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cff-version: 1.2.0
message: "If you reference this thesis, please cite it as below."
title: "Omics-driven and constraint-based modelling of microbial community metabolism"
authors:
  - family-names: Zorrilla
    given-names: Francisco
    orcid: "https://orcid.org/0000-0002-6206-8655"
    affiliation: "MRC Toxicology Unit, University of Cambridge"
year: 2024
license: CC-BY-NC-ND-4.0
url: "https://www.repository.cam.ac.uk/items/e8039120-7f95-444f-95af-78fe5ce49db6"
doi: 10.17863/CAM.114621
keywords:
  - metagenomics
  - metabolic-modelling
  - microbial-communities
  - genome-scale-models
  - constraint-based-modelling
  - microbiome
abstract: >
  This thesis outlines the development and applications of omics-driven
  metabolic modelling approaches to understand microbial community
  metabolism in diverse ecological contexts. It introduces metaGEM, a
  workflow for reconstructing context-specific genome-scale metabolic
  models from metagenome-assembled genomes (MAGs), applied across five
  datasets (lab cultures, human gut, plant-associated, soil, ocean) to
  reconstruct over 14,000 MAGs and corresponding metabolic models. The
  thesis then presents three applied case studies — amino acid
  auxotrophies across microbial communities, microbial interactions in
  cheese flavour formation, and the pathogen-suppressing ability of a
  defined gut sub-community — and develops gutDBX, a database of
  141,556 sequences associated with xenobiotic and pharmacologically
  relevant microbial metabolism.
preferred-citation:
  type: thesis
  title: "Omics-driven and constraint-based modelling of microbial community metabolism"
  authors:
    - family-names: Zorrilla
      given-names: Francisco
      orcid: "https://orcid.org/0000-0002-6206-8655"
      affiliation: "MRC Toxicology Unit, University of Cambridge"
  year: 2024
  month: 6
  institution:
    name: "University of Cambridge"
    address: "Cambridge, UK"
  doi: 10.17863/CAM.114621
  url: "https://www.repository.cam.ac.uk/items/e8039120-7f95-444f-95af-78fe5ce49db6"
  notes: "PhD thesis. Darwin College, MRC Toxicology Unit (School of the Biological Sciences)."