La consommation d'aliments riches en ellagitannins (ETs) pourrait être associée principalement à la prévention des maladies cardiovasculaires et la régulation des cancers hormono-dépendants. Néanmoins, les ETs ne sont pas biodisponibles en tant que tel et, après avoir été partiellement transformés en acide ellagique (EA) dans le tractus gastro-intestinal (GI) supérieur, ils sont métabolisés dans le côlon par la flore intestinale en urolithines, un groupe de molécules plus biodisponibles et bioactives qui peuvent persister jusqu'à 4 jours à des concentrations relativement élevées dans le plasma et l'urine. La variabilité de l'excrétion des urolithines dans l'urine est importante et à partir d'un échantillon de population de 26 volontaires sains, trois groupes principaux d'individus ont pu être distingués : "faible ou non-excréteur d'urolithin », « Excréteur prédominant d'UA et dérivés» et « Excréteur prédominant d'UB et dérivés»". Ces groupes ont également été observés en considérant la cinétique totale d'excrétion sur une période de 4 jours après ingestion du jus et à des périodes différentes tout au long d'une année. Bien que les variabilités inter-et intra-individuelles soient relativement élevées, les individus conservent leur statut au cours des différentes périodes d'intervention même en modifiant les quantités d'ETs ingérées. L'analyse par UPLC-PDA/ESI-Q-TOF/MS2 a permis d'attribuer hypothétiquement une identité à 15 autres métabolites d'ETs dans l'urine, mais le profilage métabolomique n'a pas permis de discriminer d'autres composés exceptés les dérivés d'UA ou d'UB. La fermentation in-vitro des ETs et EA, par les matières fécales a montré une voie métabolique spécifique qui débouche sur la production d'UA. Néanmoins, les métabolites excrétés in vivo sont beaucoup plus complexes ce qui met en évidence de fortes interactions entre le système excréteur de l'hôte et la composition du microbiote intestinal. La recirculation hépatique suivie par une re-conversion des métabolites de phase II dans le côlon permettrait d'expliquer l'excrétion d'UB chez certains volontaires. L'écologie spécifique de la flore intestinale évaluée par la méthode des empreintes PCR-DGGE a permis d'identifier quelques microorganismes associés à une plus grande capacité de bioconversion des ETs en urolithins / Consumption of dietary ellagitannins (ETs) could be associated mainly with prevention of cardiovascular diseases and regulation of hormone-dependent cancers. Nonetheless, ETs are not bioavailable as such; therefore, after being partially converted into ellagic acid (EA) in the upper gastrointestinal (GI) tract, they undergo sequential bioconversion in the colon by gut microbiota into urolithins, a more bioavailable and bioactive group of molecules that persist up to 4 days at relatively high concentrations in urine. Variability of urolithin excretion in urine is high and three main groups, “no or low urolithin excreters,” “predominantly UA derivatives excreters” and “predominantly UB derivatives excreters,” were observed on a cohort of 26 healthy volunteers. These categories were also unambiguously observed following the total excretion of main ETs' metabolites over a 4 day period after ingesting one shot of juice, and at different periods of time along one year. Although relatively high inter- and intra-individual variabilities were observed, individuals preserved their status during various intervention periods with different amounts of ETs ingested. UPLC-PDA and ESI-Q-TOF/MS1 and MS2 allowed the tentative assignment of an identity to 15 other ETs metabolites in urine, but this profiling did not allow the discrimination of any other compounds aside from UA or UB derivatives. In-vitro fermentation of ETs and EA with fecal stools showed a specific metabolic pathway ending in the production of UA. Nonetheless, metabolites excreted in-vivo are much more complex, highlighting strong interactions between host excretory system and composition of gut microbiota. Hepatic recirculation and additional bioconversion of Phase II metabolites in the colon may explain predominant excretion of UB in some volunteers. Microbiota ecology assessed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE) fingerprint method allowed the association of some microorganism species to higher capacity of bioconversion of dietary ETs into urolithins.Key words: Ellagitannins, blackberry, urolithin, colonic metabolites, ETs degradation patterns, gut microbiota, gastrointestinal tract,

abstract: The Human Gut Microbiome (GM) modulates a variety of structural, metabolic, and protective functions to benefit the host. A few recent studies also support the role of the gut microbiome in the regulation of bone health. The relationship between GM and bone health was analyzed based on the data collected from a group of twenty-three adolescent boys and girls who participated in a controlled feeding study, during which two different doses (0 g/d fiber and 12 g/d fiber) of Soluble Corn Fiber (SCF) were added to their diet. This analysis was performed by predicting measures of Bone Mineral Density (BMD) and Bone Mineral Content (BMC) which are indicators of bone strength, using the GM sequence of proportions of 178 microbes collected from 23 subjects, by building a machine learning regression model. The model developed was evaluated by calculating performance metrics such as Root Mean Squared Error, Pearson’s correlation coefficient, and Spearman’s rank correlation coefficient, using cross-validation. A noticeable correlation was observed between the GM and bone health, and it was observed that the overall prediction correlation was higher with SCF intervention (r ~ 0.51). The genera of microbes that played an important role in this relationship were identified. Eubacterium (g), Bacteroides (g), Megamonas (g), Acetivibrio (g), Faecalibacterium (g), and Paraprevotella (g) were some of the microbes that showed an increase in proportion with SCF intervention. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2020

Hajj, the annual Islamic pilgrimage to Makkah, Saudi Arabia, is a unique mass gathering event that brings more than 2 million individuals from around the world. Several public health considerations, such as the spread of infectious diseases, must be taken into account with this large temporary influx of people. Gastrointestinal diseases, such as diarrhea, are common at Hajj, yet little is known about the etiology. The human gut microbiome, collection of organisms residing within the intestinal tract, has been under intense study recently, since next generation DNA sequencing technologies allow for extensive surveying of genetic material found in complex biological samples, such as those containing many different organisms. Thus, using 16S rRNA and metagenomic shotgun sequencing, we have characterized the gut microbiome of over 612 pilgrims with and without diarrhea. Several metadata factors, such as hospitalization and different comorbidities, were found to have significant effects on the overall gut microbiome composition. Metagenomic shotgun sequencing efforts revealed the presence of antimicrobial resistance genes originating from disparate regions from around the world. This study provides a snapshot of information concerning the health status of the gut microbiome of Hajj pilgrims and provides more context to the investigation of how to best prepare for mass gathering events.

Under the extreme arid conditions of deserts, long periods of drought, nutrient-poor soils and high temperatures severely challenge the primary productivity of the ecosystem. Desert plants have evolved morphological and physiological adaptations against abiotic stresses. Along with these adaptation strategies they can recondition their surrounding soil, which will result in the enrichment of nutrients and moisture in the soil surrounding the plant. Although such self-fertilization may support the growth of other sympatric plant species under the plant, competitive exclusion mechanisms (i.e., allelopathy) reduce this possibility. Consequently, this will affect the diversity and functionality of the edaphic microbial communities. I hypothesize that desert xerophytes recondition the soils surrounding their body along with combining the ‘fertility’ and ‘allelopathy’ mechanisms to create a favorable new niche in desert ecosystem. I tested this hypothesis on the soil reconditioned by Welwitschia mirabilis growing in its native environment, the Namib Desert, Namibia. The collected soils were first used to confirm that Welwitschia manipulates the surrounding soil creating a ‘fertile’ but ‘exclusive’ soil area around the plant. Along with evaluating the effect of the reconditioned soil on the germination and plant development under normal irrigation and controlled drought condition, using barley as phytometer. The physio-chemical (i.e., WHC and WP) and microbial community analyses demonstrate that W. mirabilis reconditions the surrounding soil creating an environmental gradient around itself, in which the fertility is increased, through the accumulation and incorporation of shed reproductive parts of the plants (i.e., cones) in the surrounding soil, that will stimulate the plant growth under drought stress. Along with the fertilization effect, soil reconditioning also favor the antagonist effect (i.e., allelopathy) against plant competitors (e.g., new germinating seeds) to protect its ecological niche. Furthermore, the microorganisms and/or soluble/thermolabile molecules contribute to the allelopathic effect activated by the soil-reconditioning around W. mirabilis. The interactions among W. mirabilis, soil and microbes highlight an adaptive strategy that combines soil fertilization and allelopathy that I defined as “Alleolofertility” strategy. This allelofertility island surrounding the W. mirabilis may contributes to explain the evolutionary success of such a ‘living fossil’.

The role of individual soil microorganisms changes over the course of a plant's life - microorganisms that have no discernable role at one developmental stage may affect the plant later in its growth. Traditional analysis of the soil microbiome, which has focused principally on the relative abundances (RA) of individual organisms, may be incomplete, as underlying differences in population size cannot be addressed. We conducted a metagenomic analysis of soil microorganisms from various maize (Zea mays L.) fields at two depths, accompanied by crop yield components, to provide insight into influences of edaphic microbes on maize productivity under commercial maize production systems in Missouri. This study assesses the influence of fungi and bacteria, not only in terms of RA, but also in their estimated absolute abundances (EAA), derived by combining the results of Illumina HiSeq sequencing data and phospholipid fatty acid abundance data. Significant interactions were identified between maize yield components and soil microbes at critical developmental states. Most interactions between fungi and yield components were negative, with notable exceptions. Bacterial interactions were more complex, with most interactions during early ear development identified as positive, and most interactions during tasseling identified as negative. In addition to the effects that microbial populations have on yield, plant populations reciprocally changed the microbial community. Plant developmental state was the greatest predictor of bacteria, with the microbial communities present during the active growing season being most similar to each other, whereas the preplant microbiome and post-reproductive microbiome being most similar to each other. Fungal communities were primarily dependent on location.

The theoretical part of the thesis is focused on the basic description of the physiology of the skin, human microbiome and a brief summary of where individual microorganisms occur. Furthermore, there is a list of analytical and microbiological methods that are used in this thesis. In the beginning, the practical part is focused on determination of antimicrobial effects of the chosen cosmetic products using microbial tests. Then, the inhibiton and microbial effect of the chosen cosmetic products on examined microorganisms has been measured using ELISA method. The second part of the thesis is focused on the isolation of bacterial DNA in quality that would be high enough to be used for amplification in PCR. There has been an optimalization of isolation of microbial DNA that was to be found on tested subjects’ skin. The presence of chosen microorganisms on skin before and after the usage of cosmetic products was measured using a PCR method. PCR products were then detected using gel electrophoresis. From the gathered data it is clear that the number of observed microorganisms has changed significantly after the application of cosmetic products.

The presented master thesis deals with the monitoring of the influence of polysaccharides which are used as an additive in the cosmetic products, on the monitored types of bacteria which are part of the skin microbiome. And it also deals with the study the effect of polysaccharides as prebiotics on selected species of bacteria that are part of the skin microbiome. Two polysaccharides were selected to determine the effects on the skin microbiome: Nanomoist and PoLevan S. The first part of the thesis focuses on the literature search which deals with skin anatomy, skin diseases and skin microbiome and its function. The experimental part is focused on monitoring changes in the quantity of selected microorganisms of the skin microbiome, before and after application of polysaccharides to the skin using qPCR. Staphylococcus epidermidis, Cutibacterium acnes, Escherichia coli and Micrococcus luteus were monitored. The PCR products were detected by agarose gel electrophoresis. The bacterium Staphylococcus epidermidis was detected on the skin to the greatest extent, especially after the application of the polysaccharides Nanomoist and PoLevan S. Thus, a positive effect of both polysaccharides on the growth of this bacterium was found.

Content: “Red heat” is an industry term that describes the appearance of mostly red-pink coloured macroscopic microbial colonies on salt-cured hides and skins. Red heat-affected stock is undesirable as the resultant leather often shows obvious defects; but why this contamination is only superficial in other instances remains unclear. Previous work has focused on pigmented halophiles (‘salt-loving’ microbes) isolated from curing salts as the primary culprit. However, the identity of causative agents remains unspecified. Also, the involvement of non-pigmented microbes, and of microbes native to hides and skins, could be better understood. Thus, an investigation of the microbial communities that inhabit untreated bovine hide, curing salt, unaffected salt-cured bovine hide, and red heat-affected cured hide is proposed to uncover the microbial agents responsible for this contamination. This project aims to define these microbial communities using both a culture-dependent and –independent approach. Methods of microbe identification focus on marker gene amplification and sequencing. This is in contrast to earlier work which was restricted solely to phenotypic analyses. The 16S ribosomal RNA gene marker is used to identify members of Bacteria and Archaea, while the 18S and ITS2 regions of the fungal ribosomal RNA operon are targeted to detect fungi. Metagenomic amplicon sequencing using the Illumina MiSeq platform employs these same markers to determine taxonomic composition and relative abundance. Preliminary results from culturing identified different dominant species in curing salts screened for microbial growth. In agreement with earlier culture-based studies, these isolates were mostly pigmented, highly salt-tolerant members of the halophilic archaea of family Halobacteriaceae, as determined by marker gene sequencing. However, in agreement with more recent work within food preservation technology, nonpigmented isolates of halophilic archaea of genus Natrinema and bacterial genus Chromohalobacter were also found. It was also revealed that non-pigmented, quick-growing, salt-tolerant, proteolytic microbes were easily cultured from red heat-affected hide, most of the isolates were identified by marker gene sequencing as bacterial Pseudomonas halophila or Salicola. To determine red heat-causing microbes, future work involves the screening of isolates for extracellular enzyme activity; the most likely cause of red heat-associated damage. Sterile-salted hide samples will be inoculated with selected individual and combinations of isolates, and then further examined using confocal microscopy to check for reproducibility of red heat-associated damage. Take-Away: Different microbial species are found in different curing salts. Not all microbes involved in 'red heat' contamination are pigmented. The purpose is the possibility to overcome all the restrictions connected with the pin-wheel machine, the improvement of actual EN ISO methods of leather measurement and a better instrument to define tolerances considering the couple leather-machine.

Sorghum crop has become attractive to breeders due to its drought tolerance, and many uses including a human food source, animal feed, industrial fibre and bioenergy crop. Sorghum, like any other plant, is a host to a variety of microbes that can have neutral, negative or positive effects on the plant. While the majority of microorganisms are beneficial, pathogens colonize plant tissues and overwhelm its defence mechanisms. This colonization is a direct threat to the sorghum productivity. The development of microbiome-based approaches for sustainable crop productivity and yield is hindered by a lack of understanding of the main biotic factors affecting the crop microbiome. Metabarcoding has proven to be a valuable tool which has been widely used for characterizing the microbial diversity and composition of different environments and has been utilized in many research endeavours. This study analyses the relationship between the microbiota and their response to natural pathogen infection in sorghum disease groups (R, MR, S and HS) and identifies the most dominant pathogen in the highly susceptible disease group. The study also, assesses the spore viability through the use of the automated cell counter and confirms Fusarium graminearum (dominant pathogen linked to the HS disease group) through sequencing of the marker genes, to subsequently characterize pathways likely to be involved in pathogen infection resistance. To achieve the objectives, a combination of 16S rRNA (V3/V4 regions) and ITS (ITS1/ITS4) of the internal transcribed spacer regions were amplified and sequenced using NGS technologies to study the microbiota in response to natural infection. Additionally, comparative transcriptional analysis of sorghum RILs in response to Fusarium graminearum infection was conducted through RNA-Seq. Upon natural infection, the foliar symptoms assessment of the RILs was conducted and four disease groups; resistant (R), moderately resistant (MR), susceptible (S) and highly susceptible (HS) were designated. The results of the present metabarcoding study indicate that resistant sorghum leaves (R group) supported a large diversity of fungal and bacterial microbes. The genera Methylorubrum, Enterobacter and Sphingomonas with reported plant growth promoting traits were more abundant and highly enriched in the R and MR group, with members of the latter genus significantly enriched in the R group. The resistant fungal group had a majority of OTUs showing similarity to well-known plant growth-promoting fungal genus including Papiliotrema (Tremellaceae family), which are known biocontrol agents. The yeast Hannaella was also highly linked with the resistant plants. Some Hannaella species are known to produce indole acetic acid (IAA) for promoting plant growth. Metabarcoding was also used to assess the major potential disease-causing taxa associated with the highly diseased group. It identified fungal pathogenic species, that have not previously been identified as pathogens of sorghum such as Ascochyta paspali and Ustilago kamerunensis (which are known pathogenic fungi of grass species) and were associated with the susceptible disease groups (S and HS). These analyses revealed the potential sorghum fungal pathogen Epicoccum sorghinum, and was highly linked with the S disease group. It further expanded the identification of a reportedly economically importance species causing sorghum related diseases Fusarium graminearum (anamorph Gibberella zeae). This species has also been identified in this study to be highly associated with the RILs showing major disease symptoms. Fusarium graminearum a significant pathogen in winter cereals and maize has been associated with stalk rot of sorghum and sorghum grain mould. The presence of Fusarium graminearum in sorghum can be a toxicological risk, since this species has the potential to produce mycotoxins. It was further shown that natural pathogen infection results in distinct foliar microbial communities in sorghum RILs. The co-occurrence taxa represented by Tremellomycetes and Dothiomycetes fungal classes and Bacillaceae and Sphingomonadaceae bacterial family had more central roles in the network. The modules which are located centrally on the network have been expected to play important ‘topological roles’ in interconnecting pairs of other fungal and bacterial taxa in the symbiont–symbiont co-occurrence network. These taxa having a central role, are considered to be keystone microbes, and have been suggested to be drivers of microbiome structure and functioning. The results of bacterial and fungal community composition, community co-occurrences further suggested the importance of keystone taxa which may disproportionately shape the structure of foliar microbiomes. The foliar disease symptom assessments revealed that sorghum RIL 131 was highly diseased and RIL 103 did not show any visible disease symptoms and were subsequently used for transcriptomic analysis. Gene expression patterns were studied between the identified RIL that did not show visible symptoms (resistant RIL no 103) and the RIL that showed major disease symptoms (susceptible RIL no 131). Fusarium graminearum the dominant potential pathogen found in this study to be associated with the highly susceptible plants was used to inoculate RILs at seedling stage in a greenhouse and samples were collected in triplicates at 24 hours post infection (hpi), 48 hpi, 7 days post infection (dpi) and 14 dpi. Prior to that, ITS and UBC genes confirmed the identity of Fusarium graminearum, and the automated haemocytometer confirmed the cell/spore viability. Using RNA-Seq analysis it was shown that the resistant RIL had defence related pathways from early response (24- 48 hpi) to late response (7-14 dpi). And the more the infection progressed, the more the defence related genes were up-regulated in terms of fragments per kilobase of exon model per million reads mapped (FPKM) and False Discovery Rate (FDR ≤ 0.05) values. Transcriptome time series expression profiling was used to characterize the plant response to Fusarium graminearum with the Dirichlet Process Gaussian Process mixture model software (DPGP) in susceptible and resistant RILs. The susceptible RIL (number 131) transcriptional response upon Fusarium graminearum infection presented differences of the closely related clustered expression profiles across all timepoints in both RILs. Group 2 exclusively clustered the genes encoding the sesquiterpene metabolism pathway, which is one of the major physiological change occurring in response to fungal infection and has been previously reported to produce the mycotoxins associated with Fusarium head blight (FHB) of cereals. This pathway presented an increase from the initial infection phase to the late infection phase in group 4, the genes encoding starch sucrose, metabolism and cyanoamino acid pathways presented a pattern that had a sharp decline from 48 hpi -14 dpi (at a later stage of infection). This could suggest that, as the time progresses in the susceptible RIL the pathways which are important in plant defence declines at a late infection stage. Group 3 presented a pattern increase of the 5-lipoxygenase (LOX 5) gene expressed from 48 hpi-14 dpi timepoints. The loss and silencing of LOX5 function have in the past described to be linked with enhanced disease resistance. In this study the LOX5 was expressed and this could suggest that LOX5 might have a function as a susceptibility factor in disease caused by Fusarium graminearum in sorghum RILs. CBL-interacting protein kinase 6 (CIPK6) gene was also associated with this group. This gene has been associated with negative regulation of immune response to Pseudomonas syringae in Arabidopsis as plants overexpressing CIPK6 were more susceptible to Pseudomonas syringae. Transcriptional response of a resistant RIL (number 103) to infection with Fusarium graminearum presented an increase in genes encoding metabolic and biosynthesis of metabolites pathways in group 1 and group 4 at early infection phase and a sharp decline in the late infection phase. An increase in the genes encoding pathways in earlier infection state could suggest the establishment of a beneficial energy balance for defence. Additionally, genes encoding phenylpropanoid (PAL), galactose and glycolysis pathway were amongst the genes increased at early stages of infection in group 1. Sugar can play a significant role in resistance to fungal pathogens through phenylpropanoid metabolism stimulation, and previous studies showed that the phenylpropanoid pathway could play a role in resistance of wheat to Fusarium graminearum and deoxynivalenol. Overall, this study represents a first step in understanding the molecular mechanisms involved in resistance to Fusarium graminearum. This analysis has also identified the reported beneficial microbes and defence related genes and pathways. Together, the current findings suggest that different ‘resident’ consortia found in naturally infected and uninfected sorghum plants may be viable biocontrol and plant-growth promoting targets. Cultivation studies may shed light on the nature of the putative symbiotic relationships between bacteria and fungi. These results have consequences for crop breeding, and the analysis of microbial diversity and community composition can be useful biomarkers for assessing disease status in plants. The transcriptome and metabarcoding data generated will help guide further research to develop novel strategies for management of disease in sorghum RILs through the integrative approach considering both beneficial microbes and defence related genes. This provides the baseline information and will positively impact in the development of Fusarium graminearum resistant genotypes in future through the integration/incorporation of beneficial microorganisms (bacteria and fungi) and resistant genes in breeding strategies. / Life and Consumer Sciences / D. Phil. (Life Sciences)

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.