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Showing 111 to 118 of 118 (0.026 seconds)Spelling suggestions: "subject:"metagenomic"" "subject:"metagenomics""
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Exploration of microbial diversity and evolution through cultivation independent phylogenomicsMartijn, Joran January 2017 (has links)
Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.
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Capture de gènes par hybridation couplée au séquençage de nouvelle génération pour l'exploration d'échantillons métagénomiques. : Génomique et écologie microbienne / Hybridization capture coupled to next-generation sequencing to explore metagenomic samplesGasc, Cyrielle 28 October 2016 (has links)
Les microorganismes représentent la forme de vie la plus diverse et abondante sur Terre et jouent un rôle fondamental dans tous les processus biologiques. Cependant, du fait de la grande diversité des communautés microbiennes, la caractérisation fine des environnements complexes reste difficile par les approches moléculaires actuelles de PCR et de métagénomique. En effet, ces approches ne conduisent qu’à une caractérisation partielle des communautés et ne permettent pas systématiquement d’associer la structure des communautés aux fonctions métaboliques réalisées. L’approche de capture de gènes par hybridation appliquée à des échantillons métagénomiques complexes a démontré son intérêt pour révéler toute la diversité connue mais aussi inconnue des biomarqueurs fonctionnels ciblés, ainsi que pour enrichir leurs régions flanquantes sur quelques centaines de permettant en évidence des associations de gènes. Ainsi, les travaux de thèse ont visé à développer une nouvelle méthode de capture de gènes par hybridation capable d’enrichir de façon ciblée de larges régions génomiques à partir d’échantillons complexes, permettant ainsi de faire le lien entre structure et fonction des communautés microbiennes. Ces développements ont nécessité la détermination de sondes de capture, l’utilisation d’une méthode d’extraction d’ADN de haut poids moléculaire et la mise au point d’un protocole de capture permettant de piéger des fragments nucléiques de grande taille (jusqu’à 50 kb). La validation de la méthode de capture par hybridation sur un échantillon environnemental de sol a permis de révéler tout son potentiel. Appliquée au gène exprimant l’ARNr 16S, cette stratégie a permis de révéler une diversité microbienne non accessible par les approches moléculaires conventionnelles, avec une résolution d’identification jusqu'au niveau de l’espèce rendue possible grâce à la reconstruction de la séquence complète de ce marqueur phylogénétique. Appliquée à un gène fonctionnel, elle a conduit à la reconstruction de la séquence du biomarqueur et de ses régions flanquantes pouvant atteindre plusieurs dizaines de kb, permettant d’identifier les microorganismes possédant les capacités métaboliques d’intérêt. Ainsi, la capture par hybridation représente une approche alternative prometteuse pour le diagnostic environnemental en conduisant à une meilleure caractérisation des communautés microbiennes. / Microorganisms are the most diverse and abundant life forms on Earth and are key players in thefunctioning of all biological processes. Nevertheless, PCR and metagenomics strategies aiming to describemicrobial communities are hampered by their huge diversity. Indeed, these molecular methods only drive to apartial description of communities and do not systematically allow linking functions back to the identities of themicroorganisms. Hybridization capture applied to complex metagenomic samples has demonstrated its efficiency to reveal all known and unknown diversity of targeted biomarkers, and to enrich their flanking regions over a few hundred bp facilitating the discovery of gene associations.Thus, this work aimed at developing a new hybridization capture method capable of specifically enrichinglarge genomic regions from complex samples allowing to associate structure and functions of communities. Thedevelopment of this method required the design of capture probes, the use of a high molecular weight DNAextraction method, and the elaboration of a capture protocol dedicated to the enrichment of large genomicfragments (up to 50 kbp).The validation of the hybridization capture method on an environmental soil sample uncovered all itspotential. Applied to the 16S rRNA gene, this strategy revealed greater microbial diversity than conventionalmolecular methods and improved phylogenetic resolution up to the species level thanks to the reconstruction offull-length genes. Applied to a functional gene, the method enabled the reconstruction of large genomic regionscarrying the targeted biomarker and its flanking regions over several tens of kbp, leading to the identification ofmicroorganisms with specific metabolic functions. Hybridization capture thus appears as a promising alternativemethod for environmental diagnosis, through providing a better knowledge of microbial communities.
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FUNCTIONAL DIVERSITY OF FUNGI ASSOCIATED WITH DURUM WHEAT ROOTS IN DIFFERENT CROPPING SYSTEMS2013 June 1900 (has links)
Differences in pea (Pisum sativum L.) and chickpea (Cicer arietinum L.) microbial compatibility and/ or their associated farming practices may influence root fungi of the following crop and affect the yield. The main objective of this research was to explain the difference in durum wheat (Triticum turgidum L.) yield the year after pea and chickpea crops through changes in the functional diversity of wheat root fungi. The effect of fungicides used on chickpea on the root fungi of a following durum wheat crop was studied using plate culture and pyrosequencing. Pyrosequencing detected more Fusarium spp. in the roots of durum wheat after fungicide-treated chickpea than in non-fungicide treated chickpea. Plate culture revealed that the functional groups of fungi responded differently to fungicide use in the field but the effect on total community was non-significant. Highly virulent pathogens were not affected, but antagonists were suppressed. More fungal antagonists were detected after the chickpea CDC Luna than CDC Vanguard. Fungal species responded differently to the use of fungicides in vitro, but the aggregate inhibition effect on antagonists and highly virulent pathogens was similar.
The effect of chickpea vs. pea previous crop and different chickpea termination times on root fungi of a following durum wheat crop was studied. The abundance of Fusarium spp. increased after cultivation of both cultivars of chickpea as compared to pea according to pyrosequencing and was negatively correlated with durum yield. Plate culture analysis revealed that fungal antagonists were more prevalent after pea than both cultivars of chickpea and chickpea CDC Vanguard increased the abundance of highly virulent pathogens. The abundance of highly virulent pathogens in durum wheat roots was negatively correlated to durum yield. Early termination of chickpea did not change the community of culturable fungi in the roots of a following durum crop.
It is noteworthy that Fusarium redolens was identified for the first time in Saskatchewan and its pathogenicity was confirmed on durum wheat, pea and chickpea. The classical method of root disease diagnostics in cereals is based on the examination of the subcrown internode. I evaluated the method by comparing the fungal communities associated with different subterranean organs of durum wheat. The fungal community of the subcrown internode was different from that of roots and crown, suggesting cautious use of this method.
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Metagenomanalysen von zwei Habitaten mit (hemi-)cellulolytischen mikrobiellen Gemeinschaften / Metagenome analyses of two habitats with (hemi-)cellulolytic microbial communitiesWittenberg, Silja 22 January 2010 (has links)
No description available.
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Metagenomic Analyses of Glacier Ice / Metagenomanalysen von GletschereisSimon, Carola 21 January 2009 (has links)
No description available.
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Design, expression and purification of virus-like particles derived from metagenomic studies : Virus-like Particles (VLP) of novel Partitiviridae species, Hubei.PLV 11, and novel Soutern pygmy squid flavilike virus were designed, expressed using the bac-to-bac expression system and then pruified using various methodsAyranci, Diyar January 2021 (has links)
Viruses are entities which are made of a few genes and are reliant on obligate parasitism to propagate. Due to the obligate connection to their hosts, virus evolution is constrained to the type of host. Viruses however do transmit to evolutionary distinct hosts; in these cases, the phylogenetic relationship of the hosts usually are close. In some instances, RNA-viruses have made host jumps between evolutionary distant hosts, such as the host jump from invertebrates to vertebrates, and fungi to arthropod. Partitiviruses are double stranded RNA viruses which mainly infect fungi and plants. The defining characteristic of these double stranded RNA viruses are the double layered capsids which are formed by a single open reading frame (ORF). The capsid proteins form icosahedral virus particles which are in the magnitude of 30-40 nm. Metagenomic studies have discovered partitiviruses originating from an insect in the Odanata family, a finding which contradicts the fungal host specificity of partitiviruses. The finding of the Hubei.PLV 11 thus implies the existence of a partitiviruses containing structural elements in their capsids which could be involved in the infection of arthropods. Thus, this virus could be used as a model for a structural comparison with its fungi infecting relatives with hopes to identify common viral structural factors necessary for the infection of arthropods. For this purpose, the Hubei.PLV ORF was cloned and then transfected into insect Spodoptera frugiperda (Sf-9) cells using a baculovirus expression system, “bac-to-bac” expression system. The FLAG-tagged capsid proteins were expressed by the Sf-9 cells to be approximately 60 kDa. After ultra-centrifugation in a sucrose gradient, some spontaneous assembly into the expected ~40 nm icosahedral virus-like particles were observed using low resolution scanning electron microscopy. The observed particles were also confirmed by a dynamic light scattering experiment (DLS) and a higher resolution cryo-EM microscope. Thus, the bac-to-bac expression system can be used to produce VLPs from this genus of viruses, and this metagenomically derived virus genome. However, for future success in defining a high-resolution model of this virus, it is recommended that the Sf-9 culture volume is sufficiently high for enough particle production which is necessary for a high-resolution map. The other virus, the Southern pygmy squid Flavilike virus (SpSFV) has been suggested to be the oldest relative of the land based flaviviruses. The SpSFV was found to be the most divergent of the flaviviruses, and to infect invertebrates. Solving for the structure of the SpSFV and comparing it to vertebrate infecting flaviviruses could therefore lead to the identification of factors necessary for the adaptation to vertebrates and thus the humoral immunity by flaviviruses. The soluble E-protein was expressed using the bac-to-bac expression system. The protein was indicated to be multiglycosylated and approximately 50 kDa which is in line with other strains in the genus. Affinity chromatography did not elute this protein, likely due to the His-tag not being spatially available. Cation exchange could elute some protein, but not much from the small ~30 mL culture. To conclude, VLP assembly was confirmed by the Hubei.PLV, thus, solving for the structure is a distinct possibility when a larger Sf-9 culture is used to produce the VLPs. For the SpSFV soluble E-protein, the protein is secreted into the supernatant of the Sf-9 cultures, making purification a possibility. For this, a large Sf-9 culture can be used to produce this protein and then purify it with a cat-ion exchange chromatography.
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Investigation of the cross-talk between gut microbes and plasma metabolites in the development of post-traumatic epilepsyMäkinen, Nelly January 2024 (has links)
The aim of this project has been to investigate whether there are correlations to be found between gut microbes and serum metabolites, which could be involved in the development of epilepsy. To do so, metabolomics data containing metabolites and metagenomics data containing bacteria have been integrated and used in a pipeline utilizing the software package DIABLO in R Studio. DIABLO stands for Data Integration Analysis for Biomarker discovery using Latent cOmponents and utilizes multi-block pls-da to integrate multiple omics data sets to find potential biomarkers. The results in this project are mainly divided into two groups, the first group being from taking samples at an early time point, where subjects have not yet developed symptoms of epilepsy and the second group being from taking samples at a late time point, where the subjects have developed epilepsy. To find biomarkers in the data used for the integration, two subgroups are of highest interest, namely subgroup PTE, which is the group that develops epilepsy symptoms after an induced trauma to the brain, as well as subgroup TBI which do not develop epilepsy symptoms after an induced trauma to the brain. Results from the early time point suggests that bacteria such as those from Phelethenecus, Christenselellales, Ventrimonas, Ruminococcaceae and Acetatifactor, as well as metabolites such as LPC 17:0, Indole and Indole-3-carboxyaldehyde might be of interest in finding biomarkers previous to the development of epilepsy after induced brain trauma. Results from the late time point suggests that bacteria such as those from Muribaculaceae and Avidehalobacter, as well as metabolites such as Dioctyl sulfosuccinate, Canrenone, LPC 18:0, Uric acid, Arjunolic acid and Pseudouridine might be of interest in finding underlying mechanisms behind the existing condition of epilepsy. The hope is that findings in this paper might aid in future development of knowledge behind this disease as well as its underlying mechanisms.
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Identifikation von Genen und Mikroorganismen, die an der dissimilatorischen Fe(III)-Reduktion beteiligt sind / Isolation of Genes and Microorganisms Involved in Dissimilatory Fe(III)-ReductionÖzyurt, Baris 21 January 2009 (has links)
No description available.
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