Host-associated

The community of microorganisms (Bacteria, Archaea, viruses and single-celled Eukaryotes) that function and interact together in a specific location, such as the gastrointestinal tract of an animal, is called the microbiome.

In the case of host-associated microbiomes, these interactions extend to the host and are often critical for normal function and development. A dysbiosis, or imbalance of the microbiome, can lead to an increased abundance of microbes that cause disease.

See the projects that we're working on, below.

The archaeal biodiversity from native Australian herbivores

Australia’s native herbivores are among its iconic natural resources, which must be protected for the cultural, environmental and economic wellbeing of all Australians. A key feature of these animals is their 'clean and green' image because of their low methane emissions (per kilogram of food intake) compared to ruminant livestock. This project explores and characterises newly discovered microbes representing the third Domain of Life (Archaea) from these animals and a critical control point in methane emissions from animals.

These animals are unique natural resources of great cultural, environmental, and economic significance, but increasingly susceptible to habitat change and degradation. Little is known about the microbes that have co-evolved with these animals, to support their nutrition and health. The project's national benefits are timely and broad. We aim to provide a deep functional understanding of our recent discovery of novel microbes from the Domain Archaea that inhabit the digestive tracts of native Australian herbivores.

Project team: Paul Evans, Rochelle Soo, Kate Bowerman
Collaborators: Mark Morrison, Harley McRae, Phil Pope (QUT)

Discovery of bacteriophages as candidate therapeutics for treating chronic middle ear infections in Aboriginal and Torres Strait Islander children

Chronic ear infections (otitis media) are the leading cause of preventable hearing loss in Aboriginal and Torres Strait Islander children and can consequently result in negative downstream impacts on speech and social development, education and employment prospects. Current treatments have plateaued in their effectiveness and new treatment options are needed. We aim to discover and develop into novel therapies the naturally occurring viruses (bacteriophages) that infect and kill the specific otitis media causing Bacteria as well as the bacteria-killing proteins they produce.

Project team: Seweryn Bialasiewicz (CI), Julian Zaugg, Philip Hugenholtz, Max Lacour, Rylee Deehan
Collaborators: Rhiannon Baxter (UQ), Robyn Marsh (Menzies School of Health Research)

The role of the upper respiratory tract microbiome in health and chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a debilitating infection of the sinuses that can severely reduce quality of life and is a significant financial and productivity burden for the patient, the health system and the broader economy. We aim to take a holistic approach to understanding the microbial ecological networks including Bacteria, Archaea, fungi and viruses within the upper respiratory tract, and to use that information to identify key biomarkers of health and disease. These biomarkers can in turn be either used to promote a 'healthy' microbiome state or be the targets of downstream treatments if associated with specific disease-causing Bacteria.

Project team: Seweryn Bialasiewicz (CI), Julian Zaugg
Collaborators: Anders Crevin (CI)

Dairy cow mastitis biomarker discovery

Mastitis (infection of the udder) is a significant issue in the dairy industry, leading to economic losses, suffering of the animal and increased antibiotic use. Traditional detection methods have not been able to identify the causative infectious agent in a large proportion of investigated cases.

This study, in partnership with the UQ School of Veterinary Science, aims to leverage the latest sequencing technology to fill the knowledge gap and characterise the remaining common causative infectious agents. The information can be then applied to develop improved dairy herd management strategies and diagnostic tests.

Project team: Seweryn Bialasiewicz (CI), Julian Zaugg, Rylee Deehan
Collaborators: Justine Gibson, Charlotte Tinsley

Genomics of marine symbiosis

We adopt genomic approaches to assess the genetic capacity of symbiotic partners in sustaining a functional ecological unit. Central to our research are the Symbiodiniaceae microalgae, the symbionts that critically sustain the coral reefs. Breakdown of coral-alga symbiosis leads to coral bleaching.

Working with our collaborators nationally and internationally, we generate genome-scale data from coral symbionts and their relatives with the aim to understand how these microalgae evolved to sustain symbiosis with corals.

We also apply scalable methods to assess symbiont diversity directly from large number of coral hologenome datasets, and to recover genomes of symbionts without the need for strain isolation and culturing.

Project team: Cheong Xin Chan (CI), Hisatake Ishida
Collaborators: Debashish Bhattacharya (Rutgers University), Patrick Buerger (Macquarie University), Emma Camp (UTS), Yibi Chen (QUT), Ira Cooke (JCU), Jose Victor Lopez (Nova Southeastern University), Emily Howells (Southern Cross University), Matt Nitschke (AIMS), Cynthia Riginos, David Suggett (UTS), Mike Sweet (University of Derby), Madeleine van Oppen (University of Melbourne)

Establishing a model species for sponge symbiosis research

Marine sponges host a remarkably dense and diverse community of microbial symbionts that are critical to host health. However, the complexity of many sponge microbiomes hampers in-depth characterisation of sponge symbiosis.

This project aims to establish the Great Barrier Reef sponge Ianthella basta as a model species for sponge symbiosis research. In contrast to most sponge species, I. basta harbours only three well-characterised dominant microbial symbionts. We aim to assess the establishment and maintenance of microbial symbiosis in I. basta, visualise physiological interactions between host and symbionts, and assess holobiont stability under future climate conditions.

We use innovative molecular techniques, including next generation sequencing, metaproteomics and stable isotope probing to determine who eats what, where and when in this ancient symbiosis.

Project team: Nicole Webster, Steven Robbins, Laura Rix
Collaborators: Michael Wagner (University of Vienna), Bettina Glasl (University of Vienna)

Host-cyanobacteria symbioses in marine sponges

Cyanobacteria hosting sponges of the genus Phyllospongia dominate shallow-water sponge communities across the Great Barrier Reef. Like corals, these photosynthetic sponges can undergo bleaching (loss of photosynthetic symbionts) in response to climate change-induced rising seawater temperatures.

We aim to investigate the mechanisms governing the breakdown of the host-Cyanobacteria symbiosis during bleaching in the photosynthetic sponge Phyllospongia foliascens using ecophysiology, transcriptomics, metaproteomics and single-cell stable-isotope probing coupled with NanoSIMS.

Project team: Laura Rix
Collaborators: Heidi Luter (AIMS), Michael Wagner (University of Vienna), Bettina Glasl (University of Vienna), Nicole Webster (University of Tasmania), Pam Engelberts (QUT), Arno Schintlmeister (University of Vienna), Anton Legin (University of Vienna)

Evolution of the marsupial gut microbiome and adaptation to plant toxins

Culture-independent methods have been applied extensively to the gut microbiomes of mammals (in particular humans and mice), birds, fish, reptiles and insects. However, surprisingly little culture-independent work has been done with iconic Australian fauna, including marsupials of the order Diprotodontia (having two lower incisors).

Members of this marsupial order, which include kangaroos, wallabies, possums, wombats and koalas among many others, are particularly interesting in terms of their gut microbiota, as several species can digest eucalyptus leaves which are nutrient poor, high in lignified fibre and enriched in natural toxins. We aim to survey diprotodont marsupial faecal microbiomes and recover genomes of microbial populations correlated with a toxic diet.

Project team: Phil Hugenholtz (CI), Rochelle Soo, Kate Bowerman, Michaela Blyton, Pierre-Alain Chaumeil

Understanding the koala microbiome

Koalas are an iconic Australian species and true dietary specialists, surviving on a diet of almost exclusively eucalyptus leaves. While genuine obligate specialists like the koala are exceedingly rare, their narrow ecological niche also limits their ability to adapt to environmental change and places them at risk. Koalas have declined across most of their historic geographic ranges and have recently been listed as threatened in Queensland, NSW and the ACT.

There is an urgent need to understand the role of microbes in koala digestion and their potential to buffer digestive efficiency against the impacts of climate change as well as from translocation to areas with different species of eucalyptus trees.

Project team: Michaela Blyton (CI), Phil Hugenholtz, Rochelle Soo, Kate Bowerman
Collaborators: Ben Moore (Western Sydney University), Emily Hynes (Ecoplan Australia), Jack Pascoe (Conservation Ecology Trust), Desley Whisson (Deakin University), Karen Marsh (ANU)

Understanding evolution of dominant Bacteria inhabiting the rodent gut

The gut microbiome is central to animal health and immune function, however we have an incomplete understanding of how this important symbiotic ecosystem evolved. By approaching this knowledge gap from a historical perspective and using real-time observation, we will address how the gut community evolved with the rodent host and how members of that community respond to new selective pressures. The significance of these findings is in their capacity to inform our understanding of the relationship between host and microbe, not only within a key model system, but by extrapolation to other host-microbe systems.

We aim to:

catalogue and characterise the functional potential of rodent gut-associated Bacteria via genome recovery from metagenomic datasets
identify signals of evolutionary adaptation of Bacteria to the rodent gut environment via comparative genomics across related hosts occupying different environmental niches
test the adaptive capacity of Bacteria within the mouse gut in real-time using modern stressors as selective pressures.

Project team: Phil Hugenholtz (CI), Kate Bowerman, Christian Field

Point-of-care microbiome therapy in koalas during antimicrobial treatment for Chlamydia

Chlamydial disease is a major threat to the survival of koala populations. Over 15 years, half of the koalas presented to Wildlife Hospitals had overt chlamydial disease. Wildlife hospitals successfully treat many infected koalas with antimicrobial therapy, but there is a high mortality (20-25%) rate during treatment from fatal gut dysbiosis (microbial imbalance). Recent studies highlight microbiome therapy as a possible way to boost survival during treatment. Survival during antimicrobial treatment was reported to be higher in koalas with a high alpha diversity of gut microbiota or an abundance of tannin-degrading gut bacteria. Importantly, a recent study has shown that the koala’s hindgut microbiome can be modified by oral faecal inoculations using an acid-resistant capsule.

Here we will test a point-of care therapy to boost the survival of koalas during antimicrobial treatment for Chlamydia and hence contribute to the return of koalas to the wild.

Project team: Michaela Blyton
Collaborators: Jenny Seddon (JCU), Deirdre Mikkelsen, Lyndal Hulse, Amber Gillet (Australia Zoo Wildlife Hospital), Michael Pyne (Currumbin Wildlife Hospital

Harnessing the gut microbiome to improve stem cell transplant outcome

Allogeneic stem cell transplantation (SCT) is considered the gold standard procedure for the treatment of high-risk blood cancers, however, graft versus-host disease (GVHD) remains a barrier to the success of this life-saving immunotherapy. Preliminary evidence suggests the gut microbiome may play a role in modulating the tipping point in development of GVHD and its severity.

This NHMRC funded study led by Associate Professor Antiopi Varelias aims to identify the key gut microbiome species responsible for interaction with SCT subjects’ immune system and characterise those responses in both mouse models and human patients.

Project team: Seweryn Bialasiewicz (CI), Phil Hugenholtz, Julian Zaugg
Collaborators: Antiopi Varelias (CI; QIMR-B), Esteban Marcellin, Geoffrey Hill (Fred Hutchinson Cancer Centre, USA), Quan Nguyen (UQ/QIMR-B), Glen Kennedy (QLD Health), Ashleigh Scott (QLD Health)

Linking koala gut microbiome, diet and Chlamydia and comparing health between northern and southern populations across mainlands Redland Coast

We are using non-invasive sampling of koala faecal pellets to determine to determine the gut microbiomes and health status of koalas in the Redland council area. We are also using an SNP based genetic approach to determine which species of eucalypts those koalas are feeding on.

Through this project we will gain a better understanding of how diet, microbiome composition and disease interact and are affect by the urban environment.

Project team: Michaela Blyton
Collaborators: Celine Frere (CI), Nicola Jackson

Molecular analysis of koala scats for diet composition, KoRV subtypes and microbiome

We are using an SNP based genetic approach to determine which species of eucalypts koalas are feeding on from non-invasively collected faecal pellets. We are also using these samples to determine the koalas’ gut microbiome composition using 16s amplicon sequencing and what koala retrovirus subtypes they carry by env amplicon sequencing. These approaches are being applied across a range of projects to answer ecologically focus questions.

Project team: Michaela Blyton (CI), Max Lacour
Collaborators: Romane Cristescu (University of the Sunshine Coast)