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 “"metagenomic sequencing"”.
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Optimal clustering techniques for metagenomic sequencing data
Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We …
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Medical Engineering and Medical Physics: Metagenomic Sequencing for Viral Diagnostics and Discovery
The application of metagenomic sequencing is transforming microbiology by directly interrogating the entire community composition of a clinical sample in an unbiased manner, reducing reliance on culture-dependent approaches. In concert with the advent of next generation sequencing (NGS) …
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Microorganisms and Functional Genes Associated with Cometabolic Degradation of 1,4-Dioxane in Biologically-Active Carbon Biofilters Applied for Potable Reuse Treatment
… one organism or one gene at a time. Shotgun metagenomic sequencing is a high-throughput nontargeted means of broadly profiling microbial taxa and functional genes involved in various metabolic processes. In this thesis, methods for DNA extraction from granular activated carbon applied to …
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Developing a Computational Pipeline for Detecting Multi-Functional Antibiotic Resistance Genes in Metagenomics Data
… resistance. In recent years, next-generation sequencing of environmental samples (metagenomic sequencing data) has become a prolific tool for the field of surveillance. Metagenomic data are nucleic acid sequences, or nucleotides, of environmental samples. Metagenomic sequencing data has been …
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Leveraging community-based sequencing approaches to characterise the dairy microbiome
… microorganisms, advances in high-throughput DNA sequencing have enabled the study of entire microbial communities in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used …
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Human papillomaviruses of skin and genital lesions
… among women with minor cervical abnormalities. Metagenomic sequencing identified 15 known HPV types, four previously known HPV types and two novel putative types in cutaneous lesions (n=369) and swabs from top of the lesions (n=142) (SCC, AK and keratoacanthoma). The prevalence and viral load of …
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The skin microbiome in health and atopic dermatitis
… characterise skin microbial diversity is through metagenomics. A previous investigation of the skin microbiome found that more than half of the sequenced skin metagenomic reads did not align to reference genomes, complicating the analysis of skin metagenomic datasets. To address this issue, we …
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Multi-site sampling and risk prioritization of antibiotic resistance genes in sewage environments
… resistance found in wastewater by combining metagenomic sequencing of wastewater environments with risk prioritization of resistance genes. We find that many of the genes commonly found in wastewater are not readily present in humans. Ranking antibiotic resistance genes based on their …
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Necrobiome Succession in Muscle Tissue as a Potential Indicator of Postmortem Interval
… human decomposition. Utilization of 16s rRNA sequencing provided information used to assess the overall diversity and variability of the necrobiome community composition over the course of the decomposition process for three donors. Human remains were donated to Forensic Research Outdoor …
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Vaginal Microbiota : Sampling, Clinical Equivalence, and Combined Sequencing
… 100 years. The novel technologies, especially sequencing, have revealed the unforeseen complexity of vaginal microbiota communities, and revealed associations to various adverse outcomes including pre-term birth, cancer, and acquisition of sexually transmitted diseases. New data about the …
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Genomic, transcriptomic, and metagenomic approaches for detecting fungal plant pathogens and investigating the molecular basis of fungal ice nucleation activity
… that they cause are desirable. Whole genome metagenomic sequencing has the potential to enable rapid diagnosis of plant diseases without culturing pathogens and designing pathogen-specific probes. In my study, the MinION nanopore sequencer, a portable single‐molecule sequencing platform …
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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
… to significant discoveries. Motivated by this, metagenomics eliminates the culturing dependency by directly sampling DNA from an environment; successfully shedding light on the once unseen majority. The technical limitations of present-day sequencing technologies have meant, however, that in …
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Nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial resistance in a South African birth cohort
… of the NP antibiotic resistome using shotgun metagenomic sequencing. Methods: NP swabs were collected every second week from birth through the first year of life from 137 infants who were immunized with 2+1 doses of PCV13. These were the first 137 infants enrolled in the cohort who had the …
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Benign, potentially malignant & malignant oral lesions; an analysis of oral and gut microbiota
… (M) (n=7) oral lesions. Methods: Using shotgun metagenomic sequencing, we analysed the microbiota profiles to determine their potential as biomarkers for oral malignancy. We looked at alpha diversity, beta diversity, taxonomy, differential abundance, and functional profiling. Results: Our …
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Bacterial Plant Pathogen Identification using Genomics and Metagenomics
… diseases. Computational methods that rely on sequencing data have the potential to overcome these limitations. However, the diverse phenotypes among microbial species and strains within the same species pose a challenge in accurately identifying the specific pathogen responsible for the …
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Legume-rhizobia interactions in a complex microbiome
… single strain experiments. However, improved metagenomics methods have demonstrated considerable differences between single strain inoculations and strain behaviour when exposed to a complex microbiome. To identify some these differences, this experiment applies two treatment factors in a …
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Legume-rhizobia interactions in a complex microbiome
… single strain experiments. However, improved metagenomics methods have demonstrated considerable differences between single strain inoculations and strain behaviour when exposed to a complex microbiome. To identify some these differences, this experiment applies two treatment factors in a …
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Shotgun metagenomic analysis of antimicrobial resistance in wastewater
… they relate to AMR indicators identified through metagenomic sequencing. Through monitoring of local WWTPs, it was found that AMR indicators shifted over time and in relation to human behavior that changed due to the COVID-19 pandemic. Hospital wastewater did not measurably impact the microbiome …
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A genomic investigation into gastrointestinal antimicrobial resistance and clinical infection in patients undergoing transplantation
… 1.5 million lives annually. High-resolution sequencing data allows us to derive novel insights into AMR-BSIs. Immunosuppressed patients have a disrupted gut microbiome; therefore, transplant recipients provide an ideal reservoir for populations of opportunistic AMR pathogens to flourish. …
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Towards in vivo editing of the human microbiome
… called the microbiome. Efforts based on metagenomic sequencing of microbiomes associated with healthy and diseased individuals have revealed vast effects of microbiota on human health. However, compared to the expanding amount of sequence data, little is known about the function of these …
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