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Exposing dynamics in bacterial responses to antibiotic treatments using metabolomics and network analysis

Funding
Self-funded
Study mode
Full-time
Duration
4 Years
Apply by
Year round
Start date
Year round
Subject area
Biological and Biomedical Sciences
How to apply
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Overview

This is an exciting PhD project within the Centre for Metabolomics Research at the University of Liverpool. Harnessing network analysis on longitudinal metabolomics data will uncover how bacteria dynamically rewire their metabolism in response to antibiotic stress. This approach offers a powerful strategy to reveal hidden survival mechanisms and guide the development of more effective antimicrobial treatments.

About this opportunity

The aims of this PhD programme of work if to develop and apply network analysis to longitudinal metabolomics data from bacteria exposed to antibiotics to uncover dynamic metabolic responses and adaptation mechanisms.  By constructing time-resolved metabolic networks, where the nodes represent metabolites and the edges reflect biochemical relationships (e.g., enzymes or mass differences) or correlations,  we will track changes in network topology over time.  This approach enables the identification of key metabolites, pathway shifts, and potential biomarkers of antibiotic response.  Network metrics will highlight critical time points and metabolic transitions linked to antibiotic resistance or susceptibility.  Integrating network analysis with mass spectrometry-based metabolomics (including both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS)) offers a powerful strategy to elucidate bacterial survival strategies and inform the development of more effective treatments.

Training:

  • Roy Goodacre (CMR) will supervise the experimental design for bacteria exposed to antibiotics, as well as oversee the data analysis aspects of the project.
  • Howbeer Muhamadali (CMR) will supervise the experimental design for bacteria exposed to antibiotics, as well as the data generation using GC-MS and LC-MS.
  • [Yun Xu (CMR) will supervise the data analysis involving multiblock methods and network analysis.]

Papers:

  • Ahmed, S., Shams, S., Trivedi, D., Lima, C., McGalliard, R., Parry, C., Carrol, E.D., Muhamadali, H. & Goodacre, R. (2025) Metabolic response of Klebsiella oxytoca to ciprofloxacin exposure: a metabolomics approach. Metabolomics 21: 8.
  • Ahmed, S., Albahri, J., Shams, S., Sosa-Portugal, S., Lima, C., Xu, Y., McGalliard, R., Jones, T., Parry, C.M., Timofte, D., Carrol, E., Muhamadali, M. & Goodacre, R. (2024) Clinical application of FT-IR spectroscopy for the rapid identification and discrimination of bacterial and fungal sepsis pathogens isolated from children.  Microorganisms 12: 1415.

Further reading

Further work from our research group is found here: https://biospec.net/publications/  – full text is freely available for all published papers.

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Who is this for?

You should have, or expect to a 2i or above in Biochemistry, Chemistry or a related field.  Experience in analytical chemistry and chemometrics/machine learning would be advantageous.

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How to apply

  1. 1. Contact supervisors

    Supervisors:

    Roy Goodacre Roy.goodacre@liverpool.ac.uk https://biospec.net
    Howbeer Muhamadali Howbeer.Muhamad-Ali@liverpool.ac.uk https://www.liverpool.ac.uk/people/howbeer-muhamad-ali

  2. 2. Prepare your application documents

    Applications need:

    • Cover Letter with a personal statement explaining why you want to do this PhD.
    • Cover Letter should include experience in analytical science, biochemistry and or computation.
    • Detailed CV
    • As the PhD is self-funded: please provide evidence that funding is in place for the full 4 years of the PhD programme.

  3. 3. Apply

    Finally, register and apply online. You'll receive an email acknowledgment once you've submitted your application. We'll be in touch with further details about what happens next.

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Fees and funding

Your tuition fees, funding your studies, and other costs to consider.

Tuition fees

UK fees (applies to Channel Islands, Isle of Man and Republic of Ireland)

Full-time place, per year - £5,006

International fees

Full-time place, per year - £31,250

Fees applicable for academic year 2025/26

Additional costs

We understand that budgeting for your time at university is important, and we want to make sure you understand any costs that are not covered by your tuition fee. This could include buying a laptop, books, or stationery.

Find out more about the additional study costs that may apply to this project, as well as general student living costs.

Funding your PhD

The project is self-funded.  Therefore, funding needs to include tuition fees, bench fees, living expenses

If you're a UK national, or have settled status in the UK, you may be eligible to apply for a Postgraduate Doctoral Loan worth up to £30,301 to help with course fees and living costs.

There’s also a variety of alternative sources of funding. These include funded research opportunities and financial support from UK research councils, charities and trusts. Your supervisor may be able to help you secure funding.

We've set the country or region your qualifications are from as United Kingdom.

Scholarships and bursaries

We offer a range of scholarships and bursaries that could help pay your tuition fees and living expenses.

Duncan Norman Research Scholarship

If you’re awarded this prestigious scholarship, you’ll receive significant funding to support your postgraduate research. This includes full payment of your PhD fees and a cash bursary of £17,000 per year while you study. One award is available in each academic year.

John Lennon Memorial Scholarship

If you’re a UK student, either born in or with strong family connections to Merseyside, you could be eligible to apply for financial support worth up to £12,000 per year for up to three years of full-time postgraduate research (or up to five years part-time pro-rata).

Sport Liverpool Performance Programme

Apply to receive tailored training support to enhance your sporting performance. Our athlete support package includes a range of benefits, from bespoke strength and conditioning training to physiotherapy sessions and one-to-one nutritional advice.

Discover our full range of scholarships and bursaries.
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Contact us

Have a question about this research opportunity or studying a PhD with us? Please get in touch with us, using the contact details below, and we’ll be happy to assist you.

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