Jack Jonathon-Paul Lynch, BSc (Hons), MSc (Res)


I am a second-year PhD student in the School of Dentistry at the University of Leeds, funded by the Haleon-BBSRC iCase Award. I completed my Bachelor in Medical Microbiology at the University of Leeds, and then my Master of Science (By Research) on ‘Probiotic Formulations as Antimicrobial and Anti-adhesive Agents’.

My current research interests revolve around deciphering the major significant variations in oral microbiome between healthy and diseased patients, namely those with periodontitis and caries. Dysbiosis, or a shift in the taxonomic profile of the oral cavity, is already known to be associated with these diseases. My project focuses on characterising the taxonomic, functional, and resistome profiles of oral biofilms and how these change as the disease progresses. The project is split into in silico and in vitro approaches. Using in silico analyses, such as bioinformatics and machine learning, we aim to first characterise the significant differences between health and disease. We will then create algorithms for the prediction of disease or increased risk of disease from patient samples, and or prediction of antibiotic resistance phenotypes. In the lab, we aim to create a 3D co-culture model, utilising complex biofilms and host cells to accurately depict the oral cavity. We will induce dysbiosis in this model to understand how these changes affect host and microbial responses over time. We will also test new therapeutics for the reversal of dysbiosis. In combination with both wet and computational lab work, we also aim to use the in silico prediction models to verify the success of in vitro work in causing and reversing disease-associated dysbiosis.

I am also involved in the undergraduate Microbiology course, where I teach and demonstrate in the practical Microbiology lab sessions for MICR1320.

Research interests

  • Oral Microbiology
  • Bioinformatics
  • Antimicrobial Resistance
  • Oral Immunology
  • Machine Learning

Professional Memberships:

  • International Association for Dental Research (IADR)
  • Microbiology Society
  • Royal Society of Biology (RSB)


  • BSc (Hons) in Medical Microbiology- 2017-2020
  • MSc (By Research)- 2020-2021
  • PhD Student (Haleon-BBSRC iCASE Award)- 2021-Present

Research groups and institutes

  • Microbiology and cell biology