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(BBSRC DTP) Studying the effects of stressors on the cnidarian microbiome with computational models

Department of Earth and Environmental Sciences

About the Project

Coral reefs are structurally complex habitats constructed by reef-building cnidarians. These biodiversity hotspots provide important services to humans, but are among the most threatened marine ecosystems. For example, small short-term changes in ocean temperature can lead to bleaching events that weaken or destroy large areas of coral reef.6 Cnidarians including corals have complex microbiomes.3,4 Changes in the microbiome can precede bleaching events, suggesting that symbiotic interactions between cnidarians and their microbiota play a role in the response to external stressors.7

The Marine Microbial Symbioses lab at the University of Melbourne is developing methods to manipulate cnidarian microbiomes to help reefs respond to environmental stress.8,9 The efficient design and effective application of these tools demands a thorough understanding of the composition, dynamics, and function of cnidarian microbiomes in stressed and healthy states.4 This understanding is in its infancy. The Gilman and Muldoon labs at the University of Manchester work on a surprising parallel system: the human respiratory microbiome in asthma. As part of the CURE project10 (, this team is developing mathematical and computational tools to understand the composition and dynamics of healthy and asthmatic microbiomes, and to develop phage therapies that can guide asthmatic microbiomes back to healthy states. This project will bring these two lines of research together, applying tools developed for the alleviation of asthma in humans to help understand and protect coral reefs.

In this project, the student will achieve three main research objectives:

1. Develop a biological market (i.e., game theory) model to predict how multi-species symbioses will respond to environmental changes.
2. Develop classification models to characterise healthy and distressed states in the cnidarian microbiome.
3. Characterise the functional profiles of cnidarian microbiota in the presence and absence of environmental stressors.

The student will be based in Manchester for components 1 and 3, and in Melbourne for component 2. Much of the metagenomic data needed for this project has already been collected by the Blackall lab, so the project can go forward even new data cannot be obtained. However, we anticipate that the student will collect additional data and test model predictions with experimental work in the Blackall and/or Shiels labs, thus ensuring that the student gains expertise in both wet and dry aspects of metagenomics research.

Entry Requirements:
Applicants must have obtained, or be about to obtain, at least an upper second class honours degree (or equivalent) in a relevant subject. This project is offered as a Dual Award. Applicants for Dual Award projects must meet the entry requirements of both The University of Manchester and The University of Melbourne. The University of Melbourne admissions criteria can be found at:

UK applicants interested in this project should make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible. International applicants (including EU nationals) must ensure they meet the academic eligibility criteria (including English Language) as outlined before contacting potential supervisors to express an interest in their project. Eligibility can be checked via the University Country Specific information page (

If your country is not listed you must contact the Doctoral Academy Admissions Team providing a detailed CV (to include academic qualifications – stating degree classification(s) and dates awarded) and relevant transcripts.

Following the review of your qualifications and with support from potential supervisor(s), you will be informed whether you can submit a formal online application.

To be considered for this project you MUST submit a formal online application form - full details on how to apply can be found on the BBSRC DTP website

Funding Notes

Funding will cover UK tuition fees/stipend only. The University of Manchester aims to support the most outstanding applicants from outside the UK. We are able to offer a limited number of scholarships that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website View Website


Eakin CM et al. Caribbean corals in crisis: record thermal stress, bleaching, and mortality in 2005. PLoS One, 2010.

Bourne D, Iida Y, Uthicke S, Smith-Keune C. Changes in coral-associated microbial communities during a bleaching event. ISME Journal, 2008.

Blackall LL, Dugan AM, Hartman LM, van Oppen MJH. Probiotics for corals. Microbiology Australia, 2020.

Dugan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging probiotic to mitigate coral bleaching. BioRxiv, 2020.

Megremis S et al. Bacteriophage deficiency characterizes respiratory virome dysbiosis in childhood asthma. BioRxiv, 2020.

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