From Genes to Signals: Visualising Molecular Interactions in Bacterial Communities

About the Project

Microbial communities are shaped by dynamic interspecies interactions that influence gene expression, metabolite production, and ecological behaviour. Transcriptomic data suggest that biosynthetic genes in one bacterial species are differentially regulated in response to chemical signals from another, indicating a molecular-level response. However, the spatial and temporal dynamics of this response, and whether they lead to functional molecule exchange, remain poorly understood.

This project aims to develop a microscopy-based platform to visualise biosynthetic gene activation in live bacterial co-cultures and investigate interspecies exchange and sensing of secreted molecules. Engineered reporter strains expressing fluorescent or luminescent markers under the control of selected biosynthetic gene promoters will be co-cultured with another bacterial species on semi-solid agar and in microfluidic chambers, enabling controlled interaction and high-resolution imaging.

Time-lapse fluorescence microscopy will be used to track reporter activation in real time, correlating gene expression with spatial proximity and colony behaviour. Biosensor strains or fluorescent analogues of biosynthetic products may be used to assess potential molecule exchange. This approach will provide mechanistic insight into how bacterial species modulate biosynthetic pathways in response to interspecies signals and whether these pathways contribute to molecular communication or competition.

Objectives:

• Construct fluorescent reporter strains for biosynthetic genes.
• Visualise gene activation in bacterial communities using microscopy.
• Investigate potential molecular exchange between interacting species.
• Correlate gene expression with spatial and behavioural dynamics.

Training opportunities:

The candidate will gain hands-on experience in molecular cloning and live-cell microscopy. Training will include reporter construct design, co-culture assays, advanced microscopy techniques, and quantitative image analysis. The project is supported by an interdisciplinary supervisory team with expertise in microbiology, cell biology, and super-resolution microscopy. This collaborative environment offers a unique opportunity to develop skills at the interface of microbial interaction research, experimental microbiology, and advanced cellular imaging.

Outputs:

The project will generate validated reporter strains and microscopy datasets showing biosynthetic gene activation in response to interspecies interaction. It will produce protocols for reporter construction and imaging workflows, along with analytical tools for quantifying gene expression dynamics. These outputs will provide mechanistic insight into molecular exchange processes and contribute to a better understanding of microbial communication and competition.

Pre-requisite:

• A strong academic background and hands-on experience in molecular biology, bacterial genetics, and microscopy
• Excellent organisational, communication, and scientific writing skills
• Fluency in English
• A Master’s degree (300 ECTS credits) in a relevant field by the start date

Apply at:

https://le.ac.uk/study/research-degrees/research-subjects/respiratory-sciences

PhD entry requirements: https://le.ac.uk/study/research-degrees/entry-reqs

Supervisor contact details:

Katrin Schilcher, ks665@leicester.ac.uk

Yolanda Markaki, gm365@leicester.ac.uk