Impact of an Enterobacteriaceae-rich microbial community on gut health

The context of the research

Our gut is colonised by over 100 trillion microbes, which affect our wellbeing in a very complex manner. As new DNA sequencing technologies advance, we have identified our gut microbes in terms of 'who they are'; however, 'what they do' is still largely unknown. Therefore, the proposed research project aims to investigate the impact of our gut microbiota on our metabolism and disease risk. Enterobacteriaceae are Gram-negative bacteria and generally present in very low densities in the normal gut. However, Enterobacteriaceae have been found to be significantly higher in patients with inflammatory bowel disease (IBD), and patients that have undergone Roux-en-Y gastric bypass, a gold standard weight loss surgery. Although weight loss surgery is currently the most effective treatment for morbid obesity, there is thought to be an increased risk of bowel cancer following obesity surgery. Similarly, a 5-fold increase in bowel cancer cases has been observed in patients with IBD. Therefore, it is crucial to understand if the overgrowth of Enterobacteriaceae increases our risk of bowel cancer.

Aims and Objectives

Aim I is to investigate how an Enterobacteriaceae-rich microbial community affect the colon. We will use a multidisciplinary approach that includes the measurement of metabolites, microbiota, microRNAs and inflammation biomarkers, to obtain a wide landscape of disturbances of the colon after colonisation of an Enterobacteriaceae-rich microbial community. We will identify a set of altered metabolites from both the microbiota and the host, microRNAs and cytokines, in order to determine the impact of Enterobacteriaceae on our metabolism. Aim II is to investigate the way in which an Enterobacteriaceae-rich microbial community regulates our metabolism. In Aim I we will identify Enterobacteriaceae-associated products and in Aim II we will test whether or not these products have a direct impact on our colonic metabolism and whether they modulate bowel cancer risk factors such as cell proliferation (the rapid increase in the number of cells).

Potential applications and benefits

This work will help us to understand the physiological impact of Enterobacteriaceae colonisation on our colon, independent of any disease or surgery. The study will provide potential prevention and therapeutic targets for reducing the adverse effects caused by Enterobacteriaceae colonisation. If the results from the project supports my hypothesis that the overgrowth of Enterobacteriaceae increases bowel cancer risk, we will further investigate these targets derived from the project in order to control the overgrowth of Enterobacteriaceae and hence reduce the bowel cancer risk.

Aim I: To investigate the impact of an Enterobacteriaceae-rich microbial community on the colon.

Enterobacteriaceae-rich microbiota derived from RYGB-operated rats will be transplanted into non-operated rat recipients. We will analyse faecal samples collected weekly to monitor the microbial colonisation over 20 weeks post-transplant using qPCR. Microbial composition of luminal content and mucosa will be characterised using 16S rRNA gene-based sequencing. Metabolites in biofluid, luminal content and tissue samples will be measured using proton nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS)-based metabolic profiling. MicroRNAs and cytokines will be measured using an Illumina microRNA deep sequencing platform and a Meso Scale Discovery platform, respectively. Mucosal proliferative biomarker (e.g. Ki67) and inflammation biomarkers (CD3+ intraepithelial lymphocyte and CD68+ lamina propria macrophages) will be assessed using immunohistochemical staining.

Aim II: To investigate the mechanisms by which an Enterobacteriaceae-rich microbial community regulates the host phenotype

We will investigate whether an Enterobacteriaceae-rich microbial community regulates the host colonic physiology and metabolism via microbial metabolites. The luminal microbial metabolites that are found to be associated with Enterobacteriaceae and alterations of host phenotype in Aim I will be tested in the isolated colonic crypt culture. Ki67 will be measured to evaluate the impact of the metabolites on cell proliferation. Cell microRNA profiles will be obtained to predict the pathways which the microbial metabolites regulate. The mRNA targets of the microRNAs will be further confirmed using transfection and inhibition experiments in IEC-6 cells.

Academic impact

Aim I focuses on the investigation of the microbial impact on the host colon in vivo. A wide range of research scientists in the field will benefit from the results generated in Aim I. Aim II focuses on uncovering the mechanisms by which these microbial metabolites alter colonic metabolism. The microbial contributions to colon cancer risk will significantly advance research in host-microbial interaction area and provide potential microbial targets and metabolic pathways for further development of therapeutic or preventive interventions. The project will also contribute towards a greater understanding in multidisciplinary areas including metabonomics, microbiology, microRNAs and mathematical modelling. The multidisciplinary aspect of the project will provide an excellent training opportunity for the proposed research associate.

Economic and societal impact

Although the proposed project focuses on the fundamental aspects of host-microbial interactions, the research outcomes of the causal effect of Enterobacteriaceae on colon cancer risk will help to drive the development of prevention strategies that can re-create a balanced gut microbial environment. Modulating these microbes by diet or lifestyle could contribute towards a better healthcare strategy for IBD and bariatric patients. This would also be of interest for industrial R&D and lead to collaborations between industries and the university. During the project, we will work with charities such as Crohn's & Colitis UK to engage with patients and raise awareness on the socioeconomic impact of biomedical research and the significant contributions that this project would bring to the development of better patient healthcare strategies.