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 20 for “"shotgun metagenomic sequencing"”.
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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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Benign, potentially malignant & malignant oral lesions; an analysis of oral and gut microbiota
… malignant (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: …
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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
… about 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 …
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Dynamics of the human gut microbiota in very early life
… I generated 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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Microbial and Immune Signatures of Stress and Antidepressants Across Sex and Generations
… questions, we utilized 16S rRNA or whole-genome shotgun metagenomic sequencing in tandem with behavioral assays and multiplex cytokine profiling in rat and mouse models of chronic stress or perinatal SSRI exposure. Across studies, we demonstrate that the gut microbiome exhibits innate sex …
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Microbiome and Metagenomics: Statistical Methods, Computation and Applications
… and inflammatory bowel disease. High-throughput sequencing technology has been widely used to profile the microbial communities in order to understand their impact on human health. In the first part of this dissertation, we analyzed fecal samples using shotgun metagenomic sequencing from a …
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The Detection and Analysis of Pathogen-Reactive Immunoglobulins in the Urine of Men With Nongonococcal Urethritis
… 1/3 of these STI-negative individuals using shotgun metagenomic sequencing. However, we did not detect microorganisms suspected to be urethral pathogens in the remaining 2/3 of STI-negative participants. We hypothesized that these men with “pathogen-negative” urethritis had persisting …
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Applying molecular methods to investigate potential anthropogenic impacts on ageing in a free-living bat species
… stressors on biological ageing. In Chapter 3, shotgun metagenomic sequencing was used to characterise the gut microbiome of bats from both colonies. Metagenome assembled genomes (MAGs) were reconstructed and functionally annotated to assess taxonomic composition, diversity and inferred …
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Evaluating substrate utilisation to target newly identified health-promoting gut bacteria
… in culture-based techniques, advances in DNA sequencing-based approaches and improved computational pipelines. The combined use of these tools has enormous potential with respect to elucidating substrates that can be applied to specifically target microbes of interest and is the focus of this …
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Characterisation and plastic-degrading potential of plastisphere-associated microorganisms
… its potential for plastic degradation, via shotgun metagenomic sequencing. We were unable to isolate any microbial degraders of homochain plastic polymers. Marine bacterial isolates demonstrated surface erosion on LDPE films but failed to produce clearance zones or weight loss in plastic …
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Nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial resistance in a South African birth cohort
… composition 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 …
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Bioinformatic Analysis of Wastewater Metagenomes Reveals Microbial Ecological and Evolutionary Phenomena Underlying Associations of Antibiotic Resistance with Antibiotic Use
… novel bioinformatic approaches developed herein, metagenomics revealed associations between sewage-associated microbes and community antibiotic use that were in part mediated by microbial ecological processes and horizontal gene transfer (HGT). In sum, this dissertation increases the arsenal of …
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Defining the relationship between the gut microbiome and response to combination immune checkpoint blockade across cancer types
… signature of response by utilising deep shotgun metagenomic sequencing from a large, multi-centre Australian cohort of patients with advanced-stage, diverse, rare cancers (n= 106 discovery cohort). All patients were treated with combination immune checkpoint blockade (CICB), namely …
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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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Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows
… (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic …
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Listeria monocytogenes in the mushroom production environment: biofilm formation and control measures
… to identify other potential biocontrol agents, a shotgun metagenomic sequencing study was carried out which revealed other potential bacteriocin producing bacteria and clearly illustrated the changes in species dominance which occur over time. All in all, this body of work has provided beneficial …
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Pink discolouration in cheese
… manufacture, UHPLC-DAD-QTof mass spectrometry, shotgun metagenomic sequencing, and exploiting the antimicrobial activity of biopreservative nisin were used to determine the role of Thermus in causing pink defect and to investigate potential control measures. The thesis begins with a review of …
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Effect of Standard Post-harvest Interventions of Fresh Vegetables on Bacterial Community Dynamics, Pathogen Survival and Antibiotic Resistance
… the surficial carrot and lettuce microbiota by sequencing bacterial 16S rRNA gene amplicons. The effect of post-harvest treatments on the types and relative abundance of ARGs, also known as the “resistome,” were profiled by shotgun metagenomic sequencing and qPCR. Addition of a sanitizer during …
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A computational approach to understanding maternal influences on the development of ruminant neonates
… employed a computational single-nucleus RNA sequencing (snRNA-seq) approach to investigate the impact of these maternal colostral cells on mucosal immune development at the cellular level. As a first step, the snRNA-seq framework was standardized and validated by characterizing regional …
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Limitations to Use Copper as an Antimicrobial Control of Legionella in Potable Water Plumbing Systems
… the antimicrobial effects of Cu. Application of shotgun metagenomic sequencing offered the opportunity to more deeply examine the response of Legionella and other pathogens to Cu dosed to the pilot-scale hot water systems in the context of the broader microbiome. It was found that metagenomic …