Dr Amber Barton

Supervisor Details

Contact Details

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

Bacterial infections still cause an estimated 7.7 million deaths each year, despite global efforts to develop vaccines, antibiotics, and innovative treatments such as phage therapy. This is partly because bacteria are a moving target: when their survival is threatened, they evolve. For under-researched infectious diseases, such as enteric infections and neglected tropical diseases, we often do not know enough about their biology to anticipate how they will evolve and spread, or what makes a particular person susceptible to disease.

My goal is to use data-driven approaches, such as genomics and systems immunology, to explore these infections without needing preconceived hypotheses. I am particularly interested in how our various means of defending ourselves against bacteria (including our immune systems, but also bacteria-killing viruses in the gut) shape the severity and evolution of pathogens. My previous research has incorporated a number of dry lab (transcriptomics, bacterial genomics, human GWAS, metagenomics, machine learning) and wet lab (bacterial and human cell culture, ELISAs, flow cytometry) methods.

Research Groups

Microbiology & Infectious Disease

Supervision Style

In three words or phrases: Engaged, inclusive, collaborative

Provision of Training

I will provide hands-on training in technical and analytical skills at the beginning of your PhD. I expect you to be curious and motivated to develop new skills, and increasingly take ownership of your work as your confidence develops. I will also encourage you to seek out additional training and opportunities where these will support your future career.

Progression Monitoring and Management

We will have weekly meetings where we will discuss progress, come up with ideas and set targets for the following week together.

Communication

I am available by email and for informal conversations during working hours.

Meetings

PhD Students can expect scheduled meetings with me at least once per week. These meetings will be face-to-face. I am usually contactable for an instant response 3 or 4 days per week.

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. I believe in a flexible approach to working patterns, but broadly encourage a 9–5 working pattern to support a healthy work-life balance and create a cohesive, collaborative team.

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:

Determinants of bacteriophage host range among Salmonella serovars

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).

Determinants of bacteriophage host range among Salmonella serovars

Secondary Supervisor(s): Dr Antonia Sagona

University of Registration: University of Warwick

BBSRC Research Themes:

Sustainable Agriculture and Food (Microbial Food Safety)
Understanding the Rules of Life (Microbiology)

Project Outline

Salmonella enterica, a food-borne pathogen classified as a WHO priority pathogen, is in urgent need of new therapeutic approaches as it becomes increasingly antibiotic resistant. One potential solution is phage therapy, where viruses that kill bacteria are used as a treatment. However, a major challenge is that different Salmonella serovars can cause similar clinical syndromes, while phages are often serovar-specific. While broad-range phages that target not only Salmonella but also Escherichia coli do exist (Fong et al. 2021), we are only beginning to understand the factors that determine host range. For example, an acetyl esterase domain appears to be necessary for phages to target the Vi capsule of Salmonella Typhi (Pickard et al. 2010).

This project aims to better understand the features that determine phage specificity towards different Salmonella serovars and, in doing so, investigate approaches for developing therapeutic phages with broader host ranges. The project will also explore the potential for phages to target intracellular Salmonella infection.

In this project, the student will:

Isolate and sequence novel phages targeting different Salmonella serovars
Test the host range of these phages against different serovars, strains and E. coli to understand which receptors the phages target
Carry out a pangenome-wide association analysis to identify phage features, such as tail fibre proteins, that determine receptor specificity
Investigate whether these can be modified to generate phages capable of targeting multiple strains or serovars
Explore phage activity against intracellular Salmonella using human cell lines

Investigating the relationship between enteric infection, diet and the gut microbiome

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).

Investigating the relationship between enteric infection, diet and the gut microbiome

Secondary Supervisor(s): Professor Sascha Ott

University of Registration: University of Warwick

BBSRC Research Themes:

Sustainable Agriculture and Food (Microbial Food Safety,)
Understanding the Rules of Life (Microbiology)

Project Outline

Gut infections cause over one million deaths per year, and are one of the leading causes of death in children younger than five years (GBD 2023, 2026). The greatest burden falls upon children in lower and middle income countries. The microbiome is thought to play a major role in susceptibility to gut infection (Midani et al. 2018, Zhang et al. 2018, Dicksved et al. 2014) and is also significantly changed in response to infection (Hsiao et al. 2014, Zhang et al. 2018, Liechty et al. 2025, Ashton et al. 2025).

Recent studies in mice suggest that by reshaping the gut microbiome, diet has a downstream effect on susceptibility to gut infections. For example, lack of fibre or a high fat diet results in increased gut permeability, increasing susceptibility to pathogens such as Listeria and Salmonella (Wolter et al. 2021, Wotzka et al. 2019, Zhao et al. 2025). Malnutrition can also disrupt the gut barrier, resulting in a subclinical condition called Environmental Enteric Dysfunction (Syed et al. 2017). However, studies in humans are limited due to the difficulty in controlling diet and unreliable self-reporting. However, a new bioinformatics method, Metagenomic estimation of dietary intake from human stool (MEDI) (Diener et al. 2025), may provide an alternative method to estimate diet directly from metagenomic data.

In this project, the student will analyse thousands of human and livestock gut metagenomes, identifying carriage of bacterial pathogens. They will:

Analyse how the microbiome changes in those carrying gut pathogens
Infer diet using MEDI and investigate how diet shapes the microbiome
Combine these two analyses to understand whether diet relates to pathogen load or perturbation of the microbiome by infection

By doing so, it may be possible to identify diets that enhance resistance to infection.