Role of the Intestinal Microbiota in Clostridium difficile Infection and Recurrence

The human gut microbiota is often described as another organ of the body and plays an integral role in health, one such role is providing colonisation resistance against pathogens. However, the integrity of the microbiota is often lost after antibiotic treatment as the "good" bacteria are diminished, known as dysbiosis, and pathogens such as Clostridium difficile are able to invade, causing disease. Those who are >65, have been hospitalised or received antibiotic treatment are at a greater risk of infection. Clostridium difficile infection (CDI) can manifest as a range of conditions from mild diarrhoea to potentially fatal pseudomembranous colitis and is attributed to around 150 deaths in Scotland every year.
A faecal microbiota transplant (FMT) is the transfer of faecal matter from a "healthy" screened donor to the patient and they are successful in treating >90% of CDI cases however the success is undefined and comes with a plethora of safety concerns as it is not possible to identify all of the bacteria and viruses present in faeces. The gut microbiota is also being linked to conditions such as depression and obesity and it may be possible to transfer these conditions from the donor to the patient. A proposed solution is to identify the specific groups of bacteria which provide colonisation resistance and only transfer these groups to the patient.
This project will investigate the gut microbiota of patients with active CDI, those with recurring CDI, individuals who are colonised but healthy and healthy non-colonised individuals in order to identify which groups of bacteria could be providing colonisation resistance against C. difficile. To achieve this metataxonomic data of patient and volunteer microbiotas will be gathered via DNA isolation and Illumina 16s sequencing. The data will then be analysed and Python will be used to predict the functional characteristics of the microbiota. This information could be used to guide the development of probiotic cocktails which could be tailored to match a patient's specific needs and replace FMT.