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Research Studentship in Anaerobic 3D printing of gut bacterial communities

Research Studentship in Anaerobic 3D printing of gut bacterial communities

Project: Anaerobic 3D printing of gut bacterial communities

3.5-year DPhil studentship 

Supervisors: Dr Ravinash Krishna Kumar 

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.

 

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

 

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

 

See recent works for more details:

 

2022 – 3D printing of microbial communities: a new platform for understanding and engineering the microbiome

R. Krishna Kumar, K. R. Foster, Microb. Biotechnol. (2022); 00, 1-5 (https://doi.org/10.1111/1751-7915.14168)

 

​2021 – Droplet printing reveals the importance of micron-scale structure for bacterial ecology

R. Krishna Kumar, et al, Nat. Commun. 2021, 12, 857. (https://doi.org/10.1038/s41467-021-20996-w)

 

2020 – Controlled packing and single-droplet resolution of 3D-printed functional synthetic tissues

A. Alcinesio et al Nat. Commun. 2020, 11, 2105. (https://doi.org/10.1038/s41467-020-15953-y)

 

Group: 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 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. I encourage applications from under-represented groups; I am also happy to discuss potential applications informally (see contact details above).

Eligibility

This studentship is fully funded at the Home level (fees plus stipend)

Award Value

Course fees are covered at the level set for UK students (c. £8960 p.a.). The stipend (tax-free maintenance grant) is c. £18,622 p.a. for the first year, and at least this amount for a further two and a half years. 

Candidate Requirements

Prospective candidates will be judged according to how well they meet the following criteria:

• A first-class honours degree (or equivalent) in Biology, Engineering, or Materials Science
• Excellent written and spoken communication skills in English

The following skills are also highly desirable:

• We are looking for a highly motivated candidate with interest in 3D printing, and experience in engineering and method development, ideally with microbiology experience

Applicants with a good 2.1 degree are also encouraged to apply if they can demonstrate excellent laboratory skills through previous research or an undergraduate project.

Application Procedure

Candidates must submit a graduate application form and are expected to meet the graduate admissions criteria.  Details are available on the course page of the University website.

Before going through this process, applicants are strongly encouraged to make informal enquiries, which should be addressed to Prof Daniel Eakins(daniel.eakins@eng.ox.ac.uk).

Please quote 23ENGCI_DE3 in all correspondence and in your graduate application.

Application deadline: 28 July 2023 

Start date: October 2023