This PhD project, hosted at the University of Bath and part of the South West Biosciences Doctoral Training Partnership (SWBio DTP), investigates the fitness effects of loss-of-function (LoF) mutations in bacterial populations. The SWBio DTP is a BBSRC-funded collaboration among leading universities, research institutes, and industry partners across the South West and Wales, offering a structured training program for bioscience researchers. The project is supervised by Professor Edward Feil (lead), Professor Zamin Iqbal, and Dr. Alex Jeffries, with additional input from Dr. Sion Bayliss (University of Bristol). The research focuses on understanding how gene loss, specifically LoF mutations, contributes to bacterial adaptation, a process often overshadowed by studies on gene acquisition and gain-of-function mutations. LoF mutations can affect key pathways in pathogens such as Streptococcus pneumoniae, influencing vaccine escape, transmissibility, and antibiotic resistance. The project aims to systematically analyze the prevalence, distribution, and selective consequences of LoF mutations using large genomic datasets from public repositories (GPS, ENA, NCBI). A bioinformatic pipeline will be developed to detect and catalogue LoF events across hundreds of thousands of genomes and pangenomes, complemented by statistical tests to distinguish neutral, deleterious, and advantageous mutations. The research will also explore epistatic interactions and estimate essential gene sets in natural populations, providing insights into the evolution of high-priority pathogenic strains and broader adaptation in diverse niches. The studentship is open to both Home and International applicants, with funding covering tuition, a stipend (£20,780 p/a in 2025/6), research/training costs, fieldwork, conference attendance, and a 3-month placement. International applicants should note that visa and healthcare costs are not covered, and only 30% of awards are available to non-UK students. Applicants must hold a First or Upper Second Class UK Honours degree (or equivalent), with a strong background in mathematics (minimum grade B in A-level Maths or equivalent). English language proficiency (IELTS 6.5 overall, no less than 6.5 in any skill) is required for non-native speakers. The SWBio DTP supports flexible working and reasonable project adaptations to promote inclusivity. Applications close on 3 December 2025 at midday GMT. For further details and to apply, visit the SWBio DTP website.

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].