Robust Bioinformatics For Predicting Bacterial Pathogens From Microbiome Sequencing
Funder
National Health and Medical Research Council
Funding Amount
$644,151.00
Summary
We propose to develop new methods for the identification of microbial pathogens using High Throughput DNA Sequencing (HTS). Study of the microbiome - the genes encoded by the assemblage of microbial species present in an environment - using HTS technologies is revolutionising our understanding of human-microbe interactions. Our proposed work includes fundamental computational and theoretical advances and applying these techniques to solve critical problems in pathogen detection.
Decoding Bacterial Epigenetic Regulation. This project aims to characterise bacterial epigenetic regulation by determining the mechanism of action and impact of bacterial DNA methylation. This project expects to generate new knowledge about fundamental aspects of bacterial gene regulation, using a novel combination of cutting edge DNA and RNA sequencing, proteomic and bioinformatic approaches. The expected outcomes of this project will provide new tools to facilitate the integration of epigenomi ....Decoding Bacterial Epigenetic Regulation. This project aims to characterise bacterial epigenetic regulation by determining the mechanism of action and impact of bacterial DNA methylation. This project expects to generate new knowledge about fundamental aspects of bacterial gene regulation, using a novel combination of cutting edge DNA and RNA sequencing, proteomic and bioinformatic approaches. The expected outcomes of this project will provide new tools to facilitate the integration of epigenomic analysis into genomic studies, exponentially increasing the volume and value of data gathered. This would provide significant future benefits to all academic, biotechnology, agricultural, veterinary and pharmaceutical applications that involve bacterial genomic analysis.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
Unlocking the secrets of metabolic variation in a highly diverse bacterium. This project aims to explore metabolic diversity of Klebsiella pneumoniae, a bacterium relevant to the agricultural, veterinary, medical and biotechnology industries. It is expected to reveal significant insights into the biology of this diverse organism via an innovative combination of DNA sequence analyses and metabolic modelling. Expected outcomes include 4500 novel metabolic models and a novel population metabolic fr ....Unlocking the secrets of metabolic variation in a highly diverse bacterium. This project aims to explore metabolic diversity of Klebsiella pneumoniae, a bacterium relevant to the agricultural, veterinary, medical and biotechnology industries. It is expected to reveal significant insights into the biology of this diverse organism via an innovative combination of DNA sequence analyses and metabolic modelling. Expected outcomes include 4500 novel metabolic models and a novel population metabolic framework. This should provide major benefits for understanding bacterial ecology and evolution, and for future studies seeking to optimise industrial processes or prevent disease. It will also directly contribute to building Australia’s capacity in computational biology- a key driver of biotechnology innovation.Read moreRead less
Archaeal dark matter and the origin of eukaryotes. This project aims to investigate the highly controversial origin of eukaryotes and thus all multicellular life within Archaea, a domain of single-celled microorganisms. Resolving eukaryotic origins has long been hampered by an inability to cultivate archaea from the environment. This project aims to develop a novel high-throughput single-cell genomics approach to recover archaeal genomes, thus bypassing the cultivation step. The genomes will con ....Archaeal dark matter and the origin of eukaryotes. This project aims to investigate the highly controversial origin of eukaryotes and thus all multicellular life within Archaea, a domain of single-celled microorganisms. Resolving eukaryotic origins has long been hampered by an inability to cultivate archaea from the environment. This project aims to develop a novel high-throughput single-cell genomics approach to recover archaeal genomes, thus bypassing the cultivation step. The genomes will contribute to a comprehensive taxonomic framework which will facilitate the evaluation of evolutionary relationships between the eukaryotic and archaeal domains. This may uncover previously unknown archaea with novel metabolic capabilities.Read moreRead less
Commensal benefits: genomic basis for suppressing plant pathogens with Pseudomonas biocontrol species. Food security is an issue of mounting significance due to unpredictable climate trends and increasing global population growth. A feature of paramount importance to reliable crop production is the capacity to control plant diseases. This project investigates natural plant colonising bacteria as a tool for protecting plants from disease.
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
Australian Laureate Fellowships - Grant ID: FL150100038
Funder
Australian Research Council
Funding Amount
$2,982,714.00
Summary
Reconstructing the universal tree and network of life. Reconstructing the universal tree and network of life: This fellowship project aims to obtain 100 000 genome sequences and systematically organise these into natural phylogenetic relationships comprising both vertical inheritance and lateral transfers. One of the challenges in biology today is to reconstruct the complete evolutionary history of life on Earth. A major hurdle to this goal is our inability to culture most microbial species whic ....Reconstructing the universal tree and network of life. Reconstructing the universal tree and network of life: This fellowship project aims to obtain 100 000 genome sequences and systematically organise these into natural phylogenetic relationships comprising both vertical inheritance and lateral transfers. One of the challenges in biology today is to reconstruct the complete evolutionary history of life on Earth. A major hurdle to this goal is our inability to culture most microbial species which comprise the bulk of evolutionary diversity. The framework developed in this project seeks to replace the current incomplete classification of microorganisms to provide fundamental insights into ecology and evolution. It is hoped that the outcomes of the project can be applied to manage risk and capture opportunities in important Australian industries including agriculture, mining and biotechnology.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE100100130
Funder
Australian Research Council
Funding Amount
$850,000.00
Summary
Systems biology: New generation DNA sequencing to functional analysis. The technique of DNA sequencing (or 'reading' the lines of the four repeating letters that make up the genetic code) illustrates how technological developments have become the main drivers in exploring the roles of genetic factors across a spectrum of research activities. Funding provided through this ARC grant will allow the purchase of the latest DNA sequencing platform, the Illumina Solexa, as well as equipment that will b ....Systems biology: New generation DNA sequencing to functional analysis. The technique of DNA sequencing (or 'reading' the lines of the four repeating letters that make up the genetic code) illustrates how technological developments have become the main drivers in exploring the roles of genetic factors across a spectrum of research activities. Funding provided through this ARC grant will allow the purchase of the latest DNA sequencing platform, the Illumina Solexa, as well as equipment that will be used to understand the biological function of the DNA sequencing results that are obtained. The equipment will allow Australian researchers to compete on an equal footing with the international leaders in understanding the roles played by genes in plants, microorganisms, animals and humans.Read moreRead less