Background

Inflammatory bowel disease (IBD) represents a significant global health burden and is a leading cause of chronic illness among young individuals in Australia. IBD comprises two primary conditions—Crohn’s disease (CD) and ulcerative colitis (UC)—both of which are chronic, idiopathic disorders with no known cure. In Australia, approximately 1 in 250 individuals aged 5 to 40 years are affected, with nearly 75,000 people currently living with CD or UC. This number is expected to increase to 100,000 within the next five years. It is widely recognised that IBD results from a dysregulated immune response to perturbations in the gut microbiota, occurring in genetically predisposed individuals (GL Hold, et al; 2014).

IBD patients often experience recurrent episodes of active disease, or “flares,” interspersed with periods of relative remission. Despite extensive research, the precise triggers of disease onset and relapse remain poorly understood. IBD frequently imposes a lifelong burden of distressing, intrusive, and potentially severe intestinal inflammation. Current therapeutic options are constrained by suboptimal efficacy, adverse side effects, limited patient adherence, and a high likelihood of disease recurrence. The ability to identify individuals at risk of developing IBD prior to the onset of clinical symptoms—or to intervene early to prevent disease progression—holds the potential for substantial global health and economic benefits. Such advancements would align with the core objective of IBD care: to enhance long-term health outcomes and quality of life for patients.     
Until recently most IBD studies have focussed on single time-point sampling – a ‘snapshot in time’ of a patient’s disease (DN Frant, et al; 2007 and XC Morgan et al; 1012).

Advancing our understanding of IBD has revealed that traditional approaches, while informative, offer a limited view of a complex and dynamic disease that varies between individuals. This is particularly evident in the context of the gut microbiota, which undergoes significant fluctuations over the course of disease. Recent studies underscore the value of longitudinal microbiome assessment in capturing these temporal dynamics (V pascal et al; 2017 and J Halfvarson et al; 2017).

 A significant knowledge gap remains in characterising microbiota alterations in individuals with IBD within the Australian context. Population-specific differences in genetic risk loci and disease prevalence, coupled with distinct environmental exposures and dietary patterns, contribute to variations in gut microbial composition across regions.

Our focus areas

IBD research at MRC seeks to advance understanding of the role of the gut microbiota in the pathogenesis and progression of inflammatory bowel disease (IBD) within the unique genetic, environmental, and dietary context of the Australian population. By conducting longitudinal microbiome profiling of individuals with IBD, the initiative aims to:

1. Identify microbial signatures associated with disease onset, progression, and flares.
2. Define population-specific microbiota patterns in Australian IBD patients, addressing gaps in existing global datasets.
3. Explore gene-environment-microbiome interactions contributing to IBD heterogeneity.
4. Inform the development of microbiome-based diagnostics, prognostics, and therapies tailored to the Australian population.
5. Enhance early detection and personalised management strategies by identifying microbial markers predictive of disease course.

The IBD program encompasses multiple research initiatives, all aimed at enhancing patient outcomes through the integration of microbiome-derived insights into clinical management and care of inflammatory bowel disease.

Dr Paris Tavakoli (BA, BSc, MSc, PhD) is an ECR Postdoctoral Research Fellow at the Microbiome Research Centre (MRC) and is affiliated with St George and St Vincent’s Hospitals. She was awarded her PhD in Medicine in 2020 from the Faculty of Medicine at the University of New South Wales in Sydney, where her research focused on the intersection of microbiome science and clinical applications in IBD. Following the completion of her PhD, Dr. Tavakoli transitioned into a NSW Health Senior clinical project manager role whilst maintaining a significant role within the Australian IBD Microbiome (AIM) study. The AIM Study is one of the leading global initiatives in IBD microbiome research, focusing on advancing our understanding of the microbiome’s role in IBD pathogenesis and treatment. Dr. Tavakoli has made impactful contributions to the scientific literature, being the primary author of two peer-reviewed original research articles including Frontiers in Medicine (cited 116 times) and Public Health Review Journals. Additionally, she has co-authored four other peer-reviewed publications. Her research expertise extends to the management and coordination of multi-centre clinical studies, particularly in the specialised field of IBD. With substantial experience in overseeing complex clinical research projects, Dr. Tavakoli has demonstrated a strong ability to collaborate across institutions and disciplines, contributing to the advancement of IBD research on both a national and international scale.

Dr Fan Zhang, is a Senior Research Associate at the Microbiome Research Centre, St George Hospital and St George & Sutherland Clinical Campuses, University of New South Wales in Sydney. Dr Zhang obtained his PhD degree in Computer Science in 2017 from Nanyang Technological University Singapore. From 07/2016 to 10/2017, Dr Zhang joined the Genome Institute of Singapore as a Research Fellow. As one of Australia’s leading Early Career Researchers in the field of bioinformatics, Dr Zhang has already published 35 peer-reviewed publications (566 citations, h-index 13). There is an excellent distinction between each of the publications. Each of them stands well on its own and well addresses the particular research question. Dr Zhang’s papers are published in top-tier world-leading journals, including Nucleic Acids Research and Genome Biology. Dr Zhang has rich experience successfully managing bioinformatics related projects to completion. Dr Zhang is now the coordinator of more than ten national and international collaboration projects. International acknowledgement of the quality of his expertise in bioinformatics is reflected in a range of invited talks, invited reviewer activities, and other professional activities.

Ms Rachel Tennyson is a Research Registered Nurse specialising in Inflammatory Bowel Disease (IBD). With a strong background in Endoscopy nursing, she brings both clinical expertise and a deep understanding of the patient journey to her research role. Rachel is passionate about advancing IBD care through clinical research and is committed to supporting patients while contributing to studies that shape future treatments. 

Sabrina Koentgen is a third year doctoral researcher working on our AIM study 

Thisun Jayawardana is a third year doctoral researcher working on our AIM study

Yashar Houshyar is a third year doctoral researcher working on our AIM study

Anuk is our research assistant working on our AIM study

Australian IBD Microbiome (AIM) Study

This study aims to investigate the underlying causes of inflammatory bowel disease (IBD), a condition that affects approximately 1 in 250 Australians—equating to around 100,000 individuals nationwide. Despite significant advances, the aetiology of IBD remains incompletely understood. It is, however, well-established that IBD is more prevalent in developed countries, potentially due to environmental factors such as diet and lifestyle. Genetic predisposition also plays a critical role, and both genetic and environmental influences can modulate the gut microbiome. By examining longitudinal changes in the microbiome, this study seeks to determine whether microbial alterations contribute to the development and progression of IBD. The findings may improve our ability to predict disease onset and course and inform the development of novel microbiome-targeted therapies.

LOCI Project

This project aims to develop a novel pharmacogenomic assay capable of predicting individual responses to current inflammatory bowel disease (IBD) novel therapies based on patient genotype, thereby facilitating precision medicine approaches in IBD management. This initiative will leverage population-scale single-cell data generated through our internationally recognised OneK1K study, which elucidates the genetic regulation of drug target expression in specific immune cell subsets. Validation of the assay will be conducted in partnership with the AIMs study—a well-established, national, multicentre, longitudinal prospective cohort. To support clinical translation, the test will be validated within a NATA-accredited laboratory, and evidence-based guidelines will be developed to inform its implementation in routine clinical practice.

The Inhabit Project

The INHABIT Study is a four-arm randomised controlled trial exploring the effect of anthocyanins and probiotics alone and combined on quality-of-life, inflammation, and the gut microbiome in adults with Ulcerative Colitis. The gut microbiome profile of people living with UC differs from healthy controls and this may play a role in the pathogenesis and clinical management of the disease. Probiotics have been shown to induce remission in Ulcerative Colitis, however, their impact on the gut microbiome and inflammation is less clear. Anthocyanins, a bioactive compound found in purple and red fruits and vegetables, have shown anti-inflammatory and microbiota-modulating properties. However, few studies have researched their effect in Ulcerative Colitis. The aim of the INHABIT Study is to explore the combined effect and clinical significance of anthocyanins and probiotics in adults with Ulcerative Colitis. Outcomes measured include changes to quality-of-life, disease activity and disease symptoms, inflammation, cognitive function, and the gut microbiome profile.

Main investigators:

• Dr Kelly Lambert
• Denelle Cosier
• Prof Georgina Hold
• Prof Michael Grimm

Denelle Cosier, is an Accredited Practising Dietitian who is completing a PhD at the University of Wollongong, exploring the relationship between diet, inflammation, and the gut microbiome in Inflammatory Bowel Disease. Denelle is the trial manager of the INHABIT Study as it is the major study of her PhD.

Mediterranean /Anti Inflammatory Diet and IBD Project 

The study “Diet quality and IBD” is a cross-sectional, secondary analysis of baseline data from the Australian IBD Microbiome (AIM) Study cohort. It investigates the alignment of habitual dietary intake with Mediterranean and Anti-inflammatory dietary patterns in relation to intestinal inflammation and clinical disease activity, in adults with Crohn’s disease (CD) and ulcerative colitis (UC). Dietary guidance is crucial in IBD management, but maladaptive dietary behaviours and nutritional inadequacy remain prevalent. Despite various dietary approaches, consensus on the optimal strategy is lacking. Recent clinical guidelines recommend the Mediterranean diet for its anti-inflammatory properties and potential health benefits, including reduced risk of IBD onset. However, there is limited empirical research on the association between adherence to Mediterranean or Anti-inflammatory diets and objective measures of intestinal inflammation (faecal calprotectin) and validated disease activity indexes in established IBD. This study utilises comprehensive dietary, biomarker and clinical assessments to (1) quantify the extent to which habitual diets of adults with CD and UC align with Mediterranean and Anti-inflammatory dietary patterns; (2) assess associations between the diet-quality and intestinal inflammation (fecal calprotectin) and disease activity (Crohn’s Disease Activity Index; partial Mayo Score). Additionally, secondary analyses will identify specific food groups that most strongly contribute to diet quality and inflammatory status in IBD.

 Main investigators:

• Gynette L. Reyneke
• Professor Eleanor J. Beck
• Professor Kelly Lambert
• Professor Georgina Hold

Gynette Reyneke a PhD candidate in nutrition and dietetics at the University of New South Wales, is conducting doctoral research on evidence-based dietary recommendations for inflammation-related chronic diseases. Her work examines the underlying processes and methodologies that inform these recommendations, with a focus on prevention and management strategies. Gynette holds a Bachelor of Nutrition and Dietetics (Honours, Dean’s Scholar), and as an Accredited Practising Dietitian, she has gained valuable clinical experience in managing various chronic conditions, including cardiovascular disease, type 2 diabetes, and metabolic syndrome. Her research aims to contribute to the development of more effective dietary interventions for chronic diseases associated with inflammation, potentially improving patient outcomes and quality of life.

Primary Sclerosing Cholangitis (PSC) -UC

For reasons unknown, 80% of patients with primary sclerosing cholangitis (PSC; a chronic, progressing cholestatic disease) will also develop inflammatory bowel disease (IBD). PSC-IBD most commonly affects the colon and is linked clinically to ulcerative colitis (UC). However, differences include a right colon dominance, less severe inflammatory presentation, and a greater lifetime risk of developing colorectal cancer in individuals with PSC. The unique clinical presentation of PSC-IBD has led to the postulation of PSC-IBD as a distinct disease entity to IBD, but little is known about the underlying biology of colitis in PSC patients. To address this, we are using a combination of techniques such as single cell RNA sequencing, spatial transcriptomics, and bacterial amplicon sequencing to study the cells and the microbiome throughout the UC and PSC-IBD gut, providing insights to guide tailored clinical management and precision therapies. This work is being led by Dr. Jacqueline Tearle, a postdoctoral researcher within the laboratory of Dr. Kylie James at the Garvan Institute, in collaboration with the Australian IBD Microbiome Study team and St Vincent’s Hospital gastroenterologists Dr. Simon Ghaly, Dr. Andrew Kim and Dr Paris Tavakoli.

Main investigators:

• Dr Kylie James
• Dr Jacqueline Tearle
• Dr Simon Ghaly
• Professor Georgina Hold
• Dr Paris Tavakoli

Dr Kylie James is Head of the Gut Immunogenomics Laboratory at the Garvan Institute of Medical Research. She completed a PhD in T cell immunity to malaria in 2017, with Dr Ashraful Haque at QIMR Berghofer. She then undertook postdoctoral training at the Wellcome Sanger Institute in the laboratory of Dr Sarah Teichmann, and a junior research fellowship at Christ’s College, University of Cambridge. Here, she spearheaded the cell atlas of the human intestinal tract across anatomical space and developmental time and showed the influence of the neighbouring microbiota in shaping the intestinal immune cell landscape. In 2021, Kylie returned to Australia to start her team as Spinak Fellow and NHMRC Investigator Fellow.

 Dr. Jacqueline Tearle completed her Ph.D. at EMBL Australia node in Single Molecule Science, UNSW, under the supervision of A/Prof. Maté Biro, where she used live-cell microscopy and single cell transcriptomics to investigate tumour escape and invasion in melanoma. She joined the Gut Immunogenomics Lab at Garvan in 2022 as a Postdoctoral Researcher in the Gut Immunogenomics group, headed by Dr. Kylie James. Jac’s current research involves using single cell transcriptomics and computational techniques to characterise cellular and microbial drivers of intestinal disease.