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...

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The gut microbiota and its metabolites have vast impacts on the human digestive system, immune system, and health outcomes. Short chain volatile fatty acids (SCVFAs) present in feces can be representative of the interactions of the microbiota present in the gut. Low microbiota diversity in the human gut is highly associated with obesity and adverse health outcomes. Furthermore, the maternal microbiome has a direct impact on neonatal microbiota through various pathways such as environment, skin flora, breast milk composition, and vaginal secretions. This study is aimed to further understand the associations between various factors (maternal adiposity, gestational time, length of life, delivery mode, and race/ethnicity ) and neonatal microbiome and its metabolites, SCFA. Data (pre-pregnancy BMI, gestational time, length of life at time of sample collection, delivery mode, race/ethnicity, SCVFA profiles, fecal fermentation profiles, and 16s rRNA sequences, n=75) was obtained from 75 mother-infant dyads. Qiagen CLC Genomics Workbench was used to process 16s RNA data, generate quantitative and qualitative measures of alpha and beta diversity, and generate an analysis of the composition of microbiomes for differential abundances. Multiple metrics were analyzed for alpha and beta diversity and no significant differences were found for acetic acid (A), propionic acid (P), butyric acid (B), or APB combined. Shannon diversity index, a measure of Alpha diversity, showed no significant difference between groups in each subset. BMI differences were significant for no c-section vs. c-section and Black vs. White race/ethnicity. There were no significant differences found in PERMANOVA, a measure of beta diversity, or found in differential abundances among the groups.

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Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate hair microbiome and 2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we would expect significant differences in microbiome diversity across host body sites, host sex, host housing institutions, and host species. We found that the hair microbiomes of these captive primates contained high abundances of gut-, respiratory-, and environment-associated microbiota rather than skin-associated microbiota. We also found that host species identity is the strongest predictor of both hair microbiome diversity and composition, while sex and body region are strong predictors of taxonomic richness and microbiome composition, and institution is a moderate predictor for both diversity and composition. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and vary both within and across primate species, and that there may be transmission of microbes across primate body regions. These findings have important implications for understanding the biology and conservation of both wild and captive primates.