Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 77 for “"metagenome"”.
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The integration of fine-scale DNA-DNA associations by inclusion of Hi-C DNA cross-linking information into metagenomic community analysis
… individual genomes, thereby deconvoluting the metagenome. To accomplish this, first an 𝘪𝘯 𝘴𝘪𝘭𝘪𝘤𝘰 investigation of the effectiveness of graph clustering as a means of metagenome deconvolution was conducted; where Hi-C proximity interactions defined the edges and assembly contigs defined the …
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
… bioinformatics investigations is the assembly of metagenome at the strain-level resolution. This is indispensable for gaining profound insights into microbial communities and addressing pivotal biological inquiries. Despite the availability of existing assembly tools, certain challenges remain …
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Computational methods for functional interpretation of diverse omics data
… levels (e.g., genome, transcriptome, proteome, metagenome) in human health and disease. However, the massive size and heterogeneity of raw data pose substantial computational and statistical challenges in integrating and interpreting these data. To overcome these challenges, we need …
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Degenerate oligonucleotide primed amplification of genomic DNA for combinatorial screening libraries and strain enrichment
… fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a …
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Comparative Analysis of Rhizosphere and Endosphere Microbiome of Different Blueberry Species (Vaccinium sp.)
… the hypothesis by comparing the microbiome and metagenome of five different species of blueberry comprising both wild and cultivated species. The results showed that statistically significant differences were seen between the wild and cultivated species of blueberry with respect to the microbial …
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Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa
… regions (Sanger sequencing) as well as their metagenomes (Oxford Nanopore Technologies). ChromasPro and seaview.exe were used for sequence analysis and tree building, respectively. MGnify and Flye were used for assessing the metagenomics of selected samples. Parsimony-based tree fitting was …
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Metagenomic approaches for examining the diversity of large DNA viruses in the biosphere
… first chapter of the thesis, I investigated 11 metagenome-assembled genomes (MAGs) of giant viruses previously surveyed from Station ALOHA in the Pacific Ocean. St. ALOHA is located near Hawaii and represents oligotrophic gyres which the majority of the ocean is made of them. I focused on 11 …
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GENOMIC SURVEILLANCE AND RISK-BASED ASSESSMENT OF ANTIBIOTIC RESISTANCE TRANSMISSION ACROSS TROPICAL AQUATIC ENVIRONMENTS
… 189 Klebsiella pneumoniae isolates, alongside metagenome-assembled genomes, revealed three distinct ARG transmission trajectories defined by the integrity of the ARG–mobile genetic element–pathogen linkage. High-risk clones (ST131, ST147) carrying clinically significant resistance genes …
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Deep learning approach to metagenomic binning
… the diversity of these populations from whole metagenome shotgun (WMS) sequencing reads is difficult because the size of these datasets and overlapping reads limit what kinds of analysis we can do. Current methods require matching reads to a database of known microbes. These methods are either …
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Metagenomic analysis of the biodiversity and seasonal variation in the meromictic Antarctic lake, Ace Lake
… community were studied using a time-series of metagenomes utilizing the Cavlab metagenome analysis pipeline. Statistical analyses of taxa abundance and environmental factors revealed the effects of the polar light cycle, with 24 hours of daylight in summer and no sunlight in winter, on the …
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Expansion of Deltaproteobacteria diversity from marine sediment reveals unique metabolic features
… we obtained hundreds of unique, uncultured metagenome-assembled genomes (MAGs) from a variety of coastal and deep-sea sediments. These 402 Deltaproteobacteria MAGs represent a 28% increase in Deltaproteobacteria genomes. Phylogenomic analyses revealed 12 novel lineages which consist entirely …
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Studies Towards the Discovery of Novel Natural Products Through Functional Analysis of Environmental DNA-Encoded Type II Polyketide Synthases
… By directly cloning environmental DNA (eDNA or metagenome) in a surrogate host, one can exhaustively investigate the metagenome, independent of the culturability of the source organisms. Metagenomic approaches can thus provide access to previously untapped pools of chemical diversity. These …
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An investigation of the microbial population in aquarium water, using next generation sequencing
… In this project, both 16S rRNA genes and whole metagenome of a bacterial community in a freshwater aquarium were analysed using next-generation sequencing (Ion PGM). Sequencing reads were trimmed using CLC genomics workbench. De novo assembly was performed using MetaVelvet and CLC genomics …
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Bacterial Plant Pathogen Identification using Genomics and Metagenomics
… of different tools, currently used for metagenome classification, was done to illustrate effective detection of bacterial pathogens. To develop computational methods for characterization, genomes of the plant pathogen Ralstonia solanacearum were studied to understand the basis of …
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Identification and characterisation of lignin degrading bacteria and enzymes fromlarval guts of the African Palm Weevil (Rhynchophorus phoenicis)
… functional metagenomicsanalysis from whole metagenome sequencing data derived from whole gut metagenomic DNA of APW larvae to identify genes and by extension, enzymes that can deconstruct lignocellulose and degrade its lignin component. The predominant bacterial genera found across all gut …
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DELINEATING GUT-MEDIATED RESPONSE AMONG MELANOMA PATIENTS UNDERGOING ANTI-PD1 IMMUNOTHERAPY
… from which we surveyed the gut microbiota, metagenome, and systemic immune profile. For validation, fecal samples from tumor-free subjects were used as reference; gut variability measures were compared against publicly available longitudinal studies; finally, multi-cohort validation was …
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A phylogenetic framework for large-scale analysis of microbial communities
… and for the placement of thousands of unknown metagenome-reconstructed genomes leading to the definition of many new candidate species. This poses the basis for large-scale and more accurate analysis of the microbiome.
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Surveying and harnessing the genetic, (meta)genomic, and metabolic potential of the deep carbonated biosphere
… GCS environments. Through 16S rRNA amplicon and metagenome sequencing, I identified Sulfurospirillum, Rhizobium, Desulfovibrio and members of the Clostridiales family associated with reservoir fluids. Annotations of complete genomes extracted from metagenomes predict diverse mechanisms for growth …
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Dynamics of the human gut microbiota in very early life
… and analysed the largest datasets of shotgun metagenomes, isolate genomes and metagenome-assembled genomes of the neonatal gut microbiota to date. In the largest birth cohort study of its kind, I profiled the gut microbiomes of 771 UK healthy term infants and mothers through shotgun …
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