Professor Lindsay Hall

Supervisor Details

Contact Details

Institute of Microbiology and Infection, University of Birmingham

Scientific Background

Research Interests

My research focuses on understanding how the gut microbiome influences human health across the life course, with particular emphasis on early-life microbiome development and host-microbe interactions. We combine microbiology, microbial ecology, genomics, bioinformatics and experimental models to investigate how microbes shape immune development, susceptibility to infection and long-term health outcomes.

A major goal of our work is to identify microbiome-based approaches to improve human health. Current projects examine the role of beneficial microbes in infancy, microbiome responses to diet and infection, antimicrobial resistance, and the development of next-generation microbiome therapeutics. Our research is highly collaborative and spans fundamental discovery science through to translational and clinical applications.

Supervision Style

In three words or phrases: Supportive, collaborative, and empowering.

Provision of Training

I provide a structured training environment that combines hands-on support with increasing independence. Early in the PhD, students receive close guidance from me and experienced postdoctoral researchers and senior students, before gradually taking greater ownership of experimental design, data analysis and research direction as their confidence develops.

Progression Monitoring and Management

I work with students to establish clear goals and milestones, which we review regularly through individual and group meetings. I encourage students to take ownership of their projects while providing constructive feedback, troubleshooting support and strategic guidance when needed.

Communication

I operate an open and supportive communication style and encourage students to discuss scientific, professional or practical challenges early. While I am often available and responsive by email or messaging, I strongly support maintaining a healthy work-life balance.

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 3 or 4 days per week.

Work Patterns

Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team. Lab work will likely require planned and coordinated activities, but day-to-day scheduling is generally flexible.

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:

Collateral damage or ecological control? Defining how bacteriophages shape Escherichia dynamics in the early-life gut

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).

Collateral damage or ecological control? Defining how bacteriophages shape Escherichia dynamics in the early-life gut

Secondary Supervisor(s): Professor Martha Clokie

University of Registration: University of Birmingham

BBSRC Research Themes:

Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

Early life is a critical window for gut microbiome development, with lasting consequences for host health. Escherichia, including E. coli, are common but highly variable early colonisers. Some strains contribute to normal ecosystem development, whereas others carry antimicrobial-resistance or virulence traits and can cause serious infection. Bacteriophages, viruses that infect bacteria, are important drivers of bacterial population dynamics and promising precision tools, but their role in shaping the developing infant gut microbiome remains poorly understood.

This project will combine Prof Lindsay Hall’s expertise in early-life microbiomes and microbial ecology with Prof Martha Clokie’s internationally recognised expertise in bacteriophage biology. The student will have access to longitudinal early-life samples and datasets, infant-derived bacterial collections, diverse phage resources and established models of the infant gut microbiota.

The student will investigate how phage activity varies among infant-associated Escherichia and determine how these interactions influence bacterial competition and microbial community development. Using complementary experimental and computational approaches, they will explore both the direct effects of phages on their bacterial hosts and the wider consequences for microbiome composition, stability and resilience. The project will also examine how clinically relevant environmental perturbations influence these interactions.

By integrating microbiology, phage biology, genomics, microbiome science and quantitative ecology, the project will uncover fundamental rules governing phage-bacteria interactions during early life. The student will receive broad interdisciplinary training while having flexibility to shape the experimental and computational direction of the project according to their developing interests.