Mechanisms of microbiome modulation in the entero-salivary nitrate pathway

About the Project

Applications are open for a 4-Year BBSRC-funded Industrial Doctoral Landscape Award PhD Studentship in Oral Microbial Metabolism and Systems Biology at Queen Mary University of London (QMUL), Institute of Dentistry.

Project Description

The oral microbiome is a key driver of the entero-salivary nitrate–nitrite–nitric oxide (NO) pathway, linking dietary nitrate metabolism to oral ecology and systemic physiology. While oral nitrate-reducing bacteria can support NO-associated host benefits, nitrate-derived intermediates in polymicrobial biofilms can also be diverted into alternative nitrogen pathways depending on local environmental and community context. The taxa, genes, and micro-environmental conditions that determine this metabolic branching in complex oral communities remain incompletely defined.

This PhD will combine ex vivo oral biofilm models with a systematic co-culture matrix screen (pairing nitrate-reducing bacteria with representative oral commensals and pathobionts) to identify interaction- and environment-dependent shifts in nitrate metabolism. The student will investigate how variables such as oxygen availability, pH, and nutrient composition influence community function, and will apply stable isotope probing and multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) to link microbial community and gene expression to measurable metabolic outputs.

The project aims to uncover fundamental principles governing nitrate metabolism in oral biofilms, with implications for promoting microbial homeostasis and supporting systemic nitric oxide biology.

Keywords: Oral microbiome; nitrate reduction; nitric oxide; biofilms; microbial ecology; multi-omics; systems biology; oral-systemic health

Research Environment

The project will be based within a research programme at the Institute of Dentistry focused on host–microbial metabolic interactions and oral biofilm systems biology.

The student will gain interdisciplinary training in:

• Advanced oral biofilm modelling under controlled environmental conditions
• Multi-omics approaches (metagenomics, transcriptomics, metabolomics)
• Anaerobic and microaerophilic microbiology
• Quantitative data integration and systems-level analysis

QMUL offers access to state-of-the-art facilities including advanced sequencing platforms, metabolomics and mass spectrometry infrastructure, and dedicated anaerobic culture facilities.

The student will have the opportunity to spend time at the Centre for the Isotope Sciences, University of Glasgow, to gain hands-on experience in advanced mass spectrometric approaches for carbon and nitrogen isotope measurement and analysis, and to apply these methods to questions in microbial biofilm metabolism.

This project is part of the Advancing Translation of Oral Health Research (https://atohr.org/) BBSRC-funded Industrial Doctoral Landscape Award in collaboration with Haleon. This unique collaboration spans five leading UK universities, providing students with opportunities to conduct cutting-edge oral health research while gaining valuable industry experience. The programme spans four years and includes comprehensive training in oral health research and transferable skills, preparing graduates for successful careers in academia, industry, or the public sector. Our vision is to promote an interconnected network between academia and industry through state-of-the-art interdisciplinary studentships where multi-partner co-operation will facilitate a broad range of expertise that will develop world-class PhD students. This will be catalysed by identifying core technical, analytical and interpersonal skills required by Haleon’s oral health strategy. Haleon is a global leader in consumer health, with a portfolio of world-leading brands trusted by millions of people around the globe.

Personal Specification:

Essential qualities

We are looking for a highly motivated candidate with:

• A strong academic background, ideally with a First-class degree or MSc (or international equivalent) in microbiology, molecular biology, biochemistry, biomedical sciences, bioinformatics, chemistry, or a closely related discipline.
• A strong interest in understanding microbial metabolic processes and their relevance to human health.
• A willingness to engage with quantitative approaches, including metabolic flux analysis and isotope-based measurements.
• Excellent organisational skills and the ability to manage complex experimental workflows involving laboratory work, data analysis, and short research visits to collaborating institutions.
• A collaborative mindset and willingness to contribute positively to a multidisciplinary research environment spanning microbiology, analytical chemistry, and clinical research.
• Evidence of research ability through laboratory projects, dissertation work, or other independent research experience.

Desirable experience

While not required, experience in any of the following areas would strengthen your application:

• Practical experience in microbiology, including bacterial culture, anaerobic techniques, biofilm models, or molecular microbiology methods.
• Familiarity with stable isotope concepts, metabolic tracing, or mass spectrometry-based analytical techniques.
• Experience with ‘omics approaches (e.g., metagenomics, transcriptomics, metabolomics) and/or bioinformatic analysis.
• Basic programming or data analysis skills (e.g., R, Python, or similar) for handling complex datasets.

How to apply:

Formal applications must be submitted through our online form by the stated deadline for consideration. Applicants are NOT required to submit a research proposal as part of the application.

Applicants are required to submit the following documents:

• Curriculum Vitae (CV)
• Personal Statement, outlining: Previous experience relevant to the project, motivation for pursuing this position, career aspirations, and any additional information relevant to the application
• References (typically two academic referees)
• Academic transcripts and degree certificates (copies)

Informal enquiries about the project can be sent to Dr. Abish Stephen or Prof. Robert Allaker

Admissions-related queries can be sent to Dr. Aneesh Chandran

Information about the application process can be found (here)

Apply Online (here)

• Please input Dr. Abish Stephen as primary supervisor when applying to this position.

Funding Notes

This is a 4 year fully funded project, and part of the BBSRC-Haleon Industrial Doctoral Landscape Award, open to students with UK Home fees eligibility.

To classify for Home Fees, this typically means the candidate will have unrestricted access on how long they can remain in the UK (i.e. are a British National, have settled, or pre-settled status, have indefinite leave to remain etc.).

This 4-year studentship includes a tax-free stipend at London-weighted UKRI rates with an additional £3000 industry uplift per year.