PhD in Decoding Protist Parasites in Aquaculture with Single-Cell Sequencing (SWBio DTP)

This PhD project, offered through the South West Biosciences Doctoral Training Partnership (SWBio DTP) and hosted at the University of Bath, aims to decode the biology of protist parasites in aquaculture using advanced single-cell sequencing techniques. The project focuses on Ichthyodinium, a genus of parasitic dinoflagellates that infects various fish species, causing significant losses in global aquaculture. The parasite invades the yolk sac of developing fish embryos, often resulting in high mortality rates and posing a major challenge to sustainable aquaculture. The economic impact in the UK alone is estimated at £38.75–109.38M annually. Despite their importance, many protist parasites, including Ichthyodinium, lack genomic and transcriptomic data, which are crucial for understanding their biology, host interactions, and evolutionary history. The project will generate the first comprehensive molecular resources for Ichthyodinium by isolating and sequencing the parasite from both wild and captive fish embryos. The doctoral researcher will conduct regular molecular and microscopy-based health screens to identify novel parasite diversity across different environments. Using state-of-the-art single-cell sequencing, the project will: (1) generate genomic and transcriptomic datasets for targeted parasites, (2) investigate functional pathways relevant to infection and survival, (3) construct robust multi-protein phylogenies to clarify the evolutionary position of Ichthyodinium and related lineages, and (4) assess plastid retention, which could inform drug targeting strategies. The student will receive training in microscopy, single-cell sequencing library preparation and analysis, and advanced bioinformatics. The project is supervised by Dr. Corey Holt (lead, University of Bath) and Prof. Edward Feil (University of Bath), with additional input from Dr. Charlotte Davies (Swansea University). Funding is available through the SWBio DTP studentship, covering tuition, a stipend (£20,780 p/a in 2025/6), research and training costs, fieldwork, conference attendance, and a 3-month placement. The studentship is open to both Home and International students, though international funding does not cover visa or healthcare costs, and awards to international students are limited. Applicants should have a strong background in a relevant science or technology field, with a minimum of a First or Upper Second Class UK Honours degree (or equivalent), and a solid foundation in mathematics or quantitative science. English language proficiency is required for non-native speakers. The SWBio DTP is committed to supporting students from diverse backgrounds and can accommodate flexible study arrangements. Applications close on 3 December 2025. For more information or informal enquiries, contact Dr Corey Holt at [email protected].