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Surviving Perturbations: Quantitatively Understanding Microbial Community Robustness


   Department of Genetics, Evolution and Environment

   Applications accepted all year round  Funded PhD Project (UK Students Only)

About the Project

The Project:

Multispecies microbial communities can outperform single species in, for example, producing pharmaceuticals or fighting infections. However, a useful community must be “robust” in the sense that it must survive internal and external perturbations. Community robustness arises from interactions between member species and can change rapidly as members evolve. As species interactions are complex and difficult to quantify, little is understood about the quantitative basis or genetic mechanisms of robustness against different perturbations, nor how robustness may change during evolution. Theoretical work is often based on untested assumptions, while empirical work is largely phenomenological or correlative.

To quantitatively understand community robustness and how robustness might change as community members evolve, we will use genetically tractable synthetic yeast communities and mathematical modelling. With well-defined species interactions, synthetic communities are amenable to a wide range of experimental manipulations. Moreover, lessons learned from synthetic communities generally hold for communities of nonengineered microbes, as our lab and others have demonstrated. We have created and mathematically modelled a synthetic yeast cooperative community CoSMO (Cooperation that is Synthetic and Mutually Obligatory) (Hart et al., PLoS Biology 2019). It consists of two coexisting yeast strains, each supplying its partner with an essential metabolite. In this project, we will quantitively examine CoSMO’s robustness against two commonly-encountered external perturbations: 1. extreme population reduction as occurring after antibiotic treatments, or 2. gradual population reduction as what gut microbiota may experience during periodic purges from the gut. We aim to understand the quantitative and genetic bases of robustness against these two perturbations and how robustness might change as community members evolve and diversify. This understanding will be critical for engineering robust communities.

The lab:

Our new lab (relocated from Seattle, USA) is part of CLOE (Centre for Life’s Origins and Evolution https://www.ucl.ac.uk/biosciences/gee/ucl-centre-lifes-origins-and-evolution-cloe) in the Department of GEE (Genetics, Evolution and Environment https://www.ucl.ac.uk/biosciences/gee) of UCL (https://www.ucl.ac.uk/). Located in central London, UCL is a world-leading university. GEE has an illustrious history, having hosted luminaries such as JBS Haldane, RA Fisher, and John Maynard Smith. CLOE is the newest centre at GEE, along with five other centres focusing on Genetics, Healthy Ageing, Biodiversity, Computational Biology, and NatureSmart. Our lab consists of experimentalists and theorists, and our group meetings are characterized by lively and stimulating discussions where all members are intellectually engaged.

Your qualifications:

We are looking for a motivated, creative, and careful person with excellent quantitative training and communication skills. Bachelor’s or Master’s degree in Biology, Physics, Chemistry, Engineering or a related field. Undergraduate or Master’s research experience is required.

What you will get:

1.    Training in experimental biology (e.g. high-throughput microscopy, flow cytometry, chemostats, and whole genome sequencing), mathematical modelling, and how to make the two disciplines synergise.

2.    Training in science communications, both to other scientists (e.g. manuscript writing and research talks) and to the general public.

3.    Professional training opportunities offered by UCL.

Application documents: CV (Curriculum Vitae), college transcript, a list of three references, and a cover letter. These should ideally be compiled into a single pdf and uploaded. Alternatively, application materials can be sent to

References

Hart, Samuel FM, et al. "Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells." PLoS biology 17.2 (2019): e3000135.


Funding Notes

The PhD position is for a 4-year period. The expenses will be covered by a Royal Society Wolfson Fellowship awarded to the Shou lab.

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