Microbiome Research

Leading microbiome research excellence to understand the role that microorganisms play in health and diseases.

About us

Located in the Translational Research Institute in Brisbane, our Microbiome research team was founded in 2020 by Professor Gene Tyson, a world-leading expert in microbial ecology.

Professor Tyson and his team have developed novel culture-independent molecular approaches (metagenomics, metatranscriptomics and metabolomics) and open-source bioinformatic tools that have revolutionised the recovery and analysis of microbial communities in a wide range of ecosystems.

PhD opportunities

We are currently recruiting motivated individuals for PhD positions in the field of microbial ecology. Please download our list of the current PhD positions available via the link below to learn more.

To apply, please send your cover letter, CV and academic transcript to Dr Simon McIlroy.

Current PhD positions available

Research areas

Human microbiome

Our bodies are home to a vast ecosystem of microorganisms including bacteria, archaea, fungi, viruses, and bacteriophages that make up the human microbiota. These microbes and their collective genetic material, known as the microbiome, influence a wide range of physiological functions: they aid in nutrient production and absorption, help in the development and regulation of our immune system, fight off potential pathogens, and even influence our mood and mental health. While distinct microbial communities exist throughout the body, the gut microbiome has gained particular attention in recent years given its link to several diseases including inflammatory bowel disease, metabolic disorders and cancer. Like other ecosystems, exploring how inhabitants of the human microbiome influence (and are influenced by) their environment is key to understanding their role in host health and survival.

Here, we use cutting-edge technologies to study the human microbiome in the context of health and disease. By integrating meta-omic approaches including metagenomics, metatranscriptomics and metabolomics with powerful bioinformatic tools developed by our team, we can provide accurate and comprehensive characterisation of these communities at unprecedented resolution.

We are particularly interested in inflammatory bowel disease, including the subtypes ulcerative colitis and Crohn’s disease, and the neurodegenerative disorder Parkinson’s disease. Our current research aims to answer important questions about the microbiome function in human health, including their distinct role in these conditions.

Find out more about our research projects

Marine symbiosis

Microorganisms represent important components of both free-living and host-associated marine ecosystems, performing vital functional roles that maintain global ocean health and productivity. Australia’s marine estate is facing extensive and rapid change as a result of global climate change, yet our understanding of the diversity, structure, and function of the primary biotic determinants of ocean health, the marine microbiome, remains limited.

We are studying marine microbial communities using an integrated genome-centric approach to explore both functional and phylogenetic diversity. By focusing our research on Australia’s most iconic ocean habitat, reef-building corals of the Great Barrier Reef, we aim to provide detailed insights into the beneficial functional roles of the microbiome in coral health and resilience.

Find out more about our research projects

Microbes and the global carbon cycle

Microorganisms have several important roles in global carbon and nutrient cycles. Our understanding of these processes, and the microorganisms responsible, is critical to our comprehension and response to Earth’s rapidly changing climate.

We will apply meta-omics and single cell visualisation methods to characterise the microbial communities responsible for the metabolism of methane and short chain alkanes (ethane, propane and butane), which are potent greenhouse gases ubiquitous in the environment.

A key environment for this work will be permafrost wetlands, which contribute a tenth of global methane emissions and contain a quarter of the global soil carbon.

Find out more about our research projects

Microbial bioinformatics

The study of microbial ecology is almost always data-heavy since it involves the study of microbes in the context of their microbial community. Bioinformatics provides the statistical analysis, exploratory approaches and scalable computational toolsets necessary to study the structure and function of microbiomes from a wide range of environments. Given the increasing size of metagenomic data being generated, bioinformatic advances are required in order to fully realise the potential of this data and explore understudied components of microbial ecosystems.

Our work will advance the science of microbial bioinformatics by developing novel bioinformatic techniques and implementations that will be widely applicable in microbial ecology.

Find out more about our research projects

Our facilities

Housed within the Translational Research Institute, our Microbiome research team is uniquely positioned amongst top researchers and world-class facilities to drive scientific discovery and translational research. We have access to a purpose-built research environment for the study of microbial ecology and evolution using state-of-the-art molecular biology and computing facilities. Its location at the Princess Alexandra Hospital (PAH) provides access to clinical cohorts, which is critical for our work on the human microbiome.

Services

Long read sequencing

Advancements in high-throughput next-generation sequencing technologies have revolutionised genomic research. These technologies largely replaced single gene approaches by enabling paralleled sequencing of short fragments of DNA that are then pieced together into a continuous genomic sequence, offering a high-throughput and low-cost option to sequence whole genomes.

However short reads of DNA can be insufficient, with a limited ability to resolve complex and repetitive regions of the genome and the complicated task of genome reconstruction. In contrast, long-read sequencing technologies directly sequence single molecules of DNA, thus improving de novo assembly, mapping certainty, and identification of transcript isoforms and structural variants.

We aim to become the first certified service lab in Australia to offer a long-read sequencing service on the PromethION 24. This technology provides improved efficiency and accuracy over existing DNA sequencing applications, including:

  1. Direct sequencing of native DNA and RNA with capacity for real time analysis
  2. No restrictions on read length, capable of high-throughput sequencing of ultra-long reads
  3. Ability to sequence up to 24 flow cells at a time, and generate up to 200Gbp of data per flow cell

Flow cytometry

We have a dedicated high-speed cell sorter for microbial samples with the ability to sort single particles (using 96/384 well plates) and bulk populations. It is housed in a Class II biosafety cabinet and is therefore OGTR approved to handle human samples. With a dedicated operator with expertise in environmental microbiology, we are able to help with project design and development of new assays to target populations of interest.

Confocal microscopy

Confocal microscopy is an optical imaging technique for increasing the resolution and contrast of a micrograph. By capturing multiple two-dimensional images at different depths in a sample we are able to reconstruct three-dimensional structures (a process known as optical sectioning) within an object. This technique allows exploration of microbial habitats and the observation of microorganisms in situ with an unprecedented accuracy.

Students

Ms. Megan Clay

PhD candidate

Megan completed her Bachelor of Science in Liberal Arts and Sciences at Amsterdam University College. She then went on to do a master’s degree at the University of Amsterdam in Oceanography and Limnology, where she completed three mini-thesis: one on the microbiome of Caribbean Giant Barrell Sponges, one on settlement and metamorphosis in coral larvae, and one on virally mediated mortality of phytoplankton in the North Atlantic. Megan was chosen to participate in the NICO expedition, a trans-Atlantic oceanographic cruise, which solidified her love for microbial marine science. She is now a PhD candidate under the supervision of Prof Gene Tyson, where she continues to investigate microbial communities in marine ecosystems.

Ms. Kim Nguyen-Phuoc

PhD candidate

Kim completed her Bachelor of Science in Biology from Dalhousie University in Halifax, Canada, where she launched her research career in marine ecology. Here, she completed an honour’s project where she assessed how behaviour and stress response in green sea turtles is affected by popular tourist ventures, such as ‘swimming with the turtles’ excursions. During her master’s degree at the University of Alberta, Kim investigated the use of the genome editing tool CRISPR-Cas9 to create a zebrafish animal model of an eye disease called Pigmentary Glaucoma. She is now completing a PhD at Queensland University of Technology under the supervision of Prof Gene Tyson, where she is helping to develop novel techniques to study marine ecosystems.

Mr. Rhys Newell

PhD candidate

Rhys completed a Bachelor of Science majoring in Ecology and Genetics with Honours in Bioinformatics at the University of Queensland. During his Honours, Rhys developed ChIP-R, a bioinformatic tool for analysing the reproducibility of ChIP-seq and ATAC-seq peaks. Rhys is interested in the development and application of computational and statistical analyses to metagenomic and metabolomic datasets. Additionally, Rhys enjoys developing and distributing freely available code libraries which most recently includes nymph, a Rust library for performing non-negative matrix factorisation. His personal website and GitHub can be found here: https://rhysnewell.github.io

Ms. Beatriz Delgado Corrales

PhD candidate

Beatriz is a PhD candidate at the Queensland University of Technology with a background in biotechnology and environmental microbiology. She completed her bachelors and master’s degree at the Autonomous University of Madrid, Spain, where she studied the rumen microbiome, its impact on methane emissions, and its relevance in animal breeding and genetics. She did this first by studying the production of methane by methanogenic archaea, and later by doing metagenomic analysis of the rumen microbiome using short-read and nanopore sequencing with the MinION. She is now focused on applying different bioinformatic pipelines to analyse metagenomes, recovering assembled microbial and viral genomes and predicting their metabolic capacities in alkane-rich environments.

Ms. Eilish McMaster

Honours student

Eilish is completing the honours year for her Bachelor of Advanced Science through the University of Queensland, where she majors in Biology and Streaming in Genetics, with a minor in Microbiology. In her current role, she studies complex interactions between microorganisms from a thawing permafrost under the supervision of Prof. Gene Tyson (QUT), Dr. Ben Woodcroft (QUT), and Prof. Phil Hugenholtz (UQ).

Ms. Georgina H. Joyce

Honours student

Georgina is an undergraduate student at the University of Queensland completing the honours component of her Bachelor of Advanced Science, majoring in Biology. Having a keen interest in microbiology and bioinformatics, her goal is to complete a PhD within the field and continue a career in academic research.

Publications list

  1. Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rink C, Spang A. 2020. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 11, 3939. https://doi.org/10.1038/s41467-020-17408-w
  2. Emerson JB, Varner RK, Wik M, Parks DH, Neumann RB, Johnson JE, Singleton CM, Woodcroft BJ, Tollerson II R, Owusu-Dommey A, Binder M, Freitas NL, Crill PM, Saleska SR, Tyson GW, Rich VI. 2020. Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity. bioRxiv 2020.02.08.934661; https://doi.org/10.1101/2020.02.08.934661
  3. Leu AO, Chen C, McIlroy SJ, Southam G, Orphan V, Yuan Z, Hu S, Tyson, GW. 2020. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J. 14. 1030-1041.
  4. Leu AO*, McIlroy SJ*, Ye J, Parks DH, Orphan VJ, Tyson GW. Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae. 2020. mBio. 11. e01325-20. *Equal first author.
  5. Messer LF, Ostrowski M, Doblin MA, Petrou K, Baird ME, Ingleton T, Bissett A, Van de Kamp J, Nelson T, Paulsen I, Bodrossy L, Fuhrman JA, Seymour JR, Brown MV. 2020. Microbial tropicalization driven by a strengthening western ocean boundary current. Global Change Biology. DOI:10.1111/gcb.15257.
  6. Nierychlo M, McIlroy SJ, Kucheryavskiy S, Jiang C, Ziegler AS, Kondrotaite Z, Stokholm-Bjerregaard M, Nielsen PH. 2020. Candidatus Amarolinea and Candidatus Microthrix are mainly responsible for filamentous bulking in Danish municipal wastewater treatment plants. Front. Microbiol. 11. 1214.

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Future students

07 3138 2000 (Australian and NZ)

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Industry and alumni