PhD Studentship: The Skin Microbiome and Fish Health in Aquaculture (BBSRC Funded)

University of Exeter - College of Life and Environmental Sciences

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence. The partnership has a strong track record in advancing knowledge through high quality research and teaching in partnership with industry and government.

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP).  Up to 4 fully-funded studentships are being offered to start in September 2018 at the University of Exeter.

Academic Supervisors:

Main supervisor: Dr Ben Temperton
Co-supervisor: Prof Charles Tyler
Collaborator: Dr Karen Moore

Project description:

Microbiomes (the microbes associated with a host) are increasingly seen as a major component of human and animal health. Stressors that induce shifts in microbial communities can result in disease states, for example when previously low-abundance pathogens exploit environmental changes to dominate the microbiome. Advances in molecular biology and next-generation DNA sequencing have enabled the study of microbial communities at an unprecedented level. Despite this, relatively little work has been done on the microbiomes associated with aquaculture production. Global aquaculture of fish and invertebrates produced 73 Mt of food in 2014 (with an estimated value of $160Bn, FAO 2016). Disease is widely acknowledged as the prominent bottleneck to achieving global food security and poverty alleviation targets relating to aquaculture with annual losses exceeding >$6bn (FAO, 2014). Outbreaks of disease caused by endemic and emerging pathogens impact directly on farmer income and their nutritional security. Avoidance of yield-limiting disease outbreaks is a fundamental requirement for future growth and resilience of aquaculture in developing countries. Furthermore, disease outbreaks in openwater aquaculture ponds pose a risk to wild fish populations and the impact of microbiome shifts in aquaculture on the neighbouring wild populations is as yet unstudied. Advances in sequencing are of limited use to such countries when sequencing capacity is concentrated in developed nations, where prohibitive costs and time delays limit utility in disease diagnosis and management.

The recent development of the USB-powered, small-form MinION sequencer by Oxford Nanopore provides the opportunity for field-based, real-time sequencing of microbial and viral communities, by the farmers themselves. The student will develop protocols for profiling microbial communities and viral metagenomes associated with inland and coastal aquaculture facilities, using the MinION sequencer in the field. Microbial profiles will then be analysed alongside environmental data to identify putative links between emergent disease states and changes in aquaculture conditions, including antibiotic and disinfectant use. Protocols will be developed in collaboration with industrial partners to ensure robust, independent operability by farmers. The project will apply developed protocols in fieldwork based in Bangladesh (potentially also Malawi) to evaluate the impact of open-water aquaculture facilities on the microbiomes associated with wild fish stocks, for key commercial species including carp and tilapia.

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South West England