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.
Discovery Early Career Researcher Award - Grant ID: DE190100008
Funder
Australian Research Council
Funding Amount
$387,103.00
Summary
Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expect ....Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expected outcomes from this project includes providing insights into the function and evolution of non-photosynthetic Cyanobacteria and their viruses, and pure or enriched cultures to enable future studies.Read moreRead less
Hyperactive endogenous retroviruses and their impact on the koala genome. Koala populations are in steep decline with the ubiquitous koala retrovirus (KoRV) strongly linked with disease. KoRV and other less studied endogenous retrovirus (ERVs) are extremely active within the genome of koalas to a level never observed in any other vertebrate genome. This study will map ERV integration sites within koalas from across their geographic range country and use long-read genomics approaches to understan ....Hyperactive endogenous retroviruses and their impact on the koala genome. Koala populations are in steep decline with the ubiquitous koala retrovirus (KoRV) strongly linked with disease. KoRV and other less studied endogenous retrovirus (ERVs) are extremely active within the genome of koalas to a level never observed in any other vertebrate genome. This study will map ERV integration sites within koalas from across their geographic range country and use long-read genomics approaches to understand the link between KoRV and other ERVs, the impact on koala caused by dramatic genomic rewiring, and the mechanisms of genomic immunity which supress ERV activity and mitigate disease. Findings will provide insights into the ongoing arms race between virus and host and inform conservation of an iconic species.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
Smarter fermentations through starter culture genomics. Australia makes over $1 billion dollars worth of cheese each year, however fermentation can be adversely affected by virus (phage) attack or sub-optimal strain mixtures. The latest genomics and molecular biology approaches will be used to characterise and optimise starter culture strains leading to improved flavour, quality and efficiency in cheese making.
Quantitative Metagenomics. This project aims to revolutionize our view of the microbial world once more by transforming microbiome studies from relative counts of organisms to actual numbers of microbes. This project expects to impact all the microbiome studies that are being performed worldwide by unveiling the actual numbers of microbes. Expected outcomes of this project include new techniques to enumerate the number of bacteria in different environments and new approaches to measure gene expr ....Quantitative Metagenomics. This project aims to revolutionize our view of the microbial world once more by transforming microbiome studies from relative counts of organisms to actual numbers of microbes. This project expects to impact all the microbiome studies that are being performed worldwide by unveiling the actual numbers of microbes. Expected outcomes of this project include new techniques to enumerate the number of bacteria in different environments and new approaches to measure gene expression within individual bacteria in any environment that will be demonstrated with complex microbial communities. This should provide significant benefits because microbes affect every aspect of our lives and those effects are driven by how many microbes are present.Read moreRead less
Deciphering the coral minimal microbiome. This project aims to decipher the functions of coral-associated bacteria by taking advantage of low-diversity microbiomes that are naturally found in some coral species. A further aim is to unveil the importance of bacterial genome evolution in coral adaptation to climate change. Climate warming is the biggest threat to coral reefs with half of Australia’s Great Barrier Reef (GBR) corals dead due to recent summer heat waves. Expected outcomes are an incr ....Deciphering the coral minimal microbiome. This project aims to decipher the functions of coral-associated bacteria by taking advantage of low-diversity microbiomes that are naturally found in some coral species. A further aim is to unveil the importance of bacterial genome evolution in coral adaptation to climate change. Climate warming is the biggest threat to coral reefs with half of Australia’s Great Barrier Reef (GBR) corals dead due to recent summer heat waves. Expected outcomes are an increased understanding of how bacteria contribute to coral heat tolerance, and new knowledge to assist in the development of bacterial probiotics for enhancing coral thermal tolerance. This should provide significant benefits to the protection of the GBR and Australia’s economy.Read moreRead less
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 adaptive evolution of key methane-utilising microorganisms. This project aims to characterise the evolutionary adaptations of a group of microorganisms with a key role in mitigating the release of methane into the atmosphere. Innovative molecular and visualisation-based approaches will be applied to uncover their metabolic diversity and evolutionary history. An important outcome of this study will be the comprehensive understanding of the contribution and impact these microorganisms have on ....The adaptive evolution of key methane-utilising microorganisms. This project aims to characterise the evolutionary adaptations of a group of microorganisms with a key role in mitigating the release of methane into the atmosphere. Innovative molecular and visualisation-based approaches will be applied to uncover their metabolic diversity and evolutionary history. An important outcome of this study will be the comprehensive understanding of the contribution and impact these microorganisms have on the global carbon cycle, which will importantly inform accurate climate change models. This has clear benefits for society, given the precision of such models is essential in our ability to minimise the impact and associated cost of global warming.Read moreRead less
Uncovering new microbial players and processes in the global methane cycle. This project aims to utilise multiple analytical strategies (including metagenomics and metatranscriptomics) to substantially expand our understanding of the key microorganisms, metabolic strategies, and interspecies relationships involved in the formation and consumption of methane. The global methane cycle is controlled by microorganisms that produce and consume this important greenhouse gas, however it is now recognis ....Uncovering new microbial players and processes in the global methane cycle. This project aims to utilise multiple analytical strategies (including metagenomics and metatranscriptomics) to substantially expand our understanding of the key microorganisms, metabolic strategies, and interspecies relationships involved in the formation and consumption of methane. The global methane cycle is controlled by microorganisms that produce and consume this important greenhouse gas, however it is now recognised that there are many as-yet undiscovered methane-metabolising microorganisms in the environment. The project will lead to a greater understanding of the contribution of these novel microorganisms to global carbon cycling and their links to climate change. This will directly benefit modelling efforts to understand future climate change scenarios.Read moreRead less