Host-associated

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, Rhiannon Baxter, Rylee Deehan

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)

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

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.

• Project team: Cheong Xin Chan (CI), Katherine Dougan, Sarah Shah, Yibi Chen, Hisatake Ishida
• Collaborators: Debashish Bhattacharya (Rutgers University), Patrick Buerger (Macquarie University), Ira Cooke (JCU), Jose Victor Lopez (Nova Southeastern University), Lauren Messer (QUT), Cynthia Riginos, Mauricio Rodriguez-Lanetty (Florida International University), David Suggett (UTS), Mike Sweet (University of Derby), Madeleine van Oppen (University of Melbourne), Heroen Verbruggen (University of Melbourne)

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, Pam Engelberts, Steven Robbins, Laura Rix
• Collaborators: Michael Wagner (University of Vienna), Bettina Glasl (University of Vienna)

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: Nicole Webster, Laura Rix, Pam Engelberts 
• Collaborators: Heidi Luter (AIMS), Michael Wagner (University of Vienna), Bettina Glasl (University of Vienna)

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
• Collaborators: Mark Morrison, Thomas Sicheritz-Ponten (Technical University of Denmark), Birger Moeller (University of Copenhagen)

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)

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:

1. catalogue and characterise the functional potential of rodent gut-associated Bacteria via genome recovery from metagenomic datasets
2. identify signals of evolutionary adaptation of Bacteria to the rodent gut environment via comparative genomics across related hosts occupying different environmental niches
3. 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

Koala populations in northern Australia continue to decline due to habitat loss and disease, with the recent mega-fires devastating previous koala strongholds. It is critical that sick and injured koalas brought into rehabilitation centres can be returned to health and released to contribute to the ongoing viability of local populations. In the Brisbane region, many koalas that are admitted to rehabilitation centres are given antibiotics to treat infections such as chlamydial disease (cystitis, infertility and/or conjunctivitis), which affects more than half of all koalas brought into care.

These antibiotic treatments can decimate the koalas’ community of symbiotic gut microbes or microbiome, causing gastrointestinal dysbiosis and death. As specialist herbivores, koalas rely on their gut microbiomes to help them digest their toxic and fibrous diet of eucalyptus leaves. Without these critical microbes, koalas may not be able to obtain the nutrients and energy they need to survive, leading to poor rehabilitation outcomes for antibiotic-treated koalas. We propose to further improve microbial inoculation capsules that we have developed previously, into koala probiotics and test their effectiveness at improving koala digestion and survival during and after antibiotic treatment.

• Project team: Michaela Blyton (CI), Phil Hugenholtz, Leanne Dierens, Max Lacour
• Collaborators: Ben Moore (Western Sydney University), Michael Pyne (Currumbin Wildlife Hospital), Stephanie Shaw (Moggill Koala Hospital), Tim Portas (RSPCA), Ryley Staunton (Daisy Hill Koala Centre)

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

Koalas eat gum leaves ... right? The koala is one of the world's best-known and loved mammals, and even schoolchildren know that koalas eat gum leaves. This is true, but the real answer is also a little more complicated. Our project aims to provide a more detailed picture of what eucalypts (there are 900 species) and other plants koalas eat throughout their range. To do this, we have developed a new technique to identify plant DNA in the faecal pellets (poo) of koalas. Eventually, we hope that we'll be able to tell anybody who sends us a koala faecal pellet, what that koala had been eating.

• Project team: Michaela Blyton (CI), Max Lacour
• Collaborators: Ben Moore (Western Sydney University), Kasia Heller (Diversity Arrays Technologies), Damian Jaccoud (Diversity Arrays Technologies)

After fire, many eucalypts produce new leaves from epicormic buds under the bark. These leaves can differ substantially in nutritional quality from mature intact canopy, which likely affects their relative value as browse for koalas and the capacity of the landscape to support koalas. However, little is known about whether koalas alter their diet after fire in response to these changes in the relative value of available browse.

The objectives of the proposed project are to:

1. quantify the types and proportions of eucalypt species eaten by koalas living in burnt and nearby unburnt habitat,
2. compare the relative quality of diets eaten by koalas in the two environmental settings
3. identify the most appropriate sampling strategy to characterise the tree species composition and nutritional quality of the landscape, and
4. determine how dietary selection is related to the relative value of available browse.

This project will answer key questions about the impact of fire on koala diet choices and habitat nutritional quality, which will assist with the future management of koala populations after fire. This includes the capacity of burnt habitat to support koala population recovery, and whether pre-fire rankings of eucalypt browse preferences and habitat quality are appropriate when eucalypts are producing epicormic leaves after fire. The findings could also be used to inform revegetation activities to ensure that restored habitats can support koalas under a range of environmental conditions.

• Project team: Michaela Blyton (CI), Max Lacour
• Collaborators: Karen Marsh (ANU), Ben Moore (Western Sydney University), Romane Cristescu (University of the Sunshine Coast)