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Computational Design of Synthetic Microbial Communities

Karkaria, Behzad Darius; (2021) Computational Design of Synthetic Microbial Communities. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Abstract

In naturally occurring microbial systems, species rarely exist in isolation. There is strong ecological evidence for a positive relationship between species diversity and the functional output of communities. The pervasiveness of these communities in nature highlights that there may be advantages for engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially when functional complexity is increasing. The establishment of synthetic microbial communities is a major challenge we must overcome in order to implement coordinated multicellular systems. Here I present computational tools that help us design engineering strategies for establishing synthetic microbial communities. Using these tools I identify promising candidates for several design scenarios. This work highlights the importance of parameter inference and model selection to build robust communities. The findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and tuning the community composition. Additionally, I show that fundamental interactions in small synthetic communities can produce chaotic behaviour that is unforecastable. Together these findings have important ramifications for how we build synthetic communities in the lab, and the considerations of interactions in microbiomes we manipulate.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Computational Design of Synthetic Microbial Communities
Event: UCL (University College London
Open access status: An open access version is available from UCL Discovery
Language: English
Additional information: Copyright © The Author 2021. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request.
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10126407
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