The Australian Inflammatory Bowel Disease Microbiome Study - The AIM Study

Patients with Inflammatory Bowel Disease Male and female (nonpregnant) patients with either ulcerative colitis or Crohn's disease undergoing follow-up colonoscopy for disease activity assessment will have samples of large bowel mucosa, peripheral blood, urine and stool collected at colonoscopy (stool and urine collection tubes/instructions will be provided in advance, so patients can bring samples to their colonoscopy appointment). IBD patients who are eligible for the study but are not requiring colonoscopy, will be invited to participate in the study by local research teams either at the current clinic visit, a future scheduled clinic visit or a separate visit to the local clinical research facility. At this appointment, peripheral blood, urine oral swab and stool will be collected (stool and urine collection tubes/instructions will be provided in advance, so patients can bring samples to their appointment). All IBD patients will be asked to complete a series of validated questionnaires detailing patient reported outcomes/environmental exposures as well as dietary habits. Completion of the questionnaires will be requested at study entry and at the end of 12 and 24 months. A limited patient reported measure of disease activity will also be requested alongside 3 monthly stool sampling. To allow further detailed analyses of the gut microbiota, patients will be asked to provide oral swab and stool samples, for microbiota analysis and measurement of host protein levels including faecal calprotectin, every 3 months for 24 months. In the event that patients experience an increase in symptoms, they will be advised to contact their IBD clinical team as per usual clinical management, but they will be requested to provide additional oral swab and stool samples during the episode of flare (defined by a standardised clinical definition), in addition to the 3-monthly regular request. Sample and Data Collection For participants undergoing colonoscopies, up to six additional intestinal tissue samples will be collected along with the biopsy samples that are routinely taken during this procedure for clinical management. Approximately 20ml of blood (4 teaspoons) will also be collected along with the blood tests that are routinely taken at this time. In addition, patients will be asked to provide a urine sample (50 ml) in individual sterile collection tubes, an oral swab, and a stool sample will be collected by the participant before commencing bowel preparation the previous night (collection kit/instructions provided in advance). For participants attending IBD outpatient clinics or participants attending a clinical research facility, 30ml of blood (6 teaspoons), 50 mL of urine, oral swab, and a stool sample will be collected when they initially enter the study. At subsequent appointments if participants are having blood collected as part of routine clinical management, we will collect an additional sample. Questionnaires Participants will be asked to fill in a Food Frequency Questionnaire and a food avoidance questionnaire online in one of their visits to the clinic (or they can be given a user login and password to fill in the questionnaire at home). These questionnaires are aiming to evaluate the participants’ usual eating and drinking habits over the last 12 months (e.g. What type of spread or oil did you usually put on your bread? with the following answers to select from: none, butter, butter-margarine blends [e.g. Devondale Extra Soft or Dairy Soft, Western Star spreadable varieties], margarine, olive oil). Participants will be asked to record every food item they eat in a specialised smartphone application for 5 days (4-week days and 1 weekend day, not necessarily consecutive). If they are not smartphone users, they will be provided with a 5-day diet diary which they will be asked to fill in and return in their next visit to the clinic. Participants will complete this at study entry, at 12 and 24 months. All participants will also complete a limited participant reported outcomes measures score which will be returned with their 3 monthly stool and oral samples. Participants will also be asked to complete a lifestyle factor questionnaire during their visits to the clinic (or they can be given a user login and password to fill in the questionnaire at home). This lifestyle questionnaire is aiming to evaluate the participants’ usual lifestyle habits over the last 12 months (e.g. level of exercise, sleep habits, travel habits, use of health supplements and complementary medicines. A paper-based format will be available for participants who cannot complete it online. Participants will complete this at study entry, at 12 and 24 months. For all participants in this study, the researchers may access their hospital records for demographic and/or clinical information solely for the purposes of this study.