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Comprehensive strain-level characterisation of microbial communities associated with inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder driven by complex interactions between environmental, microbial and immune-mediated factors 1,2. An unfavourable shift in gut microbiome composition, known as dysbiosis, is now considered a key feature of IBD 2-5, however it is unclear how specific microorganisms and their interactions with host cells contribute to disease onset and progression.Previous IBD studies have been largely limited to older sequencing methods with low phylogenetic and functional resolution. Furthermore, these studies have predominantly …

Study level
Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Centre for Microbiome Research

Illuminating the microbial world using genome-based fluorescence microscopy

Our understanding of microbial diversity on earth has been fundamentally changed by metagenomic characterisation of natural ecosystems. Traditional approaches for visualising microbial communities are time-consuming and provide limited information about the identity of specific microorganisms.The proposed research aims to combine single cell genomics and super resolution microscopy for novel, high-throughput, genome-based techniques to visualise microorganisms, plasmids and viruses, with strain level specificity.The application of these highly scalable approaches will provide comprehensive and unprecedented insight into the fine-scale dynamics and evolution …

Study level
PhD
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Centre for Microbiome Research

Strain-level characterisation and visualisation of microbial communities associated with inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder driven by complex interactions between environmental, microbial and immune-mediated factors. An unfavourable shift in gut microbiome composition, known as dysbiosis, is now considered a key feature of IBD, however it is unclear how specific microorganisms and their interactions with host cells contribute to disease onset and progression. Previous IBD studies have been largely limited to older sequencing methods with low resolution. Furthermore, these studies have predominantly focused on bacterial populations, …

Study level
PhD
Faculty
Faculty of Health
School
School of Biomedical Sciences

Adaptive evolution of anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments (PhD)

The as-yet-uncultured archaeal lineage Methanoperedenaceae are anaerobic methanotrophs with a key role in mitigating the atmospheric release of methane in freshwater environments. The metabolic diversity of these microorganisms directly links methane with several key biochemical cycles and suggests a remarkable ability of these microorganisms to adapt to diverse environmental conditions.The overall aim of this PhD project will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.Methods and ResourcesThe project will …

Study level
PhD
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Centre for Microbiome Research

Application of fluorescence-activated cell sorting and confocal microscopy for the study of the microbial communities responsible for nutrient removal from domestic wastewater

The removal of nutrients like carbon, nitrogen and phosphorus from wastewater is critical to the prevention of eutrophication in receiving water systems and is carried out by complex microbial communities.Eutrophication can have devastating consequences on aquatic life and natural ecosystems, with toxic algal blooms also posing a risk to human health.Understanding the microbiology of phosphorus (P) removal from wastewater is considered essential to knowledge-based optimisation of enhanced biological P removal (EBPR) systems.Most of the species in these systems are novel …

Study level
Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Centre for Microbiome Research

Metabolic diversity of the anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments

The as-yet-uncultured archaeal lineage Methanoperedenaceae are anaerobic methanotrophs with a key role in mitigating the atmospheric release of methane in freshwater environments. The metabolic diversity of these microorganisms directly links methane with several key biochemical cycles and suggests a remarkable ability of these microorganisms to adapt to diverse environmental conditions.The overall aims for a potential Honours/MSc project will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.

Study level
Master of Philosophy, Honours, Vacation research experience scheme
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Centre for Microbiome Research

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