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Fully-funded White Rose BBSRC DTP Biology project: Modelling microbial metabolic islands in the (waste) stream

   White Rose Doctoral Training Partnership in Mechanistic Biology

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  Prof J Chong, Dr AJ Wood, Prof G Thomas  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Lead supervisor: Prof James Chong (Department of Biology)

Co-supervisors: Prof Jamie Wood (Departments of Biology & Mathematics) and Prof Gavin Thomas (Department of Biology)

The student will be registered with the Department of Biology

Mixed microbial communities underpin anaerobic digestion (AD) – a robust biotechnology used to recover resources from variable waste materials such as sewage, food waste and agricultural residues. AD communities adapt to changes in the composition and concentration of organic matter, with functional guilds within the community integrating complex environmental and community signals into a resilient response. Understanding the parameters that might drive individual species to change their metabolic activities, and the consequences that might cascade from such changes, could provide a powerful tool for community manipulation. The microbial communities found in AD contain hundreds of different species, which presents a challenge for building predictive metabolic models, a technique which can be very powerful for understanding single species systems.

The aim of this project is to build a metabolic model of an individual microbial species found in AD and develop methods to understand how this individual interacts with the “meta-organism” around it. 

During the project you will build a two-organism metabolic model, where one model represents a single species in the community and the other represents the rest of the community as a “meta-organism”. These two models will be populated with available data, using metagenome assembled genome (MAG) DNA sequences to predict the metabolic pathways available. You will make use of available datasets and methodologies to build and populate these models. Where more information is required to inform and/or test your models (e.g. to provide accurate parameterization, to confirm predictions, or to confirm the ability of target organisms to make use of specific metabolites) you will carry out laboratory work to collect data from carefully designed, targeted, experiments using appropriate methods including multi-omics measurements (e.g. meta-transcriptomics, isotope labelling).

 Your combined model will be used to predict the behavior of the single species as it interacts with the community meta-organism. The validity of your model will then be tested by comparing these predictions to measurements you make in our laboratory AD systems. You will be supported by expertise in building models and making multi-omics measurements, gaining experience in both these areas during the course of your studies.

The Department of Biology holds an Athena SWAN Gold Award. We are committed to supporting equality and diversity and strive to provide a positive working environment for all staff and students. 

The WR DTP and the University of York are committed to recruiting future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and we have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with any biological, chemical, and/or physical science backgrounds, or students with mathematical background who are interested in using their skills in addressing biological questions. 

Programme: PhD in Mechanistic Biology (4 years)

Start Date: 1st October 2023

Interviews: Friday 10 February 2023 or Monday 13 February 2023. Please keep these dates free.

Funding Notes

This project is part of the BBSRC White Rose Doctoral Training Partnership in Mechanistic Biology. Appointed candidates will be fully-funded for 4 years. The funding includes:
Tax-free annual UKRI stipend (£17,668 for 2022/23 academic year)
UK tuition fees
Research support and training charges (RSTC)
International students will need to have sufficient funds to cover the costs of their student visa, NHS health surcharge, travel insurance and transport to the UK as these are excluded from UKRI funding.

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