Investigations into the microbiology and antimicrobial resistance associated with Noma

Project Summary

Noma is a devastating, rapidly progressive disease of the mouth and face that predominantly affects children living in conditions of extreme poverty. Despite its severe consequences, the microbiological causes of disease remain poorly understood, and there is a major gap in knowledge concerning antimicrobial resistance (AMR) among bacteria associated with Noma.

This PhD will investigate the microbiology and AMR of Noma using a unique collection of hundreds of clinical samples obtained from Noma patients. The project will characterise the bacterial communities associated with Noma and determine how these microbial populations vary according to disease severity, clinical presentation and patient characteristics. A combination of culture-based microbiology, antimicrobial susceptibility testing and whole-genome sequencing will be used to identify bacterial pathogens, resistance determinants and associated mobile genetic elements.

The project will move beyond identifying individual pathogens to investigate Noma as a polymicrobial disease.

By integrating microbiological, genomic and clinical data, the PhD will establish the first detailed picture of the microbial and AMR landscape associated with Noma. The research will address fundamental questions about the role of bacteria in Noma while generating evidence that could inform antimicrobial treatment, infection management and future diagnostic approaches. More broadly, the work will provide important insights into AMR and neglected infectious diseases affecting some of the world’s most vulnerable populations.

Background/rationale

Noma is widely regarded as polymicrobial, with previous culture-based and molecular studies implicating organisms including Fusobacterium, Prevotella, Porphyromonas and spirochaetes, but no definitive causative organism or microbial mechanism has been established.

This knowledge gap is particularly important because treatment relies on broad-spectrum antibiotics, yet there is remarkably little information on the antimicrobial susceptibility and resistance determinants of bacteria associated with noma. Consequently, clinicians have limited evidence on which to base antimicrobial therapy, while repeated or inappropriate antibiotic exposure may contribute to AMR.

The research is especially timely following the WHO’s recognition of noma as a neglected tropical disease in 2023, which has increased international attention and created an opportunity to develop the evidence base needed for improved diagnosis, treatment and prevention. Our recent work using Nigerian samples has demonstrated substantial disruption of the oral microbiome and identified a previously undescribed Treponema species strongly associated with noma, providing an important new direction for understanding disease biology.

The availability of hundreds of well-characterised Nigerian samples now provides an exceptional opportunity to move beyond small, descriptive studies. Combining culture, antimicrobial susceptibility testing, metagenomics and whole-genome sequencing will allow this PhD to investigate microbial communities, pathogens, virulence and AMR together, potentially identifying biomarkers and therapeutic targets while informing more rational, targeted treatment of this neglected disease.

Training & development

The candidate will receive comprehensive multidisciplinary training spanning clinical microbiology, antimicrobial resistance, genomics, bioinformatics and infectious disease research. The student will develop practical expertise in analysing bacterial genomes, identifying AMR genes, virulence factors and mobile genetic elements, and applying comparative genomic and microbiome approaches to complex clinical datasets.

A strong computational component will provide training in bioinformatics, statistical analysis, data visualisation and reproducible research, with opportunities to develop programming and command-line skills. Training will be supported by experienced microbiologists, molecular biologists and bioinformaticians, with access to appropriate sequencing and high-performance computing infrastructure.

The PhD will also provide extensive transferable skills development, including scientific writing, critical appraisal of literature, presentation of research, data management, project planning, teamwork, collaboration and communication with clinical and non-specialist audiences. The candidate will be encouraged to present their findings at national and international conferences and to publish their work in peer-reviewed journals.

Professional development will include formal doctoral training, research integrity, responsible research conduct, statistics, leadership and career development. Where appropriate, the student will have opportunities for short placements with collaborating laboratories in other partner institutions, providing experience of research in different settings and strengthening international collaboration.

The candidate will also participate in cohort activities, seminars, journal clubs and interdisciplinary workshops, providing opportunities to build networks, share expertise and learn from researchers working across microbiology, global health, genomics and AMR.

Supervisory Team

• Prof. Adam Roberts, molecular microbiologist specialising in AMR, metagenomics, genomics and microbiome analysis.
• Dr Stuart Ainsworth, microbiologist and snake biologist, specialising in virulence factors and microbiome analysis.

What we’re looking for

The ideal candidate will demonstrate expertise in microbiology, experience of bioinformatic approaches, and a strong understanding of both Noma-associated microbiology and the mechanisms and epidemiology of antimicrobial resistance, with enthusiasm for translational research and emerging infectious diseases.

Indicative Start Date: 1st October 2026

Funding Package: The funding packages includes:

• Programme fees paid at the Full-time, Liverpool Campus, UK rate (LSTM – Fees and Funding for UK Students)
• Stipend at the UKRI minimum doctoral standard rate (see Support for UKRI-funded students – UKRI). For 26/27 this is set at £21,805.
• Direct costs associated with delivery of project (laboratory consumables etc.) will be met by the studentship
• The duration of the funding package is 3 years.

Eligibility

Academic

Applicants must hold at least a first class or high upper second-class Honours degree, or a degree of comparable standard awarded from outside the UK.

A Masters degree (at merit or distinction preferable) is also a pre-requisite.

Where an applicant does not meet the Honours degree requirement (e.g. they hold a lower second-class Honours degree), they may be eligible to apply if they also hold a Master’s degree with an awarded distinction in an area relevant to the research theme of the project. To be considered for this exemption, the qualification must be awarded at time of application and candidates must provide an award certificate and transcript for both qualifications. Unfortunately, we are unable to consider Master’s qualifications that have not yet been awarded for this purpose.

Residence

This opportunity is only available to candidates holding a ‘home’ fee status and with valid immigration permission to live and study in the UK for the full duration of the studentship at the point of application.

‘Home’ fee status typically applies to students who are ‘settled’ in the UK—meaning they have no immigration restriction on the length of stay—and who have been ordinarily resident in the UK, the Republic of Ireland, the Channel Islands, or the Isle of Man for the three years immediately before the first day of their course. Eligibility also extends to certain groups such as British or Irish nationals, those with Indefinite Leave to Remain or equivalent rights, refugees or individuals with humanitarian protection, and some family members of qualifying persons.

Applicants must hold valid immigration permission to live and study in the UK for the full duration of the studentship at the point of application. This includes ensuring that your current visa category permits postgraduate study and will remain valid throughout the funded period.

If you are unable to provide evidence of both of the above requirements, your application will be rejected.

How to Apply

Candidates are encouraged to apply as soon as possible.

In order to be considered for this opportunity, candidates must:

Submit a copy of their Curriculum Vitae to pgr@lstmed.ac.uk

Complete the following form: Investigations into the microbiology and antimicrobial resistance associated with Noma

This application form will ask you to:

• Provide your personal details
• Answer questions related to your knowledge of the research area and motivation for doctoral study (up to 1250 characters [approx 250 words] per question)
• Detail your qualifications, any relevant research experience and your English language proficiency
• List any contextual information that you feel is important for assessors to know (optional)
• Provide diversity monitoring information

Deadline for application is noon UK time 2nd September. Applications are only considered complete if LSTM has received a copy of your Curriculum Vitae and a completed form.

Successful Candidates

Candidates that are successfully shortlisted for interview will be notified week commencing 7th September.

Successful candidates will be invited to submit documentation in support of the information they provided in their initial application prior to interviews expected to take place week commencing 14th September.