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, Kate Bowerman
- Collaborators: Mark Morrison, Harley McRae, Phil Pope (QUT), Rochelle Soo
Bacteriophage-derived antimicrobial 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 novel therapies originating from naturally occurring viruses (bacteriophages) that infect and kill the specific otitis media causing bacteria.
- Project team: Seweryn Bialasiewicz (CI), Julian Zaugg, Phil Hugenholtz, Rylee Deehan
- Collaborators: Andrea Coleman (Queensland Health), Anders Cervin, Diane Maresco-Pennisi, Rhiannon Baxter, Robyn Marsh (Menzies School of Health Research), Max Lacour
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
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), Kate Bowerman, Michaela Blyton, Pierre-Alain Chaumeil
- Collaborators: Rochelle Soo
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, Kate Bowerman
- Collaborators: Ben Moore (Western Sydney University), Emily Hynes (Ecoplan Australia), Jack Pascoe (Conservation Ecology Trust), Desley Whisson (Deakin University), Karen Marsh (ANU), Rochelle Soo
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
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 (QIMR), 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)
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)
- Collaborators: Romane Cristescu (University of the Sunshine Coast), Max Lacour
Oral microbiome biomarkers of periodontitis in gestational diabetes
Gestational diabetes has been associated with increased risk of developing oral diseases, including periodontitis. In collaboration with the UQ School of Dentistry and led by Duke-NUS Medical School researchers, we aim to use multi-omic approaches to search for oral microbial community changes to identify potential mechanisms between the observed diseases and candidate targets for therapeutic intervention.
- Project team: Seweryn Bialasiewicz (CI), Julian Zaugg
- Collaborators: Chaminda Seneviratne, Prajod Preethi (Duke-NUS)
Pathogen survey in ticks
Ticks are well-known vectors of infectious diseases in both humans, companion animals and livestock, however the true range of potential pathogens is underexplored. In collaboration with UQ's School of Veterinary Sciences, we are using transcriptomic methods to characterise both unknown viral and bacterial pathogens, as well as the emerging canine pathogen Ehrlichia canis in dog ticks on the Australian East coast.
- Project team: Seweryn Bialasiewicz (CI), Julian Zaugg
- Collaborators: Swaid Abdullah, Rhys Parry, Justine Gibson
Enhancing metagenomics of host-associated low microbial biomass samples using nanopore sequencing
A key constraint of most host-associated metagenomic studies (e.g. clinical samples) is the high host to low microbial DNA ratios, resulting in poor microbial sensitivity and genome assembly due to the overwhelming interference of the host DNA. In this study, we aim to leverage the recent development of adaptive sampling on the MinION nanopore sequencing platform in combination with field-friendly sample preparation techniques to develop a metagenomic sequencing method that reduces the burden of high host DNA on low microbial biomass samples.
- Project team: Seweryn Bialasiewicz (CI), Julian Zaugg, Rylee Deehan
- Collaborators: Stacey Andersen (QIMR), Subash Rai, Rhiannon Baxter, Sohye Yoon, Brooke Purdue