Open PhD position

Application deadline: January 12th 2024

Key details

3.5-year funded PhD position
Lead Supervisor: Dr Ravinash Krishna Kumar
Department: Department of Infectious Disease
Location: Sir Alexander Fleming Building, Imperial College London, London, UK

Key words:

3D printing, bacterial communities, gut bacteria, synthetic biology

Project

Bacteria often live together and interact with each other in densely packed communities. Such communities live in our digestive tract and are essential for our health. Critically, changes in the community diversity (number of species), productivity (total biomass), and structure (who-is-next-to-who) can lead to chronic and life-threatening diseases. It is a great challenge to study and understand these bacterial communities, especially at the micrometre length-scales at which they naturally occur. New methods are urgently needed to build simplified bacterial communities that capture the complex arrangements and interactions of different bacteria found within us.

To fill this gap, we have developed a new droplet-based 3D printing technology for building micrometre structured bacterial communities. We now want to apply this technology to understand the structure/function relationships of our gut microbiota, in particular, the Bacteroides. These are one of the most abundant anaerobic groups of bacteria in our gut responsible for nutrition, pathogen protection, and immune training. We aim to use our printing technology to interrogate how community structure controls the diversity and productivity of Bacteroides communities, and in turn, how they provide us with health benefits.

Goals

The goals of this PhD project will be to:
1) develop our technologies to be able to print anaerobic Bacteroides gut strains
2) develop real-time imaging of printed Bacteroides communities
3) use this technology to understand how to build diverse and productive Bacteroides communities through changing the spatial patterning of species

For more details see:

2022 – 3D printing of microbial communities: a new platform for understanding and engineering the microbiome R. Krishna Kumar, K. R. Foster, Microb. Biotechnol. (2023); 00, 1-5 DOI

2021 – Droplet printing reveals the importance of micron-scale structure for bacterial ecology R. Krishna Kumar, et al, Nat. Commun. 2021, 12, 857. DOI

2020 – Controlled packing and single-droplet resolution of 3D-printed functional synthetic tissues A. Alcinesio et al Nat. Commun. 2020, 11, 2105. DOI

This project is highly interdisciplinary – you will gain expertise in 3D printing, method development, materials science, microbiology, and microbial ecology.

Microbiome Printing Lab (visit our group webpage here for more information)

Our research group focuses on building tractable gut microbiome models using 3D printing and flow systems. With this work, we hope to set a new standard for in vitro models of our gut microbiome, where we will be able to image in real time the development of gut bacterial communities (which is currently not possible when using mouse models). To achieve these objectives, we will collaborate with Professor Laurie Comstock (University of Chicago) who is a world-expert in Bacteroides molecular biology, and with Professor Kevin Foster (University of Oxford) who is world-expert in microbial ecology and evolution.

Our research group prioritises a healthy research culture, collaboration, and flexible work hours as needed. I will provide a personalised mentorship, including working towards different career choices following the PhD.

How to apply

Please send your CV (including contact details of two referees) and a motivation letter for the project and lab to Dr Ravinash Krishna Kumar: r.krishnakumar@imperial.ac.uk by the 12th of January 2024.

The project aims to start as early Feb 2024, with flexibility to start after this date.

Informal enquiries are most welcome via email, video calling, and lab visits. Please get in touch again with Dr Ravinash Krishna Kumar: r.krishnakumar@imperial.ac.uk

Eligibiltiy

The studentship is funded by the Department of Infectious Diseases, Faculty of Medicine for 3.5 year home (fee-status) PhD studentship, which includes tuition fees, bursary commensurate with UKRI rates (£20,622 pa tax free) and £5,000 pa for research and training support.

Internatioal students can apply with us for a fully funded Presidents Scholarship).

Applicants must have or expect to gain a First or Upper Second class undergraduate degree in Synthetic Biology, Systems Biology, Molecular Biology, Microbiology or other related field. A Masters Degree is desirable but not essential. Applicants are also required to meet Imperial College’s English language requirements

Imperial College London

Imperial College is a hub for the advancement of synthetic biology and microbiome sciences. Moreover, you will be positioned to take advantage of the London BioFoundry and the Advanced Hackspace, along with the Department’s close ties with clinical scientists across the Faculty of Medicine and researchers in the Life Sciences and Bioengineering departments. The Department provides a well-developed teaching and support network for PhD students, and the research project will be pursued in the Sir Alexander Fleming Building at the vibrant South Kensington Campus in central London.