Title:PhD: How do the interactions between temperate and lytic phages
shape microbial communities? (University of Manchester)

Bacteriophages, the viruses that infect bacteria, are the most abundant
biological entities on Earth. These phages often compete for the same
resources - bacterial hosts -but still find ways to coexist. This
is particularly interesting for two types of phages: obligately lytic
phages, which infect and kill bacterial cells to release new virions,
and temperate phages, which can either follow the lytic pathway or
enter a dormant state by integrating into the bacterial genome as a
prophage. The dormant prophage maybe at risk if the host is infected by
another lytic phage, which would destroy both the host and the resident
prophage. However, other resident prophages may also be activated and
kill the host. Such complex interactions likely influence phage ecology
and evolution, as evidenced by phages carrying mechanisms to avoid
superinfection by other phages. Yet, we have a very limited understanding
of phage interactions and their influence on microbial communities.

This project aims to understand how phages, particularly temperate and
lytic phages, interact and coexist within bacterial communities. We
will combine ecological theory,mathematical modelling, bioreactor
experiments, and synthetic engineering to develop a predictive model
of phage dynamics. Building on our previous theoretical work, we will
develop novel mathematical models that incorporate phage ecology and
evolution, then use continuous culture experiments in bioreactors to
test and iteratively refine our mathematical predictions. Engineered
phages with fluorescent markers and OD measurements will allow us to
track prophage and bacterial populations in real-time,while qPCR and
plating will provide co-resident prophage and free phage numbers. By
iterating between mathematical simulations and bioreactor experiments,
we will refine our theory on phage interactions and microbial community
dynamics. This research will provide novel insights into the dynamics
of phage infections and offer practical tools for manipulating microbial
communities, such as fostering healthy microbiomes and managing microbial
infections. The results can be applied to human health, conservation,
and agriculture/food security.

This project offers an exciting opportunity for interdisciplinary
research, where participants will acquire diverse skills, including
computational modelling, mathematical theory, microbiological
experimentation, machine learning, and synthetic engineering. The
successful applicant will be funded (tuition and stipend) by the UK
Engineering and Physical Sciences Research Council and by the University
of Manchester.

For information on how to apply, please visit
https://www.findaphd.com/phds/project/epsrc-dtp-how-do-the-interactions-between-temperate-and-lytic-phages-shape-microbial-communities/?p185126.
If you have questions, email the advisory team at
claudia.igler@manchester.ac.uk (Claudia Igler),
katharine.coyte@manchester.ac.uk (Kat Coyte), and/or
tucker.gilman@manchester.ac.uk (Tucker Gilman).

R. Tucker Gilman (he/him)

Department of Earth and Environmental Sciences
University of Manchester
Office:C.1249a Michael Smith Building
Tel: +44 (0)161 275 1544
Twitter: @GilmanTucker
Zoom: https://zoom.us/my/tucker.gilman

Tucker Gilman <tucker.gilman@manchester.ac.uk>

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