HoliCOW – A holobiont strategy to decipher core host-microbiota interactions in cows

Overview

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.

Research activities

These projects are uniquely placed within the junction of several active international research consortiums and are supported both intellectually and technologically by the world-leading Centre for Microbiome Research (CMR). Both students will participate in experimental design, data analysis, biological interpretation and manuscript preparation and will be presented with opportunities to visit external partners in Europe for short-term research visits. Candidates will have supervisory support from both CMR members and international partners to facilitate both learning objectives and to successfully publish research findings in high-impact peer reviewed journals.

Project 1

A PhD student with bioinformatics experience will generate and analyze complex microbiome sequence data to complement existing rumen microbiome datasets. Via multi-omics analyses, they will create an inventory of microbial genomes and lists of expressed metabolic features that are signature for the keystone microorganisms that drive rumen function. It is expected that this project will formulate a dedicated 'wish-list' of cultivation targets and will engage other project partners in guiding cultivation work that uses CMR’s world leading high-throughput cultivation platform.

Project 2

A PhD student with molecular lab experience will primarily engage in the high throughput cultivation and characterization of core microbiota. To characterise core microbiota, they will design and implement synthetic consortia to focus on core metabolic features that drive rumen digestion and methane formation. They will collaborate with project partners and utilize meta-omic technologies to characterize microbiota of interest and additionally verify the importance of their cultivation targets against global datasets from European consortiums.

Outcomes

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 a collective effort to reduce global methane emissions by at least 30%, which could eliminate over 0.2°C warming by 2050.

Skills and experience

Project 1

Required PhD student academic qualifications:

• honours degree or MSc in microbiology/bioinformatics, with specific emphasis on functional microbial multi-omic data analysis
• knowledge of a programming language e.g. Python / R.

Desirable experience:

• molecular laboratory, bacteriology and/or cultivation-based experimental work
• network-based analysis of multi-omics data.

Project 2

Required PhD student academic qualifications:

• honours degree or MSc in microbiology/bacteriology/biochemistry with specific emphasis on molecular techniques.

Desirable experience:

• anaerobic microbiology
• single-cell sorting/sequencing
• bioinformatic analyses of microbial functional omic data
• knowledge of a programming language e.g. Python / R.

Scholarships

You may be eligible to apply for a research scholarship.

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Keywords

• Microbiome
• Methanogenesis
• Global warming

Contact

Contact the supervisor Professor Phil Pope via email phil.pope@qut.edu.au for more information.