Professor Yin Chen

Supervisor Details

Contact Details

School of Biosciences, University of Birmingham

Scientific Background

Research Interests

Current research in the group focuses on microbial diversity, genetics and biochemistry of microorganisms involved in the metabolism of one-carbon (C1) compounds and lipids in human body as well as a variety of terrestrial and marine ecosystems.

There are three main strands of research in my group

Methylated amines and nitrogenous osmolytes. We have pioneered in the understanding of novel metabolic pathways and new enzymes leading to the re-mineralization of ammonium from organic nitrogen species, particularly methylated amines, in the surface marine waters.

Microbial interactions, particularly the role of the cell surface and membrane lipids in the stress and nutrient limitation response of bacteria. We recently demonstrated that marine heterotrophic bacteria can remodel their lipid composition in response to nutrient limitation. Key to the lipid remodelling process in these marine heterotrophs is a novel intracellular phospholipase C, which is particularly abundant in natural marine bacterial communities, especially in areas characterised by low phosphate concentrations. We have recently characterised a novel pathway leading to the formation of these unique aminolipids in marine bacteria. These results pointed to the previously overlooked key role of lipid substitution as an adaptive strategy, enabling heterotrophs to thrive in the vast phosphorus-depleted areas of the oceans and resolved the paradox of SAR11-phytoplankton competition in oligotrophic oceans. Such a membrane remodelling strategy also comes with unforeseen ecophysiological consequences in trade-offs of certain traits. In parallel, we also begin to understand the role of lipid remodelling in bacterial pathogens, some of which can substitute membrane lipids in order to become resistant to antibiotics.

Interplay of diet, gut microbiota and host health and disease. We are particularly interested in understanding the role of quaternary amine metabolism and methylated amine formation in human gut. In the study published in 2014, we have identified a novel Rieske-containing oxygenase involved in gut microbial catabolism of carnitine to trimethylamine. We recently solved the structure of this key enzyme CntA, help us better understand the mechanisms responsible for carnitine degradation by gut microbiota, providing a reliable biomarker for investigating key gut microbes involved in carnitine-diet induced cardiovascular diseases.

Research Groups

Chen Lab

Supervision Style

In three words or phrases: Supportive, student-centred, spontaneous, collaborative.

Provision of Training

You will be expected to identify your training needs in discussion with the supervisors’ team.

Your training will be provided by the supervisors or their teams (experienced post docs/PhD students in our groups).

Alternatively, we may send you to our collaborators’ network around the UK and the world for specific training.

Progression Monitoring and Management

I will expect you to take full ownership of your project but come to me at least once a month when you need help, troubleshooting or just general chat.

I like to be kept up to date, and will expect to see evidence of method development/data generation results/trouble shooting on a monthly basis.

Communication

I have an open office policy which means you can come to see me when you need to.

Additional communication can be via email/teams/skype etc.

You are expected to set up a monthly meeting with myself and co-supervisors for general update and future plans.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per month

In year 1 of PhD study

At least once per month

In year 2 of PhD study

At least once per month

In year 3 of PhD study

At least once per month

The meetings will be face to face and I am usually contactable for an instant response (if required) on every working day.

Working Pattern

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.

Notice Period for Feedback

I need at least 1 week's notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Uncovering the role of lipid renovation in bacteria-host interactions

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).

Uncovering the role of lipid renovation in bacteria-host interactions

Secondary Supervisor(s): Professor Ioannis Nezis (Warwick)

University of Registration: University of Birmingham

BBSRC Research Themes: Sustainable Agriculture and Food (Plant and Crop Science)

Project Outline

Antimicrobial resistance is one of the most serious threats to humans in the 21st century. Hence, understanding antimicrobial resistance mechanisms is pivotal for combating superbugs that are constantly emerging.

Pathogens use many strategies to combat challenges by antimicrobial compounds in order to better adapt or survive antibiotic insults. These include the induction of efflux pumps or the synthesis of enzymes involved in degrading or modifying antibiotics (e.g. β-lactamases) (Blair et al 2015).

This project aims to determine whether there is another, previously overlooked, dimension to antimicrobial resistance mechanisms, namely the remodelling of membrane lipids. Lipid remodelling is a process whereby bacteria selectively modify their membrane lipid composition in response to a particular environmental stimulus, e.g. the availability of a specific nutrient (see Sebastian et al 2016). Such remodelling potentially plays a role in dictating the permeability and selectivity of the outer membrane, hence mediating antimicrobial resistance. After all, from a pathogen’s perspective, the membrane lipid bilayer forms the first-line of defence against the invasion of an antibiotic (Nikaido 2003). We hypothesize that changes in membrane lipid composition will result in selective recruitment of outer membrane proteins (such as efflux pumps, porins etc), therefore affecting antibiotic trafficking through the membrane. We have recently discovered the central pathway responsible for bacterial lipid remodelling, involving an unusual intracellular phospholipase (PlcP) and demonstrated that lipid remodelling is a common adaptation strategy for a diverse range of bacteria (Sebastian et al., 2016; Jones et al., 2021). This PlcP-mediated pathway is present in many clinically important pathogens such as Pseudomonas aeruginosa and Burkholderia cenocepacia. Interesting, this PlcP-mediated pathway is also essential for intracellular survival and plays a key role in subverting host autophagy and the innate immunity response, thus contributing to the success and spread of these PlcP-containing pathogens during infection. Using cutting-edge omics (lipidomics, transcriptomics and proteomics), advanced imaging (confocal) and cellular biology approaches (macrophages, autophagy biomarkers), this project aims to determine the link between lipid remodelling and antimicrobial resistance and intracellular survival using P. aeruginosa and B. cenocepacia as model organisms.

References

Blair JM, et al 2015 Molecular mechanisms of antimicrobial resistance. Nature Reviews Microbiology 13:42-51.

Sebastian et al 2016 Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. ISME J 10 (4), 968-978.

Jones et al., 2021 Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic. ISME J https://doi.org/10.1038/s41396-021-01008-7.

Nikaido H 2003 Molecular basis of bacterial outer membrane permeability revisited. Microbiology and Molecular Biology Reviews 67(4)593-656.

Previous Projects (2024-25)

Co-supervisor on a project with Professor James McDonald.