• About
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Our research focuses on the role of the gut microbiome and diet in inflammatory bowel disease (IBD) and other gut disorders with the overarching aim of improving patient outcomes and quality of life. We are investigating interventional approaches to manipulate the gut microbiome for therapeutic effect, in particular using dietary therapies and faecal microbiota transplantation; alongside clinical research in the area of IBD and gastrointestinal ultrasound.

Our research group strives to incorporate high quality clinical studies coupled with novel basic science methodology in a collaborative framework, to yield translational therapeutic advancement for IBD. Insights from our research aim to shed light on IBD pathogenesis and thereby progress the field toward cure.

What is IBD?

Inflammatory bowel diseases (IBD) are chronic inflammatory conditions, which are relapsing and remitting in nature, without medical cure. The incidence of prevalence of IBD is dramatically rising globally, and Australia has one of the highest rates in the world. IBD is associated with high rates of surgery and hospitalisation, with a concordant loss of quality of life (QoL) and disability. Despite an expanding therapeutic armamentarium, current treatments targeting the immune system remain inadequate with an efficacy of <40%.

Microbial manipulation in IBD

Microbial manipulation represents a new treatment paradigm that has the potential to bridge the therapeutic gap in IBD. Whilst most research to date has focused on immunological mechanisms, inflammation in IBD may be the sequelae of interactions occurring between the gut microbiota and epithelial cells lining the digestive tract. Epidemiological trends in IBD closely correlate with widespread loss of gut microbial diversity, attributable to changes in dietary intake and broad adoption of a Western diet. Gut microbial dysbiosis and changes in fermentation are consistently observed in patients with IBD. Microbial manipulation in IBD is a therapeutic option for patients that is non-immunosuppressive, harnessing an alternative mechanism of action to conventional IBD therapies.

Pioneering novel microbial and diet therapies

Emerging data suggests that microbial manipulation, using faecal microbiota transplantation (FMT) and prescribed dietary strategies, holds promise for effective management of IBD. 

FMT is defined as the transfer of faecal material from a healthy donor to a person with an illness with the aim of treating disease. We have demonstrated that FMT can safely induce remission of active ulcerative colitis. Our group is actively studying the role of FMT to maintain remission of ulcerative colitis as well as its ability to treat Crohn’s disease. We are also exploring the role of FMT in a broader range of indications, including in neurodegenerative disorders and in the oncological setting.

Our research group has also published a pilot dietary intervention study, testing a novel dietary strategy which has the potential to influence management paradigms for patients with ulcerative colitis. The diet was well-tolerated and improved inflammation and symptoms in participants. This study has informed the rationale and methodology for a high-impact randomised controlled trial exploring the efficacy of this diet in patients with ulcerative colitis, which is currently underway at BHI/TQEH. The current trial has attracted competitive grant funding from multiple sources, including The Hospital Research Foundation, European Crohn’s and Colitis Organisation, and the Gutsy Foundation. The outcome of this trial is expected not only to influence clinical practice but to shed light on the pathogenesis of ulcerative colitis, through deep exploration of the functional microbial impacts of diet in inflammatory bowel disease.

Improving patient outcomes with IBD

Our group is dedicated to research which lead to tangible improvements in outcomes and quality of life for patients with IBD. Intestinal ultrasound (IUS) is a novel non-invasive tool for monitoring disease activity in IBD, which can be performed at the point-of-care. IUS can expedite clinical decision-making and appropriately direct therapy in IBD, in many instances avoiding expensive and invasive tests such as colonoscopy. IUS also allows real-time assess of bowel contents, which can allow directed management of non-inflammatory causes of gut symptoms, including constipation. Our group is leader for both training and research in IUS in Australia.

Potential research students are encouraged to contact [email protected] , [email protected] or [email protected] to discuss possible projects.





Student Alumni

NameDegreeYearThesis titleSupervisors
Alice DayPhD, The University of Adelaide2021Exploring a patient-centered, diet-focused treatment paradigm for Inflammatory Bowel DiseaseAndrews J, Bryant R
Rachel DavisFirst Class Honours, Flinders University of South Australia2019Diet and inflammatory bowel diseaseDay A, Bryant R, Miller M
Sam CostelloPhD, The University of Adelaide2019The role of faecal transplantation in the treatment of ulcerative colitisRoberts-Thomson I, Hughes P, Conlon M, Andrews J
Current trials and projects underway within IBD

Project: Examining a Sulphide-Reducing Diet as Therapy in Ulcerative Colitis: A Randomised, Single-Blind, Placebo-Controlled Dietary Advice Trial (EAT-UC RCT)

Principle investigators: Dr Alice Day & Associate Professor Rob Bryant

Associate investigators & collaborators: Dr Sam Costello, Prof Peter Gibson, Dr Sam Forster, Dr CK Yao, Prof Chris Probert, Malcolm Hebblewhite


Project: Faecal microbiota transplantation for maintenance of remission of Crohn’s disease

Principle investigator: Dr Karmen Telfer, MBBS, studying for MPhil

Supervisors: Prof Philip Weinstein, University of Adelaide, Dr Sam Costello


Project: Faecal microbiota transplantation for refractory ulcerative proctitis.

Principle investigator: Dr Sreecanth Raja, MBBS, studying for MPhil

Supervisors: Professor Christopher Rayner, University of Adelaide, A/Prof Robert Bryant, Dr Sam Costello


Project: Exclusive enteral nutrition in Inflammatory Bowel Disease

Principle investigator: Dr Matthew Chu, MBBS, studying for MPhil

Supervisors: A/Prof Robert Bryant, Dr Alice Day


Project: Helicobacter pylori resistance patterns in Australia

Principle investigator: Dr Jonathon Schubert, MBBS, studying for PhD

Supervisors: Professor Christopher Rayner, University of Adelaide, A/Prof Robert Bryant, Prof Ian Roberts-Thompson


Project: Intestinal ultrasound in Crohn’s disease

Dr Thomas Goodsall, MBBS, studying for PhD

Supervisors: Prof Jane Andrews, University of Adelaide, A/Prof Robert Bryant, A/Prof Chris Ma, University of Calgary


Project: Dietitian First clinic in Functional Gastrointestinal Disorders

Principle investigator: Samantha Plush, APD, studying for PhD

Supervisors: A/Prof Robert Bryant, Dr Alice Day, Professor Saravana Kumar, University South Australia


Project: Intestinal ultrasound to identify gastrointestinal contents

Principle investigator: Dr Ryan Mathias, MBBS, studying for PhD

Supervisors: A/Prof Robert Bryant, Dr Sam Costello, Dr Alice Day


Project: A dedicated Inflammatory Bowel Disease diet clinic (IBDDC): evaluating patient outcome measures, new modes of service delivery, and cost utility.

Principle investigator: Dr Alice Day

Associate investigators & collaborators: A/Prof Rob Bryant, Sangwoo Han, Dr Jyoti Khadka University of South Australia, Dr Matthew Chu

Please refer to the financial year Publication Lists for an annual updated list or researcher profiles for a full list of publications.

Microbial manipulation

Costello, S., Hughes, P., Waters, O., Bryant, R., Vincent, A., Blatchford, P., . . . Andrews, J. (2019). Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial. JAMA – Journal of the American Medical Association, 321(2), 156-164.

Raja, S. S., Bryant, R. V., Costello, S. P., Barnett, M., Schubert, J., & Rayner, C. K. (2023). Systematic review of therapies for refractory ulcerative proctitis. Journal of Gastroenterology and Hepatology (Australia), 38(4), 14 pages.

Tucker, E. C., Haylock-Jacobs, S., Rapaic, M., Dann, L. M., Bryant, R. V., & Costello, S. P. (2023). Stool donor screening within a Therapeutic Goods Administration compliant donor screening program for fecal microbiota transplantation. JGH Open, 7(3), 172-177.

Bogatic, D, Bryant, RV, Lynch, KD, Costello, SP. Systematic review: microbial manipulation as therapy for primary sclerosing cholangitis. Aliment Pharmacol Ther. 2023; 57: 23– 36. https://doi.org/10.1111/apt.17251

Bryant, R. V., Day, A. S., McGrath, K. C., Telfer, K., Yao, C. K., & Costello, S. P. (2021). Fecal microbiota transplantation augmented by a sulfide-reducing diet for refractory ulcerative colitis: A case report with functional metagenomic analysis. JGH Open, 5(9), 1099-1102.

Costello, S. P., Day, A., Yao, C. K., & Bryant, R. V. (2020). Faecal microbiota transplantation (FMT) with dietary therapy for acute severe ulcerative colitis.. BMJ Case Rep, 13(8), e233135.

Soo, W. T., Bryant, R. V., & Costello, S. P. (2020). Faecal microbiota transplantation: Indications, evidence and safety. Australian Prescriber, 43(2), 36-38.

Diet & IBD

Day, A. S., Yao, C. K., Costello, S. P., Ruszkiewicz, A., Andrews, J. M., Gibson, P. R., & Bryant, R. V. (2022). Therapeutic Potential of the 4 Strategies to SUlfide-REduction (4-SURE) Diet in Adults with Mild to Moderately Active Ulcerative Colitis: An Open-Label Feasibility Study. Journal of Nutrition, 152(7), 1690-1701.

Day, A. S., Yao, C. K., Costello, S. P., Andrews, J. M., & Bryant, R. V. (2022). Food-related quality of life in adults with inflammatory bowel disease is associated with restrictive eating behaviour, disease activity and surgery: A prospective multicentre observational study. Journal of Human Nutrition and Dietetics, 35(1), 234-244.

Davis, R., Day, A., Barrett, J., Vanlint, A., Andrews, J. M., Costello, S. P., & Bryant, R. V. (2020). Habitual dietary fibre and prebiotic intake is inadequate in patients with inflammatory bowel disease: findings from a multicentre cross-sectional study.. Journal of Human Nutrition and Dietetics, 34(2), 420-428.

Gastrointestinal Ultrasound

Goodsall, T. M., Nguyen, T. M., Parker, C. E., Ma, C., Andrews, J. M., Jairath, V., & Bryant, R. V. (2021). Systematic review: Gastrointestinal ultrasound scoring indices for inflammatory bowel disease.. J Crohns Colitis, 15(1), 125-142.

Helicobacter pylori

Schubert, J. P., Woodman, R. J., Mangoni, A. A., Rayner, C. K., Warner, M. S., Roberts-Thomson, I. C., . . . Bryant, R. V. (2022). Geospatial analysis of Helicobacter pylori infection in South Australia: Should location influence eradication therapy?. Journal of Gastroenterology and Hepatology (Australia), 37(7), 1263-1274.

Schubert, J. P., Rayner, C. K., Costello, S. P., Roberts-Thomson, I. C., Forster, S. C., & Bryant, R. V. (2022). Helicobacter pylori: Have potential benefits been overlooked?. JGH Open, 6(11), 735-737.

Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial

Costello SP, Hughes PA, Waters O, Bryant RV, Vincent AD, Blatchford P, Katsikeros R, Makanyanga J, Campaniello MA, Mavrangelos C, Rosewarne CP, Bickley C, Peters C, Schoeman MN, Conlon MA, Roberts-Thomson IC, Andrews JM. Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial. JAMA; 2019. 321(2): 156-164

InvestigatorsGranting bodyProject TitleType of GrantTotal Grant AmountFunding Period
Associate Professor Robert BryantThe Hospital Research Foundation GroupMicrobial manipulation in inflammatory bowel diseases: a novel therapeutic paradigmMichell McGrath Fellowship$1,875,0002023-2028
Kristy Burfield, Dr Alice Day, Samantha Plush, Dr Matt Sutton, Robert Barnard, A/Prof Rob Bryant, Sangwoo HanFlinders University South AustraliaFIND-IBD; Flinders student-led interdisciplinary nutrition, mental health, and physical performance screening for holistic care planning in inflammatory bowel disease in a tertiary outpatient setting.NEXUS Grant$10,0002023-2024
Prof Guy Maddern, Professor Tim Price, A/Prof Rob Bryant, Dr Sam Costello, Dr Virginie Gaget, Dr L Kuan, Dr Hugh, A/Prof AfzaliMRFFFaecal microbiota transplantation to improve pain, symptoms management and treatment efficacy in patients with pancreatic cancerPancreatic Cancer Research Stream$1,521,8312023-2026
Dr Alice Day, A/Prof Robert Bryant, Dr Sam Costello, Prof Peter Gibson, Dr Sam Forster, Dr CK Yao, Prof Chris Probert, Malcolm HebblewhiteThe Gutsy GroupExamining a Sulphide-Reducing Diet as Therapy in Ulcerative Colitis: A Randomised, Single-Blind, Placebo-Controlled Dietary Advice Trial (EAT-UC RCTProject grant$150,0002022-2025
Dr Alice Day, A/Prof Robert Bryant, Dr Sam Costello, Prof Peter Gibson, Dr Sam Forster, Dr CK Yao, Dr Tom Goodsall, Prof Chris Probert, Malcolm HebblewhiteEuropean Crohn’s Colitis OrganisationExamining a novel sulphide-reducing diet As Therapy in Ulcerative Colitis (EAT-UC trial)Project grant€80,000 ($130,000)2021-2022
A/Prof Rob Bryant, Dr Alice Day, Dr Sam Costello, Prof Peter Gibson, Dr Sam Forster, Dr CK YaoThe Hospital Research Foundation GroupThe 4-SURE project: pioneering a new diet paradigm in the management of ulcerative colitisProject grant$129,9802020-2023

Industry collaboration with Microbiotica announced on 21 June 2018.

Associate Professor Sam ForsterResearch Group Head, Microbiota and Systems BiologyHudson Institute of Medical Research,
Sanger Institute
Melbourne, CambridgeAustralia, UK
Professor Peter GibsonProfessor of GastroenterologyMonash UniversityMelbourneAustralia
Professor Chris ProbertProfessor of GastroenterologyLiverpool UniversityLiverpoolUK
Professor Michael KammKamm Research Group Lead & GastroenterologistUniversity of MelbourneMelbourneAustralia
Dr Emma HalmosAdjunct Senior Research FellowMonash UniversityMelbourneAustralia
Dr CK YaoAdjunct Senior Research FellowMonash UniversityMelbourneAustralia
Professor Rupert LeongClinical Professor of MedicineMacquarie University & University of SydneySydneyAustralia
Associate Professor Jakob BegunIBD Group leader in the Immunity, Infection, and Inflammation ProgramMater Research University of QueenslandBrisbaneAustralia
Philip WeinsteinProfessorial Research Fellow School of Public Health; Adjunct Professor Biological SciencesThe University of AdelaideAdelaideAustralia
Professor Christopher RaynerGwendolyn Michell Professor, Adelaide Medical SchoolThe University of AdelaideAdelaideAustralia
Dr Hannah WardillSupportive Oncology Group LeadThe University of AdelaideAdelaideAustralia
Dr Trevor LawleyGroup Leader of Lawley LabWellcome Sanger InstituteCambridgeUK
Professor Simon TravisProfessor of Clinical GastroenterologyUniversity of OxfordOxfordUK
Dr Vipul JairathProfessor of MedicineAlimentiv Clincial TrialsLondon, OntarioUK, Canada
Dr Christopher MaSenior Medical DirectorAlimentiv Clincial TrialsLondon, OntarioUK, Canada
Professor Saravana KumarProfessor in Allied Health and Health Services ResearchUniversity of South AustraliaAdelaideAustralia
Dr Sarah SaxonConsultant PathologistSA Pathology & Royal Adelaide HospitalAdelaideAustralia
Associate Professor Lorraine MackenzieAssociate Research ProfessorBasil Hetzel InstituteAdelaideAustralia
Associate Professor Sarah VreugdeSenior ScientistBasil Hetzel InstituteAdelaideAustralia