Work at CMR
CMR is seeking exceptional postdoctoral researchers and professional staff to join us on our mission to become a global leader in microbiome research.
We are dedicated to supporting the continuing professional development of our early- and mid-career researchers. Here you will have access to state-of-the-art molecular biology and computing facilities, as well as a highly collaborative research community. Furthermore, our location at the Translational Research Institute will help you foster diverse academic and industry relationships.
Please contact us to learn more about a career with CMR and see our current research opportunities below:
Academic Roles
We are not currently advertising any academic roles.
Professional Roles
We are not currently advertising any professional roles.
Study with us
At CMR, we are always on the lookout for Undergraduate, Honours, Masters and PhD students who want to take part in impactful research that promotes human and environmental health.
Our students receive outstanding cross-disciplinary research training in microbial ecology, helping to prepare you for diverse career paths. Furthermore, our location within the Translational Research Institute will uniquely position you amongst top researchers and world-class facilities to help drive scientific discovery.
There are many opportunities available within our areas of research. Please contact us to learn more about a future with CMR.
Student Opportunities
From a descriptive to a predictive understanding of the human microbiome
Microorganisms have a profound influence on biological, environmental, and industrial processes, but understanding the complex dynamics of microbial communities and how to manipulate them to our advantage remains a challenge. CMR Director Professor Gene Tyson has recently been awarded a prestigious ARC Laureate Fellowship that aims to overcome current technological limitations and transform microbial ecology from a descriptive to a predictive science. This will be achieved using as a model the most intensively studied ecosystem on the planet: the human gut microbiome.
We are looking for motivated PhD students to join the Laureate research team. The team will be led by Professor Tyson and will include four postdoctoral researchers and five PhD students who will work closely together to achieve the aims of this ambitious research program. As a PhD student, you will benefit from the mentorship and multidisciplinary expertise of Professor Tyson and the postdoctoral researchers, as well as the state-of-the-art research facilities available at CMR. You will learn broad skills across microbiology, including microbial ecology, multi-omics, biochemistry, molecular biology, and bioinformatics.
Study level: PhD
HoliCOW – A holobiont strategy to decipher core host-microbiota interactions in cows
To meet the goal of limiting global warming to 1.5°C, methane emissions from ruminants such as beef and dairy cattle must be reduced by 11–30% by 2030 and by 24–47% by 2050 compared to 2010 levels. A newly funded Future Fellowship project is hiring 2 PhD students who will tackle this challenge by creating a thorough mechanistic understanding of the microbiological, biochemical and genetic processes that cause methanogenesis in the cow rumen. These activities will identify core beneficial microbiota that are critical to cow performance and methane production across different breeds of animals, which is essential to accelerate development of microbiome-based interventions that benefit animal production and reduce its carbon footprint. Expected research outcomes will impact Australia’s ability to meet its commitment to the Global Methane Pledge—a collective effort recently signed by 120+ nations to take voluntary actions to contribute to reduce global methane emissions by at least 30%, which could eliminate over 0.2°C warming by 2050.
Study level: PhD
Using machine learning to understand how the world’s microbiomes are changing due to climate
Shotgun metagenomic sequencing has become commonplace when studying microbial communities and their relationship with the health of our planet, and their direct effects on our own health. Currently, there are >180,000 shotgun metagenomes publicly available, but until recently trying to treat these data as a resource has been challenging due to its extreme size (>700 trillion base pairs). Recently we have developed a tool that can efficiently convert this base pair information into a straightforward assessment of which microorganisms are present in a sample, and what their abundances are. Searching this dataset can now be undertaken in milliseconds.
This project will apply machine learning tools to predict one particular property of these microbial communities – the temperature at which they grow.
Study level: Honours
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 and have never been cultured in a laboratory.
In the proposed project you will develop and apply novel cutting-edge flow cytometric methods for the identification, visualisation and metabolic characterisation of the microorganisms responsible for phosphorus removal from wastewater in Australia.
Study level: Honours
Giant viruses in the human gut microbiome
Viruses that infect bacteria and archaea are particularly unstudied in the human microbiome, due to their extreme diversity. Recently it has been shown that large viruses with genomes in excess of 500,000 base pairs are present in both human and animal gut microbiomes (Devoto et. al. 2020), suggesting that many more groups of these ‘megaphages’ remain to be discovered. In contrast to the recovery of draft bacterial and archaeal genomes, which is now relatively routine, finding novel viruses directly from metagenomic datasets is comparatively challenging. While collections of bacterial and archaeal sequences assembled from metagenomic datasets can be assessed as being near-complete with well-established tools, there are no similar tools for viruses. Thus, we may already have thousands of viral genomes assembled in our databases, and simply not know it.
This project will use a newly developed tool which is able to find megaphages genomes derived from metagenomic sequencing of human gut samples. It is anticipated that application of this tool to hundreds to thousands of human microbiomes will yield many such megaphages. Further project work will focus on characterising these viruses in terms of their gene complement, determining which bacteria or archaea they infect, and their relationship to human disease state.
Study level: Master of Philosophy, Honours
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. 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 phylogenetic and functional resolution. Furthermore, these studies have predominantly focused on bacterial populations, while other important elements of intestinal ecology (e.g. viruses and plasmids) remain poorly characterised.
We hypothesise that the compositional and functional organisation of microbial communities in the mucosal lining contribute to the initiation and progression of IBD.
Study level: Master of Philosophy, Honours
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, while other important elements of intestinal ecology (e.g. viruses and plasmids) remain poorly characterised. Together, these limitations have prohibited the comprehensive characterisation of microbial perturbations observed in IBD. The overall aim of this project is to understand how the composition, function and organisation of microbial communities in the epithelial mucosa differ between individuals with IBD and healthy controls.
In this project, high-resolution metagenomics – the sequencing and reconstruction of all microbial DNA from an environmental or clinical sample – will be applied to epithelial mucosa biopsy samples from individuals with and without IBD. Advanced bioinformatic tools will be used to identify microorganisms, including all bacteria, viruses and plasmids associated with IBD, along with functions underpinning disease pathogenesis. Novel fluorescence in situ hybridisation (FISH) approaches will be applied to epithelial mucosa samples, allowing strain-level visualisation of key IBD-associated microorganisms, their spatial arrangement, and interactions with gut epithelial cells.
Study level: PhD
Defining human immune responses to a healthy gut microbiome
Many human diseases are thought to involve interactions between the gut microbiome and the immune system which shape the nature and function of immunity. These interactions between host and environment are thought to be critical regulators of health and disease. In autoimmune diseases many studies have associated presence or absence of particular microbial species with diseases and some studies have shown influence of disease-related genetics on the composition of the gut microbiome. However, no studies to date have formally addressed the question of how a healthy immune system responds to components of a healthy microbiome and whether immune cells from autoimmune patients behave differently to the same microbial challenge.
We aim to understand whether the immune response to a healthy microbiome differs between healthy controls and patients with autoimmune disorders.
Study level: PhD
Exploring global viral diversity with conserved sequence tags
Viruses control much of the world indirectly through infection of microbial cells. Modern metagenomics provides the raw data to investigate their dynamics and patterns of co-occurrence with the microbial hosts, but extracting signal from these datasets at the large scale remains challenging. Marker-gene based approaches, such as SingleM, have shown great promise for microbial data, converting metagenomic datasets into community profiles by concentrating on reads which derive from conserved sections of prevalent genes.
This project will investigate ways that viral metagenome datasets can be profiled by extending SingleM to target the marker genes encoded in viral genomes. This will be achieved by determining which genes are conserved phylogenetically across substantial numbers of viruses, and then applying the optimised workflows and cloud-run assets already developed for SingleM to profile >200,000 public metagenomes.
Study level: PhD
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.
Study level: PhD
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.
Study level: PhD
Development of a Microfluidic Gut-Brain Axis Chip
The gut microbiome refers to the collection of micro-organisms that are living symbiotically in the human or animal gastrointestinal tract (defined as the “microbiota”), their genetic material as well as the surrounding environmental habitat. It is now appreciated that the microbiome plays an important role in human health and diseases. Many neurodegenerative diseases, such as Parkinson’s Disease have been linked to dysregulation of the gut microbiota. However, it is difficult to study gut-brain axis using animal models due to inter-species differences. There is a need to develop human-specific experimental systems that emulate the gut microenvironment to functionally investigate how microbiome composition affects neuronal cells and function.
This project aims to utilise microfluidic organs-on-chip technology to mimic cellular processes involved in gut-brain axis and perform pilot screen on drug candidate to modulate these interactions.
Study level: PhD, Master of Philosophy
Development of a multiplexed gut micro-bioreactor for functional screening of gut microbiome
The human microbiome refers to the collection of micro-organisms that are living symbiotically in the human body (defined as the “microbiota”), their genetic material as well as the surrounding environmental habitat. It is now appreciated that the microbiome plays an important role in human health and diseases. Various disease states have been linked to dysregulation of the gut microbiota, including neurodegenerative, cardiovascular and metabolic diseases. The composition of the gut microbiome can also affect responses to therapies, most notably in cancer treatment.
A key engineering challenge is to create gut bioreactor system that can generate the aerobic (oxygen-requiring) intestinal epithelium and anaerobic microbiota interface since most gut microbes are obligate anaerobes and cannot tolerate oxygen.
Study level: PhD, Master of Philosophy
Improving human health through the microbiome
Every person harbours a unique collection of microorganisms – the majority of which reside in the gastrointestinal tract – that influences nearly every aspect of human health. As such, the gut microbiome is emerging as a potential tool for the diagnosis and treatment of a wide range of diseases. However, microbiome studies yield vast amounts of data, and the complexity of the microbiome makes it difficult to decipher interactions between microorganisms, host cells and environmental factors.
This project will integrate high-throughput metagenomic, metatranscriptomic and metabolomic techniques with advanced machine learning approaches to address this challenge, providing a comprehensive view of the microbial role in a range of human diseases.
Study level: PhD, Master of Philosophy, Honours
Estimating the evolutionary history of plasmids and viruses
Concatenated gene phylogenies have been used to infer phylogeny in a subset of viruses, but neither viruses nor plasmids have sufficient numbers of genes common to all entities to apply concatenated gene-based phylogenetics. Working with collaborators in local and international universities, the proposed project will develop new phylogenetic methods to estimate the evolutionary history of non-cellular genomic elements.
This estimated history will then be related the evolution of these entities to that of cellular life to form a unified view, reshaping our understanding of evolution globally.
Study level: PhD, Master of Philosophy, Honours
Identifying emergent ecosystem responses through genes-to-ecosystems integration at Stordalen Mire
Permafrost thaw induced by climate change is predicted to make up to 174 Pg of near-surface carbon (less than 3m below the surface) available for microbial degradation by 2100. Despite having major implications for human health, prediction of the magnitude of carbon loss as carbon dioxide (CO2) or methane (CH4) is hampered by our limited knowledge of microbial metabolism of organic matter in these environments. Genome-centric meta-omic analysis of microbial communities provides the necessary information to examine how specific lineages transform organic matter during permafrost thaw. Stordalen Mire in northern Sweden has been subject to a decade of intense molecular and biogeochemical study, and almost 50 years of climate and vegetation research providing a unique opportunity to examine how microbial communities are changing alongside our climate.
The overall aim of this project will be to examine how individual microbial community members and entire communities assemble, adapt and acclimatise to changing environmental conditions.
Study level: PhD, Master of Philosophy, Honours
Symbiosis in microbial ecosystems
Soil systems are fundamentally important to the health of our planet, but the complexity of soil microbial communities makes them particularly challenging to study. Soil systems are amongst the most diverse microbial ecosystems on Earth in terms of the number of microbial species (and strains) present within individual samples, and in the breadth of functions encoded. Beyond complexity measured by counting distinct community members, interactions between microbial species including symbiosis, parasitism or commensalism are widespread and yet barely studied.
The proposed PhD project will build bioinformatic pipelines to identify and characterise symbioses in metagenome datasets. Most of the research will be computational in nature, developing methods that are grounded in our understanding of microbial systems, while at the same time realising how minuscule our understanding of these systems is.
Study level: PhD, Master of Philosophy, Honours