Dr Jonathan Cox

Supervisor Details

Contact Details

School of Medicine, Pharmacy and Biosciences, Aston University

Scientific Background

Research Interests

Dr Jonathan A. G. Cox is a microbiologist and translational research leader whose work focuses on tackling antimicrobial resistance (AMR) through the discovery and development of new antimicrobial therapies for respiratory and other clinically important bacterial pathogens. His research spans antibiotic discovery, antimicrobial potentiators, anti-biofilm agents, and natural-product therapeutics, with a particular emphasis on overcoming drug resistance and extending the effectiveness of existing antibiotics. Through multidisciplinary collaborations with academia, healthcare providers, industry, and policymakers, he has built a research programme that bridges fundamental microbiology with real-world clinical and commercial impact. His work has attracted significant research funding, and produced in excess of 37 peer-reviewed publications, and contributed to the training of the next generation of infection scientists through doctoral and postgraduate research supervision.

As Senior Lecturer in Microbiology at Aston University, Dr Cox combines scientific leadership with a strong commitment to research translation, innovation, and societal impact. His research has generated partnerships with organisations including healthcare providers and biotechnology companies, advancing novel interventions against respiratory infections and antimicrobial-resistant pathogens. Beyond the laboratory, he is actively engaged in shaping research strategy, fostering collaborative networks, supporting knowledge exchange, and translating discoveries towards healthcare and commercial application. Through public engagement, media contributions, policy engagement, and industry collaboration, he seeks to ensure that research delivers tangible benefits for patients, healthcare systems, and society while addressing one of the most significant global health challenges of the 21st century.

Supervision Style

In three words or phrases: Supportive; Challenging; Inclusive.

Provision of Training

I provide tailored training plans that combine technical, professional, and transferable skills development, ensuring researchers have the knowledge and confidence needed to achieve their goals. I also encourage experiential learning through research projects, collaboration, conference participation, public engagement, and funding applications to support long-term career development.

Progression Monitoring and Management

I use regular supervisory meetings with clearly defined milestones, deliverables, and development goals to monitor progress and identify challenges early. Expectations are agreed collaboratively, with constructive feedback and support provided to ensure researchers remain on track and achieve their academic, professional, and career objectives.

Communication

Open, regular, and constructive communication through scheduled meetings and responsive day-to-day support, creating an environment where challenges can be discussed early and progress can be reviewed honestly. My approach emphasises clear expectations, timely feedback, and mutual respect, fostering both independence and confidence.

Meetings

PhD Students can expect scheduled meetings with me at least once per fortnight. These meetings will be face-to-face. I am usually contactable for an instant response on every working day.

Work Patterns

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings) I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

Decoding community assembly, spatial organisation and antimicrobial tolerance in polymicrobial biofilms

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Decoding community assembly, spatial organisation and antimicrobial tolerance in polymicrobial biofilms

Secondary Supervisor(s): Dr Georgina Hopkins, Professor Kim Hardie

University of Registration: Aston University

BBSRC Research Themes:

Understanding the Rules of Life (Microbiology)

Project Outline

Chronic lung infections are a major cause of morbidity in people with cystic fibrosis. Although multiple bacterial species frequently coexist within the respiratory tract, the biological interactions that govern community assembly, persistence and antimicrobial tolerance remain poorly understood. Current experimental approaches often focus on individual pathogens in isolation and therefore fail to capture the complexity of polymicrobial infection.

This PhD project will investigate interactions between three clinically important cystic fibrosis-associated pathogens: Mycobacterium abscessus, Pseudomonas aeruginosa and Staphylococcus aureus. Using fluorescently labelled bacterial strains, advanced microscopy and physiologically relevant cystic fibrosis culture models, the student will establish three-dimensional polymicrobial biofilms and quantify the spatial organisation, population dynamics and interspecies interactions within these communities.

The student will determine how competition, cooperation and niche partitioning influence community structure and stability, and assess how colonisation history affects subsequent biofilm development. Particular emphasis will be placed on identifying the biological mechanisms that drive antimicrobial tolerance within polymicrobial communities. Quantitative microscopy data will be integrated with image analysis, microbiological measurements and mathematical/statistical modelling to identify predictive relationships between community architecture, microbial interactions and treatment outcomes.

By combining microbiology, microbial ecology, quantitative bioscience and computational approaches, the project addresses key BBSRC priorities in understanding complex biological systems and the fundamental mechanisms underpinning host-associated microbial communities. The work will provide interdisciplinary training in microbiology, biofilm biology, fluorescence imaging, data science, statistics and predictive modelling, generating new insights into the biology of chronic polymicrobial infection.