture and its resistance to low pH, bile and antibiotics in comparison with the planktonic cell form. The antimicrobial effect of probiotic strains in the form of a biofilm was studied. The cultivation of the multispecies biofilm on the combined carrier was optimized and the stability of the biofilm and the final viability of probiotic bacteria were confirmed. Furthermore, the influence of various foods and beverages on the viability of probiotic bacteria was evaluated with emphasis on the simulation of passage through the gastrointestinal tract. Both models, solutions with standardised concentrations of alcohol, sugar, salts, proteins or different pH and different types of real foods and beverages were tested. The effect of food and beverages was tested on monocultures of Lactobacillus acidophilus, Bifidobacterium breve and on probiotic capsules containing a mixed culture of probiotic microorganisms. The survival of probiotics in various food matrices in the simulated gastrointestinal tract was quantitatively different. We managed to define foods suitable for supporting the multiplication of probiotic bacteria. A separate part of the work was focused on the targeted modulation of the intestinal microbiome by individualized probiotics that were prepared on the basis of molecular biological analyzes of the intestinal microbiome aimed at detecting the percentage of lactobacilli, bifidobacteria and phylum Firmicutes and Bacteroidetes. Personalized probiotic supplementation confirmed the positive effect of this approach on microbiome changes, especially on the increase of the content of lactobacilli, bifidobacteria and the overall diversity of the microbiome.
|
|
|
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.
|
|
|
Bacteria Classification Based on Marker Genes
Pelantová, Lucie ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
The aim of this work is proposal of new method for bacteria classification based on sequences of marker genes. For this purpose was chosen 10 marker genes. Resulting MultiGene classifier processes data set by dividing it in several groups and choosing gene for each group which can distinguish this group with best results. This work describes implementation of MultiGene classifier and its results in comparison with other bacteria classifiers and with classification based entirely on gene 16S rRNA.
|
|
|
Vliv změny stravovacího režimu na vybrané ukazatele mikrobiomu lidského trávicího traktu
Patloka, Ondřej
The literature review of this thesis discusses the intestinal microbiome of the human gastrointestinal tract. The main attention is paid to the chapters on the development of the intestinal microflora within the life stages of a person, the importance of the microbiota in terms of metabolism and influencing the health of the host, and the influence of the way of eating in terms of the intake of basic nutrients and specific food components of the diet, which can change the bacterial diversity and composition of the intestinal microflora. In the practical part, a microbiological analysis of the fecal microflora of six individuals (n=6) who underwent a weight reduction course was performed. During the experiment, 3 microbiological analyzes of the stool of the probands were performed within the monitored period, i.e. (at the beginning of the weight reduction course, at its end and in the period after the end of the weight reduction course). Microbiological analysis was performed by the plate method, where the number of KTJ/g stool of the probands was evaluated after cultivation. For each of the probands, one sample was analyzed in each phase of the experiment. For statistical evaluation, the averages of log KTJ/g from the stool of all probands within each phase of the experiment were used. At the same time, there was a detailed evaluation of the intake of basic nutrients and other food components of the diet from the dietary records of the probands within the individual periods of the experiment. At the end, a correlation analysis was performed between the observed parameters. During the experiment, there was a decrease in the intake of total carbohydrates, monoenoic and trans fatty acids (P<0.05). In the group of probands, a tendency to decrease total energy intake and increased fiber intake was also noted. As part of the reduction course, there was a decrease in the abundance of Bacteroides spp. and lactic acid bacteria (P<0.05). In contrast, the numbers of Lb were increased at the end of the reduction program. acidophilus and Lb. rhamnosus in the stool of probands (P<0.05). In addition, in the period after the end of the reduction course, there was an increase in the abundance of fecal Bifidobacterium spp. (P<0.05) and a reduction in the number of Enterococcus spp. in the proband group (P<0.05). Based on the detected changes in the abundance of the bacterial composition of the cultured taxa, a possible reduction in the body weight of the probands within the monitored experiment can be assumed.
|
|
|
The modification of gut microbiota composition by dietary intervention: the effect of plant-based and western-type diet
Ďásková, Nikola ; Cahová, Monika (advisor) ; Beneš, Jiří (referee) ; Tlaskalová - Hogenová, Helena (referee)
This thesis explores the relationship between diet, gut microbiota, and metabolic health, with a particular focus on their association with non-communicable metabolic diseases (NCDs) such as obesity and type 2 diabetes (T2D). The aim of the first study is to assess compositional and metabolic differences in gut microbiota between healthy lean long-term vegans and omnivores. The study reveals that while the gut microbiota composition is not significantly different between the two groups, there are significant differences in the fecal, serum and urinary metabolome. These differences may be attributed to the different availability of substrates in the diet, as the vegan diet is associated with a shift from a proteolytic to a saccharolytic fermentation program. Our results support the hypothesis of both resilience and metabolic flexibility of the adult gut microbiota. In addition to taxonomic analyses, this dissertation also includes metabolomics to evaluate the functional manifestations of the gut microbiota. We introduce a novel method to assess the ability of the gut microbiota to produce beneficial metabolites with a specific focus on butyrate synthesis using qPCR quantification of bacterial butyryl-CoA:acetate CoA-transferase. In silico, we identified bacteria among the human gut microbiota that...
|
|
|
Opioid-induced microbial dysbiosis
Popjak, Šimon ; Drastichová, Zdeňka (advisor) ; Stehlíková, Zuzana (referee)
The aim of this bachelor thesis is to describe the consequences of opioids in relation to the gut microbiome. Chronic opioid use induces microbial dysbiosis in the gut, where both functional and structural changes in the composition of the microbiome occur. This disrupts gut homeostasis and leads to diseases. The diversity of microbial organisms decreases and the expression of neurotransmitters changes. Opioids interfere with the microbiomeň-gut-brain axis, which normally functions in symbiosis. They alter the composition of the gut microbiota, affect the function and structure of the gut epithelium and the expression of neurotransmitters in the nervous system. This thesis focuses primarily on the action of morphine, the action of which has been desribed the most. Keywords: opioids, microbiome, dysbiosis, microbiome-gut-brain axis, gut homeostasis
|
|
|
Role of basidiomycete yeasts in the lichen symbiosis
Jerhot, Štěpán ; Steinová, Jana (advisor) ; Černajová, Ivana (referee)
Lichens are, according to the latest definition considered ecosystems, which consist of a fungus, one or more photosynthesizing partners and an undefined number of additional microorganisms. The role of basidiomycete yeasts, which were shown to appear in many lichen species, has been discussed in the latest lichenological scientific papers. This bachelor thesis summarizes the knowledge about the distribution of lichen-associated yeasts and their importance in these symbioses. It also presents some of the methods newly used to study yeasts in lichen symbioses and compares the often inconsistent results based on the methods used in the papers. The topic is not sufficiently covered to draw sufficiently robust conclusions about the role of yeasts in lichen symbiosis. However, the results to date suggest that lichen yeasts do not have any significant specificity of association with mycobiont species, and there has been no support that yeasts directly enhance host fitness. A more detailed depiction of the structures that yeasts form at sites of contact with the host and a description of the mechanisms by which the participating partners communicate with each other could help to definitively determine their role in the lichen symbiosis.
|
|
|
Interactions among free-living prokaryotes and protists in microbial communities
Jirouchová, Kateřina ; Pánek, Tomáš (advisor) ; Fiala, Ivan (referee)
Protists and prokaryotes live in the natural environment in complex microbial communities whose members interact with each other. These communities consist of a few to many species that interact with each other in many ways such as predation/prey, ecto/endosymbiosis, parasitism, modulation of development or behaviour and harmful algicidal/bactericidal interactions, resulting in a complex network of interactions that influence structure of the microbial community as well as metabolism and behaviour of present species. This bachelor thesis is an overview of the interactions between free-living protists and prokaryotes within microbial communities, excluding well-studied interactions such as predation, parasitism, and ecto/endosymbiosis, while focusing on the diversity of lesser- known interactions, highlighting their importance and future research opportunities.
|
|
|
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...
|
guest ::
