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.
Black Death Genomics And The Evolution Of Pathogen Virulence
Funder
National Health and Medical Research Council
Funding Amount
$525,412.00
Summary
The Black Death was one of the most lethal plagues of antiquity and changed the course of human history. We will reconstruct and analyse the evolution of its causative agent – the bacterium Yersinia pestis – sampled from human skeletal remains dating back to the Black Death and beyond. We will determine the mutations that changed the virulence of plague epidemics through time, enabling a unique insight into the most dramatic example of pathogen emergence that has ever been available for study.
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
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
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
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.
To eat or not to eat? How symbiotic bacteria manipulate the phagocytic behaviour of their eukaryotic host. Bacteria often live in close association with eukaryotic cells, ranging from simple amoeba to humans. This project will identify key factors that control their interactions and will yield important information on the evolution of beneficial or harmful relationships.
The dynamics of evolution: How horizontal gene transfer drives the diversification and adaptation of complex, bacterial communities. The genetic exchange between populations is a prerequisite for the long-term evolution of bacteria, however its short-term dynamics are largely unexplored. This project aims to define the temporal dynamics of gene transfer and how it shapes the genetic composition of entire bacterial communities. Using innovative DNA sequencing technologies and bioinformatics, This ....The dynamics of evolution: How horizontal gene transfer drives the diversification and adaptation of complex, bacterial communities. The genetic exchange between populations is a prerequisite for the long-term evolution of bacteria, however its short-term dynamics are largely unexplored. This project aims to define the temporal dynamics of gene transfer and how it shapes the genetic composition of entire bacterial communities. Using innovative DNA sequencing technologies and bioinformatics, This project aims to offer a significant new understanding of the short-term diversification of communities and how different evolutionary forces shape bacterial function. It will show how bacterial systems can adapt to new environmental conditions and the effect on essential ecosystem functions.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE170100428
Funder
Australian Research Council
Funding Amount
$368,968.00
Summary
Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microo ....Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microorganisms’ metabolic pathways using DNA sequencing, bioinformatics and cultivation techniques. By understanding these microorganisms’ metabolisms, researchers expect to assess how they affect global carbon cycling and climate change.Read moreRead less
Lifestyle choices: genomic analysis of niche adaptations in marine Synechococcus. Photosynthetic marine bacteria are very important in the global carbon cycle. This project aims to discover how these bacteria adapt to survive in different marine environments. This is important for understanding how they will be affected by climate change and other environmental alterations.