PhD Project: The Fitness Effects of Loss-of-Function Mutations in Bacterial Populations (SWBio DTP)

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.