Studying bacterial competition in the gut microbiome and its influence on chronic intestinal inflammation and colorectal cancer

   School of Medicine, Dentistry & Biomedical Sciences

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  Dr David Cisneros, Dr R Ingram  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

The gut microbiome is composed by trillions of bacteria that inhabit the human intestine. These microorganisms generate metabolites from diet and the environment, which directly regulate physiological states. Therefore, manipulation of the microbiome is a research area with great potential to directly change disease prevention and treatment. In most cases, bacteria in the intestine contribute to digestion and intestinal health. However, some strains of bacteria are linked to chronic inflammation and colorectal cancer and in this project, we want to study these link using state-of the-art genetic techniques to study an inflammation model.

About the lab: 

The Cisneros lab is a brand-new team at Queen’s University Belfast (QUB). We have fresh ideas to study the gut microbiome and how it influences human health. Our goal is to integrate the newest technologies with classical molecular genetics to understand how the gut microbiome is established and how it can cause disease when this process goes wrong. Our team is based on a people-centric view of research. To help these aims, the Wellcome-Wolfson Institute for Experimental Medicine counts with state-of-the-art facilities and an its research environment encompasses an integrative view of health. Moreover, QUB excels on equality and diversity charters. 

Get more detailed information about the lab here: 

About the project: 

Trillions of bacteria comprise the gut microbiome and contribute to human health by producing metabolites that regulate intestinal health and contribute to human metabolism and homeaostasis. Therefore, the microbiome represents an innovative approach to develop new therapies. Our team studies how bacterial competition for nutrients and space shapes the biodiversity of the gut. This is important because gut biodiversity is a determinant of human health. Moreover, few key species can affect biodiversity, by direct competition with other bacteria. 

Many microbiome bacteria contribute to homeostasis and contribute to reduce inflammation in the gut. However, like Dr Jekyll and Mr Hyde, some species called pathobionts have strains associated with cancer and chronic inflammation. Moreover, modern lifestyles contribute to dysregulation of the gut microbiome and establish vicious circles contributing to various metabolic diseases, obesity and cancer. 

In this project, we will study genes that allow pathobiont bacterial species to stably colonize the intestinal environment in the first place using state-of-the-art techniques such as microbiome sequencing and CRISPR‒Cas9 gene editing as demonstrated in one of our recent papers (click here) . Furthermore, we will study how do pathobionts affect acute and chronic inflammation in a colitis model. The results of this research will contribute to design strategies to manipulate the microbiome and to reduce digestive tract cancer incidence, which in the UK represents ~40,000 new cases per year with an economic cost of £17.1 billion. 

The successful candidate will acquire training in cell biology, microbiology, genome editing and high-throughput sequencing. The project should provide experience to pursue industrial or academic R&D in the new field of microbiome therapeutic biologicals, synthetic biology, or biotechnology.

Biological Sciences (4) Medicine (26)

Funding Notes

Funded by the Department for the Economy (DfE). For UK domiciled students the value of an award includes the cost of approved tuition fees and maintenance support the 2024/25 rates are still to be confirmed (current rates for 2023/24 are Fees £4,712, Stipend £18,622). To be considered eligible you must have been ordinarily resident in the UK for the full 3-year period prior to the start of the studentship and you must be ordinarily resident in Northern Ireland on the first day of the start of the studentship. For further information about eligibility criteria please refer to


Please visit the School of Medicine, Dentistry and Biomedical Sciences, The Wellcome-Wolfson Institute for Experimental Medicine website for further details about the Centre.
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