Biological Sciences: Fully-funded Swansea University and Mowi Feed PhD Scholarship: Functional Microbiomes: Unravelling Diet, Environment and Host Pathogen Interactions (RS531)

Subject areas: Biosciences, Microbiome, Metabolomics, Host-pathogen interactions, Aquaculture, Animal health 

Project start date:

• 1 October 2024 (Enrolment open from mid-September)

Project supervisors: 

• Dr Tamsyn Uren Webster (T.M.UrenWebster@swansea.ac.uk)
• Dr Konstans Wells
• Dr Claudio Greco

Aligned programme of study: PhD in Biological Sciences

Mode of study: Full-time

Project description:

Microbiota can positively influence animal physiology and health in many ways, including by enhancing nutrient uptake, immunity and pathogen resistance. At the same time, microbiomes are readily influenced by both various host and environmental factors, including diet and temperature. However, key questions remain regarding the functional nature of host-microbiome relationships and, especially, interactions with pathogens and the environment.

Aquaculture will likely make an important contribution to future global food security, given the depletion of wild fish stocks and increasing demand for high-quality protein. Functional feeds offer great promise for improving fish health and productivity, including by enhancing nutrient uptake and pathogen resilience. This will be crucial for the sustainability of the industry, especially under climate change scenarios predicted to increase pathogen transmission. We expect that the gut microbiome plays an important role in mediating these dietary benefits, we do not yet know how.

This PhD will focus on unravelling microbiome-pathogen interactions in Atlantic salmon, and how this relationship is shaped by diet and environment. The project represents an exciting collaboration between Swansea University and Mowi Feed, where we ultimately aim to better understand how functional feeds can improve fish health and disease resistance. All dietary & pathogen experiments will be conducted by Mowi Feed, in Norway and Scotland. The student, based in Swansea, will be focused on conducting molecular, bioinformatic and community-modelling analyses to determine microbiome-pathogen-environment interactions, including 16S rRNA sequencing, metabolomics and transcriptional profiling, as well as some in vitro microbial interaction assays. The main objectives are:

1. Determine the impacts of functional feeds on microbiome diversity, structure and function.
2. Establish causal links between feed, microbiome, host immunity and pathogen resistance.
3. Characterise temporal microbiome-pathogen interactions in fluctuating environments.

The student will join a dynamic, supportive and enthusiastic research team in Swansea, broadly focusing on impacts of environmental factors on microbiomes, pathogens and animal physiology, with complementary supervision from Drs Tamsyn Uren Webster, Konstans Wells and Claudio Greco. The student will also closely collaborate with the industry partner, Mowi-Feed, with supervision from Dr Laura Martinez Rubio.

The project would suit a student with a keen interest in microbiomes, host-pathogen interactions and (eco)physiology, as well as enthusiasm for unravelling complex interactions. Some experience in molecular techniques, metabolomics, microbiology, bioinformatics and statistical analysis in R would be an advantage.

The candidate will adopt an exciting interdisciplinary approach that combines laboratory work, bioinformatics and ecological modelling. The student will capitalise on the well-established and newly refurbished laboratories and computational facilities in Swansea, and world-leading experimental facilities for aquaculture nutrition from Mowi. A comprehensive training programme will be provided by the interdisciplinary supervisory team’s expertise in microbiomes and molecular physiology (Dr Uren Webster), animal health and disease ecology (Dr Wells), metabolomics and natural products (Dr Greco), and aquaculture nutrition (Dr Martinez Rubrio).