Reducing greenhouse gas emissions from cattle using microbiome variation

Project opportunity

This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.

Project goal

This project will develop a new tool for methane mitigation from livestock – a saliva-based test that will allow producers to rank animals based on the amount of methane they will produce. The test is called “LESTR” (Low Emission Saliva Test for Ruminants). The key project outcome will be a predictive equation and testing methodology that allows identification of low methane emitting “commercial” animals based on a biological sample (e.g., saliva).

Project skills

The project will involved the the analysis of the microbiome of cattle, and will include sampling of microbiome, molecular genetics, the application of new 'long read' sequencing technology, bioinformatics and statistical analysis. 

Project support

This project directly aligns with the newly awarded "LESTR" grant. The student will work closely with the Post-Doctoral Research fellow on the project, as well as the experienced researcher team that is based across the university (QAAFI, SCMB and SAFS). The student will be based in the Centre for Animal Science team at QAAFI, with the Agri-Genomics team. The student will have access to the vast knowledge of the other HDR and postdoctoral researchers in the team, to support the students research progress and success.

Project background

The Queensland beef industry is a major contributor to export income (approximately $9 billion in 2019) and regional jobs, with over 30,000 people employed on farm and in the meat processing sector. However, methane emissions from cattle account for approximately 8% of Australia’s greenhouse gas emissions. The future sustainability and social licence of the beef industry will depend on a reduction in this level of emissions. This proposal develops a method to rank animals by the amount of methane an individual animal is likely to emit – allowing producers to make decisions around their approach to breeding and management decisions.

Cattle and sheep vary naturally in the amount of methane they produce, even when grazed on the same pasture and at the same age (van Gastelen, Dijkstra et al. 2019, Newbold and Ramos-Morales 2020). This is a result of the composition of their rumen microbiomes - which we term their “rumen microbiome profile” – the presence and relative abundance of microbial species (Ross, Moate et al. 2013, Wallace, Sasson et al. 2019). We have previously demonstrated that it is possible to use this rumen microbiome profiles to identify which animals will be high or low methane producers (Ross, Moate et al. 2013, Ross, Hayes et al. 2020). While this method can identify naturally low methane emitting cattle, the practicality of obtaining rumen fluid from commercial cattle is prohibitive.

An alternative to direct rumen sampling is using the oral microbiome. Tapio, Shingfield et al. (2016) illustrated that oral microbiome samples could be used as non-invasive indications of the rumen microbiome. Methodological optimisations have been undertaken that identified optimal sampling conditions regarding time from feeding, as well as corrections of oral specific (i.e., non-rumen sourced) microbial species (Young, Skarlupka et al. 2020). This method has recently successfully been applied to examine rumen microbiome changes at weaning (Amin, Schwarzkopf et al. 2021).

The ability of the rumen microbiome profile to predict low methane emitting cattle, and the suitability of the oral or salivary microbiome as a suitable non-invasive sampling method has been demonstrated in multiple studies. However these studies have been small, generally less than 10 animals per treatment group. While past research has demonstrated the potential, large numbers of animals are required to develop prediction equations that are suitable for use in industry. Hence, we have developed a large study  that will be assessed under production settings. The animals will have methane measurements and saliva samples taken, which will be used to develop a predictive test for low methane emitting cattle.

This project aims to develop methods to rapidly identify cattle with low methane emitting microbiome profiles using non-invasive sampling.

Scholarship value

As a scholarship recipient, you'll receive: 

  • living stipend of $32,192 per annum tax free (2023 rate), indexed annually
  • tuition fees covered
  • single Overseas Student Health Cover (OSHC)


Dr Elizabeth Ross

Queensland Alliance for Agriculture and Food Innovation


Preferred educational background

Your application will be assessed on a competitive basis.

We take into account your

  • previous academic record
  • publication record
  • honours and awards
  • employment history.

A working knowledge of metagenomics, genetics, genomics, bioinformatics, programming or statistics would be of benefit to someone working on this project.

The applicant will demonstrate academic achievement in the field(s) of biology or agriculture and the potential for scholastic success.

A background or knowledge of the Australian beef industry or the agricultural sector is highly desirable.

Latest commencement date

If you are the successful candidate, you must commence by Research Quarter 3, 2024. You should apply at least 3 months prior to the research quarter commencement date.

If you are an international applicant, you may need to apply much earlier for visa requirements.

How to apply

You apply for this project as part of your PhD program application.

View application process