Genome-level insight into the dynamics of a model coral microbiome. The aim of the project is to examine structural and functional microbiome dynamics in an ecologically important coral on the Great Barrier Reef along a natural temperature gradient. Microorganisms form an intimate symbiotic relationship with corals and are critical to their health. However, the microbiome can be disrupted by environmental perturbations, including higher-than-normal ocean temperatures, leaving the coral susceptib ....Genome-level insight into the dynamics of a model coral microbiome. The aim of the project is to examine structural and functional microbiome dynamics in an ecologically important coral on the Great Barrier Reef along a natural temperature gradient. Microorganisms form an intimate symbiotic relationship with corals and are critical to their health. However, the microbiome can be disrupted by environmental perturbations, including higher-than-normal ocean temperatures, leaving the coral susceptible to disease and bleaching. Currently, our understanding of how the microbiome composition and metabolic function change in response to seasonal temperature variation and disease is limited. This project is designed to provide insight into the role the microbiome plays in maintaining coral health and may aid in the long-term preservation of the reefs.Read moreRead less
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-b ....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 of environmentally and biotechnologically important microbial communities.Read moreRead less
Epigenetic regulation in bacteria. This project aims to understand the effect of DNA modification on gene regulation in the bacterial organism Escherichia coli, which causes urinary tract infection worldwide. High-throughput DNA sequencing technologies mean one can determine the entire genetic blueprint of a bacterium – its genome – accurately, quickly and cheaply. Single-molecule real-time sequencing provides a complete read-out of a bacterial genome (genetic data) and chemical modifications of ....Epigenetic regulation in bacteria. This project aims to understand the effect of DNA modification on gene regulation in the bacterial organism Escherichia coli, which causes urinary tract infection worldwide. High-throughput DNA sequencing technologies mean one can determine the entire genetic blueprint of a bacterium – its genome – accurately, quickly and cheaply. Single-molecule real-time sequencing provides a complete read-out of a bacterial genome (genetic data) and chemical modifications of the DNA (epigenetic data). Epigenetic data can affect regulation: how genes are switched off and on. This project seeks to harness the power of single-molecule DNA sequencing, together with state-of-the-art genomic and molecular approaches, to better understand the impact of DNA modification on gene regulation in the model bacterial organism, Escherichia coli. This work will support advanced training in bioinformatics and microbiology and improve our understanding of regulation in all bacteria.Read moreRead less
Changing the classification status quo with a global genome-based taxonomy. A grand challenge in biology is the reconstruction of the complete evolutionary history of life on our planet. A major hurdle to this goal has been the inability to culture most microbial species which comprise the bulk of evolutionary diversity. However, new molecular techniques have removed this hurdle and >1,000 new microbial species are being revealed each month through sequencing of environmental samples. This proje ....Changing the classification status quo with a global genome-based taxonomy. A grand challenge in biology is the reconstruction of the complete evolutionary history of life on our planet. A major hurdle to this goal has been the inability to culture most microbial species which comprise the bulk of evolutionary diversity. However, new molecular techniques have removed this hurdle and >1,000 new microbial species are being revealed each month through sequencing of environmental samples. This project aims to organise both cultured and uncultured microbial diversity into a systematic evolutionary framework to replace the current highly flawed and incomplete classification of microorganisms. The systematic classification of the microbial world is timely and will enable fundamental insights into ecology and evolution.Read moreRead less
Safety in numbers: Bacterial aggregation and adaptation to oxidative stress. This project is a new collaboration which links two molecular microbiologists with the complementary skills required to make new insights into the molecular processes that underpin bacterial aggregation and biofilm formation. Biofilms are of immense significance in medical, industrial and environmental settings and so the fundamental information gained from this project will have wider relevance to the field of microbio ....Safety in numbers: Bacterial aggregation and adaptation to oxidative stress. This project is a new collaboration which links two molecular microbiologists with the complementary skills required to make new insights into the molecular processes that underpin bacterial aggregation and biofilm formation. Biofilms are of immense significance in medical, industrial and environmental settings and so the fundamental information gained from this project will have wider relevance to the field of microbiology. An outcome of this proposal will be fundamental knowledge about the production of surface adhesins that will form the basis for rational treatment of disease in the future. Prevention of aggregation and biofilm formation would make bacterial populations more susceptible to conventional antibiotic treatment.Read moreRead less
Phase-variable epigenetic regulators in bacterial veterinary pathogens. This project aims to identify phasevarion regulated genes in the major bacterial swine pathogens Streptococcus suis and Actinobacillus pleuropneumoniae. Both species contain randomly switching epigenetic regulators that control expression of multiple genes by epigenetic mechanisms. Identifying phasevarion controlled genes will inform and direct future vaccine development for important livestock species.
Phasevarions of Haemophilus influenzae: mechanisms and origins of a novel epigenetic system controlling coordinated random switching in expression of multiple genes. Central to the utilisation of biological information is our ability to identify and interpret DNA sequence information from genomes. In bacteria that cause disease, these investigations can identify key aspects of the infectious process or potential components of vaccines or new targets for antibiotics. Our recent work has identifie ....Phasevarions of Haemophilus influenzae: mechanisms and origins of a novel epigenetic system controlling coordinated random switching in expression of multiple genes. Central to the utilisation of biological information is our ability to identify and interpret DNA sequence information from genomes. In bacteria that cause disease, these investigations can identify key aspects of the infectious process or potential components of vaccines or new targets for antibiotics. Our recent work has identified a new genetic system, the 'phasevarion', that mediates random expression of multiple genes. The proposed research aims to advance our understanding of gene expression at the most basic level, revealing how bacteria generate diverse populations to evade environmental and immune stresses, and facilitating improved interpretation and use of DNA sequences for researchers and industry in this field.Read moreRead less
YhcB, a crucial player in the control of bacterial cell envelope biogenesis. All life depends on a cell envelope to enclose the chemical reactions that make life possible. But how do cell envelopes grow? How each component of the cell envelope is incorporated into the envelope at the right amount and in the right time to prevent cell death, has been a longstanding question in bacteriology. Using a unique combination of high through put genetic screens and biochemical approaches, this project wil ....YhcB, a crucial player in the control of bacterial cell envelope biogenesis. All life depends on a cell envelope to enclose the chemical reactions that make life possible. But how do cell envelopes grow? How each component of the cell envelope is incorporated into the envelope at the right amount and in the right time to prevent cell death, has been a longstanding question in bacteriology. Using a unique combination of high through put genetic screens and biochemical approaches, this project will characterise a key regulator of cell envelope growth in Gram-negative bacteria. Knowledge arising from this research will provide insight into a fundamental process in bacteria, will develop new technology to probe protein interactions, and will provide novel avenues to solve infection in plants, humans and animals.Read moreRead less
The evolution of bacterial pathogenesis: a genomic approach. The outcome of this research will be a better understanding of the genes involved with adaptation to particular pathogenic lifestyles. Specifically, genes that are rapidly evolving in selected bacterial pathogens of medical and veterinary importance will be identified using a bioinformatics approach that exploits the existence of multiple closely-related genome sequences. Such genes encode potential new targets for therapeutic interv ....The evolution of bacterial pathogenesis: a genomic approach. The outcome of this research will be a better understanding of the genes involved with adaptation to particular pathogenic lifestyles. Specifically, genes that are rapidly evolving in selected bacterial pathogens of medical and veterinary importance will be identified using a bioinformatics approach that exploits the existence of multiple closely-related genome sequences. Such genes encode potential new targets for therapeutic intervention that provide alternatives in the face of emerging antibiotic resistance. Importantly, the methodology developed in this project is broadly applicable to the study of evolution of bacterial pathogenesis in any background: medical, agricultural or horticultural.Read moreRead less
Unravelling a novel stress-signalling system in bacteria. This project aims to investigate the cyclic-di-AMP signalling system in industrially important bacteria. The recently discovered cyclic-di-AMP is essential for normal bacterial growth and plays key roles in heat and antibiotic resistance, metabolism and virulence. This project will develop new biological assays to shed light on how bacteria sense and respond to environmental stress. Expected outcomes include a much deeper understanding of ....Unravelling a novel stress-signalling system in bacteria. This project aims to investigate the cyclic-di-AMP signalling system in industrially important bacteria. The recently discovered cyclic-di-AMP is essential for normal bacterial growth and plays key roles in heat and antibiotic resistance, metabolism and virulence. This project will develop new biological assays to shed light on how bacteria sense and respond to environmental stress. Expected outcomes include a much deeper understanding of signalling inputs and outputs. This should lead to benefits such as guiding the improvement of bacterial strains used in food and biochemical biotechnological applications, and may provide the foundation for the development of novel antibiotics.Read moreRead less