The innate and adaptive immune processes are modulated by hormones including glucocorticoids and by microbiota. The exact mechanisms underlying the microbial and hormonal contributions to this control are not completely clear. Present study is therefore focused to crosstalk between microbiota and de novo biogenesis or local regeneration of glucocorticoids. In particular, the study analysed the effect of commensal microbiota on expression of genes encoding steroidogenic enzymes (Star, Cyp11a1, Hsd3b1, Cyp21a1, Cyp11b1) and regeneration of glucocorticoids (Hsd11b1) in adrenal glands, colon, spleen and mesenteric lymph nodes using conventional and germ-free mice. The expression of all 5 components of steroidogenesis was identified only in the adrenal gland and colon, whereas the lymphoid organs expressed predominantly Star, Cyp11a1 and Hsd3b1 indicating the ability to produce only progesterone but not corticosterone. Microbiota decreased the expression of Star in all studied tissues but the expression of other genes was insensitive to microbiota or did not respond homogenously depending on the tissue and gene. Hsd11b1 expression was upregulated by microbiota in the spleen but not in other tissues. Similarly, the in vitro treatment of immune cells isolated from mesenteric lymph nodes by microbial...

Diabetes has caused many deaths worldwide but can be combated at least partially by diet and physical activity. The gut microbiome shows correlation with both type 1 and type 2 diabetes, has modulatory effects on the immune system and implicates brain functions through the gut-brain axis, in part by microbial metabolites. Diet has long been known to impact the microbiome but exercise has gained interest within the last decade, with studies mostly done on rodents and athletes with somewhat positive results on its modulation of the microbiome. This literature study aims to evaluate whether exercise can influence the microbiome for healthy, prediabetic, and diabetic cohorts and what this might mean for host health. The database PubMed was searched for articles in January 2021 and inclusion criteria yielded 7 articles for review. These differed in methods, cohorts, and exercise interventions, and therefore cannot grant any strong evidence but indicate along with previous research that exercise affects the microbiome, with slight differences in responses depending on the individual’s current state and exercising methods. / Diabetes har orsakat många dödsfall världen över men kan bekämpas åtminstone delvis med hjälp av diet och fysisk aktivitet. Tarmens mikrobiom har visats korrelera med både typ 1 och typ 2 diabetes, har reglerande effekter på immunsystemet och inverkar på hjärnfunktioner genom tarm-hjärna-axeln, delvis via metaboliter från mikroberna. Det har länge varit känt att mat kan påverka mikrobiomet, men träning har också väckt intresse över det senaste årtiondet med studier som fokuserat mest på möss och atleter med någorlunda positiva resultat för dess förändring av mikrobiomet. Denna litteraturstudie syftar till att undersöka om träning kan ha effekt på mikrobiomet hos såväl friska människor som prediabetiker och diabetiker, och vad detta kan betyda för hälsan. En litteratursökning gjordes i databasen PubMed i januari 2021 som efter sortering enligt inkluderande kriterier gav 7 artiklar för granskning. Dessa använde olika metoder, undersökta grupper och träningsupplägg, vilket försvårar jämförelser men indikerar i linje med tidigare forskning att träning påverkar mikrobiomet, med en del skillnader i resultat beroende på individens status och träningsupplägg.

Deadwood is a hotspot of microbial diversity and its decomposition contributes to carbon and nitrogen cycling in temperate forests. The historically recognized importance of fungi in the decomposition of deadwood has recently been complemented by the description of bacterial functions thanks to the rapid progress of culture-independent methods based on the analysis of nucleic acids. To study different aspects of deadwood decomposition, a temperate mixed forest in Zofinsky prales National Nature Reserve was selected as a site with rich historical forestry data where deadwood decomposition represents an important process in wood turnover. The aim of this thesis is to describe role of bacteria in deadwood decomposition at fine scale resolution with respect to community composition, enzyme transcription, and metabolic potential of dominant species. Effects of deadwood age together with pH and water content on the bacterial community composition proved to be more important than tree species identity. Bacteria showed distinct composition between early and late community in decomposing deadwood. The bacterial community was also under a significant influence of fungal community composition. Despite being in a close contact, bacterial and fungal communities differed significantly between deadwood and the...

Inflammatory bowel disease is a serious condition with an incomplete etiology and pathogenesis. In this thesis, a mouse model of sodium dextran sulfate-induced inflammation was used to study different changes in the metabolism of germ-free and conventionally raised mice due to the development of the inflammatory process. NMR metabolomics of fecal, urine and serum samples, combined with uni- and multivariate statistical analysis, were used to characterize the changes. It was shown that the metabolic signature differs between germ-free and conventional mice. In germ-free mice, significant amounts of carbohydrates were found in feces. Their levels decreased during inflammation as they were excreted in urine. In contrast to conventional mice, germ-free mice also excreted large amounts of amino acids in feces during the developing inflammation. Disorders of sugar and protein metabolism found in germ-free mice indicate severe malnutrition caused by inflammation. The results show that the presence of a microbiome represents a protective mechanism against significant disruption in the body. A stability study of fecal extracts of healthy conventionally colonized mice confirmed that none of the identified and quantified metabolites showed significant systemic changes in several consecutively collected...

Inflammatory Bowel Disease (IBD) is a chronic and incurable condition that is increasing inprevalence across the globe. This illness consist of two forms: Crohn’s Disease (CD) andUlcerative Colitis (UC). CD is characterised by a patch inflammation pattern across the gut anda multitude of different factors, such as diet. Contemporary research has found a link betweengut dysbiosis and the development of IBD, suggesting that the microbial flora colonising the guthave a vital part to play in the development of CD.This paper aims to identify taxa associated with CD. This is done through the application ofmachine learning algorithms as standard univariate statistical methods fail to apply in the highlyinterdependent domain of the gut microbiome. The compositionally of the data and externalfactors influencing variance in the data will be taken into account.After applying a Center Log ratio transformation (CLR) to a MetaPhlAn3 taxonomic profile andusing a random forest classifier the following five taxa were identified as the most important inthe association to CD: Ruminococcaceae bacterium, Akkermansia muciniphila, Streptococcusparasanguinis, Flavonifractor plautii and Bifidobacterium bifidum.

Storage mite Acarus siro is one of the most distributed stored product mites in the world. It infests various products (grains, dried fruits, meat products, animal feed etc.) and causes allergic reactions in humans. For these reasons, it is important to find an effective strategy to suppress or even better to eliminate the mite from the storing facilities. Historically, there have been reported cases of the mite being resistant to several pesticides. In this thesis, four populations of Acarus siro were exposed to pesticides in different concentrations - first in the form of solutions and next as a diet additive. The populations showed divergent sensitivity to four selected pesticides (pirimiphos-methyl, chlorpyriphos-methyl, deltamethrin and deltamethrin in combination with piperonyl butoxide). The biggest differences were recorded in response to solutions of pirimiphos-methyl. This pesticide was then added to standard rearing diet in five concentrations. The mite populations were exposed to this died for 3 weeks. Control and pesticide-treated diet microbiome analyses revealed that 0.0125 µg×g-1 concentration causes hormoligosis in 6L and 6Tu strains. The same concentration was responsible for microbiome change in 6Z strain. Exposure to 1,25 µg×g-1 concentration caused microbial shifts in 6Z and...

Chronic Pseudomonas aeruginosa infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial microbiome profiles in the airway are associated with less inflammation. Thus, the hypothesis was raised that certain commensal bacteria might protect the host from inflammation. We therefore performed a screening study with commensals isolated from CF airway microbiome samples to identify potential beneficial commensals. We isolated more than 80 aerobic or facultative anaerobic commensal strains, including strains from genera Streptococcus, Neisseria, Actinomyces, Corynebacterium, Dermabacter, Micrococcus and Rothia. Through a screening experiment of co-infection in human epithelial cell lines, we identified multiple commensal strains, especially strains belonging to Streptococcus mitis, that reduced P. aeruginosa triggered inflammatory responses. The results were confirmed by co-infection experiments in ex-vivo precision cut lung slices (PCLS) from mice. The underlying mechanisms of the complex host-pathogen-commensal crosstalk were investigated from both the host and the bacterial sides with a focus on S. mitis. Transcriptome changes in the host in response to co-infection and mono-infection were evaluated, and the results indicated that several signalling pathways mediating inflammatory responses were downregulated by co-infection with S. mitis and P. aeruginosa compared to P. aeruginosa mono-infection, such as neutrophil extracellular trap formation. The genomic differences among S. mitis strains with and without protective effects were investigated by whole genome sequencing, revealing genes only present in the S. mitis strains showing protective effects. In summary, through both in vitro and ex vivo studies, we could identify a variety of commensal strains that may reduce host inflammatory responses induced by P. aeruginosa infection. These findings support the hypothesis that CF airway commensals may protect the host from inflammation.

The effect of gluten-free diet on β-cell residual capacity, immune function and gut microbiome in children with newly diagnosed type 1. diabetes Abstract The pathophysiology of the onset and progression of type 1 diabetes (T1D) is not fully understood. Gluten has a proinflammatory effect on the immune system and is therefore considered as one of the factors affecting the onset and progression of T1D. The aim of the thesis is to allow a complex insight into the role of the GFD on the residual β-cell capacity, T1D control, gut microbiome, gut permeability, subtypes of immune cells and the effect of gut microbiome transfer into germ-free non-obese diabetic (NOD) mice on the incidence of diabetes. On the group of 45 children with T1D (26 intervention group, 19 control group) we proved the association of the GFD with slower decrease of β-cell residual capacity (the difference in the trend of C-peptide decrease 409 pmol/l/year; p = 0,04) and lower HbA1c (by 7,8 mmol/mol; p=0,02). We also described the changes in the gut bacteria that were differentially abundant after the administration of the GFD and the changes in abundance of the regulatory and effector immune cells. We showed there was no change in the gut permeability with respect to the study group. We also proved that the transfer of human gut microbiota...

Introduction:Uveitis in an ocular inflammation affecting mostly people of working age. Uveitis is responsible for severe visual impairment despite of expanding new therapeutics. The animal models of uveitis were established, because the wide clinical variability of uveitis limits the studies in human medicine. The goal our project was to establish a reproducible model of experimental autoimmune uveitis in Czech Republic, and further on this model to observe the frequency of CD3+ and F4/80+ cells in retina, to assess the influence of microbial environment on intensity of intraocular inflammation and to test the therapeutical possibilities. Material and methods: The C57BL/6J mice were immunized by retinal antigen (IRBP 1-20, interphotoreceptor retinoid binding protein), enhanced by complete Freund's adjuvant and pertussis toxin and mild posterior autoimmune uveitis was induced. The mice were bred in conventional and germ-free (gnotobiotic) conditions. The uveitis intensity was evaluated in vivo biomicroscopically and post mortem histologically on hematoxylin eosin stained sections according to the standard protocol. The histological eye specimen were analyzed also by imunohistochemisty and by flow cytometry. Each experiment was performed for 35 days. The conventional mice with uveitis were treated...

The aim of this work was to gain new knowledge about mechanisms of autoimmune uveitis and to test new therapeutic possibilities that have not yet been studied in uveitis or whose effect is questionable. The main emphasis was placed on the role of microorganisms in the process of uveitis. A mouse model of experimental autoimmune uveitis including a germ-free model was used to achieve the aims and samples of patients' intraocular fluids were analyzed. In the experimental model, the intensity of inflammation was evaluated in vivo clinically and post mortem histologically. The effect of immunomodulatory treatment was evaluated. The intensity of inflammation was compared between groups of germ-free and conventional mice. The therapeutic effect of antibiotics administered to affect microbiome was investigated in conventional mice. In intraocular fluid samples of patients with autoimmune uveitis signs of infection were monitored and levels of cytokines and other factors were evaluated. Evaluation of the effect of immunomodulatory therapy has demonstrated the efficacy of mycophenolate mofetil, which supports its wider use in the treatment of autoimmune posterior uveitis in human medicine. The decrease in bacterial load has led to a decrease in the intensity of inflammation, thereby confirming the importance of...