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Developing an artificial gut microbiome platform to understand the role of symbiotic and pathogenic microbes in health & disease

   School of Biosciences

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  Dr A Tsaousis, Dr Alexis Vlandas, Dr Yannick Coffinier  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Applications must be received by Sunday 28 February 2022 – 23.59  

Over the last decade, scientists have discovered a new interplay between health, disease and a previously unknown factor. This factor is the human microbiota, i.e. the collection of organisms that live in the human body. These organisms are microscopic and are nearly as numerous as our human cells. Moreover, these microorganisms encode 150-fold more genes than the humans that harbour them. While microbiota reside in all parts of our body, most inhabit the gut where there is an abundance of nutrients. Gut microbiotas have many functions in the human body. For example, they help with digestion of fibre, production of some vitamins (K and B) and they also provide protection from intestinal infections and other diseases.

While there is a huge amount of published work on the composition of gut microbiome and their association with health, disease and aging, not much is known about the microbe-microbe or microbes-host interactions within the gut. So far, studies include large scale genomics, quantification studies (presence and abundance of microbes) and metabolomics of the entirety or part of the gut. However, none of these directions are directly associated with the contribution of specific microbes. This is mainly due to the difficulty of cultivating individual groups of microorganisms separately from each other, while monitoring their interactions and the effects, if any, they have to each other. For example, some of these microbes cannot easily be monocultured (grow by themselves in culture) in a laboratory setting or at least do not exhibit desired physiological activities as seen in their natural environments, but the presence of other microbial populations may improve culturing success and/or cell behaviour.

The purpose of this multidisciplinary PhD project is to overcome these complications by developing a hydrogel-based technology based on a microfluidic device that will enable not only the development of synthetic ecologies of gut microbes but will also allow to monitor their individual growth and communications: substances that each microbe excretes in an artificial gut environment. Thus, the aims of the project are fourfold:

1.    Use ‘omics to understand the basic biology of the gut.

2.    Develop various forms of two-dimensional (2D) and three-dimensional (3D) culturing apparatuses using hydrogel and microfluidics technologies.

3.    Evaluate the function of these apparatuses by incorporating and monitoring the growth of various microbial organisms (bacteria, viruses and parasites).

4.    Assess the efficacy of the above apparatuses, by integrating gut microbial communities from humans (infected and no infected with pathogens) and subsequently monitoring their ecology, growth, and communications.

Overall, we anticipate that this pioneer study will establish microbiota baselines and expand our understanding of gut microbiome biology. This will aid in identifying the suite of unique features of the gut microbiome, which will allow us to investigate mutualism in the gastrointestinal tract in relation to unique features of microbes. This project will provide the platform for spearheading future investigations on exploring the gut microbiome and its role in health and diseases (e.g. infections by pathogens), including parasitic, viral, immunological, metabolic, cardiovascular and neurological diseases.

Key attributes and skills for prospective applicants 

·      The successful candidate is expected to be a highly motivated, efficient, creative and punctual student with an interest in multidisciplinary research.

·      He/she will be expected to have an undergraduate (BSc) degree at 2(i) or higher in Biosciences, Chemistry, or a related discipline, with some experience in cell culturing and/or microbiome-related work. 

·      The candidate will have access to a range of samples and should be able to work with large-scale data.

·      Good interpersonal skills and ability to communicate technical information This project will provide the candidate with a broad multidisciplinary scientific training.

·      Good technical lab skills.

·      Ability to set up experiments with due care and attention

·      Ability to take direction, follow protocols and pick up techniques quickly

·      Keen to learn new technical skills with regard to operation.

·      Candidates applying for a PhD degree must normally hold a good Honours degree (First or 2:1) or an MSc  Degree (at Merit or Distinction) in a relevant, appropriate subject, or the equivalent from an internationally recognised institution.

How to apply 

To apply please go to

You will need to apply through the online application form on the main University website. Please note that you will be expected to provide personal details, education and employment history and supporting documentation (Curriculum Vitae, transcript of results, two academic references). Please provide a statement to explain your reasons for study and your suitability and interest for this project.

Funding Notes

Tuition fees and stipend at the standard Research Council rate (Home rate only: £4,500 (fees) and £15,609 (stipend) in 2021/22). The 2022/2023 rate is yet to be announced by the UK Research Councils.
Open to overseas/home/EU fee paying students.
The scholarship covers home fees only, however international students are welcome to apply and fund the difference.
Scholarships are available on a cotutelle (dual award) basis only.
Students have to spend at least 12 months at Kent and Lille.

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