Anaerobic 3D printing of gut bacterial communities

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)

Our research group (https://www.sems.qmul.ac.uk/staff/r.krishnakumar) 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). This project will be co-supervised by Dr Lee Henry (https://www.qmul.ac.uk/sbbs/staff/leehenry.html) at the School for Biological and Behavioural Sciences. 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. The work will be based in the supportive Centre for Bioengineering (https://www.sems.qmul.ac.uk/research/bioengineering/) in the School of Engineering and Materials Sciences at QMUL, as well as having access to SBBS (https://www.qmul.ac.uk/sbbs/) and the Blizard Institute (https://www.qmul.ac.uk/blizard/) for characterisation techniques.

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 am an active member of the EDI Steering Group at the School of Engineering and Materials Science (https://www.sems.qmul.ac.uk/edi/) and encourage applications from under-represented groups; I am also happy to discuss potential applications informally (see contact details above).

Funding

This studentship is fully funded and includes a 3-year stipend (set at £19,668 for 2022/23) and Home tuition Fees.

Eligibility

We are looking for a highly motivated candidate with interest in 3D printing, and experience in engineering and method development, ideally with microbiology experience (but not essential as you will be trained in this).

• Available to applicants with UK Home Fee Status only. (See: http://www.welfare.qmul.ac.uk/money/feestatus/ for details of UK Home status)

• The minimum requirement for this studentship opportunity is a good Honours degree (minimum 2:1 honours or equivalent) or MSc/MRes in a relevant discipline.

• If English is not your first language, you will require a valid English certificate equivalent to IELTS 6.5+ overall with a minimum score of 6.0 in Writing and 5.5 in all sections (Reading, Listening, Speaking).

• Candidates are expected to start from October 2023

Supervisor Contact Details:

For informal enquiries about this position, please contact Dr Ravinash Krishna Kumar, E-mail: [Email Address Removed]

Application Method:

To apply for this studentship and for entry on to the PhD Full-time the Medical Engineering - Semester 1 (September Start), please follow the instructions detailed on the following webpage:

Research degrees in Engineering: http://www.qmul.ac.uk/postgraduate/research/subjects/engineering.html

Further Guidance: http://www.qmul.ac.uk/postgraduate/research/

Please be sure to include a reference to ‘2023 QMRS RKK’ to associate your application with this studentship opportunity.

Website: http://www.qmul.ac.uk/postgraduate/research/subjects/engineering.html