Inflammatory Bowel Disease (IBD) affects over 100,000 Australians and costs $400M annually. Worryingly, nearly 1/3 of patients do not respond to current treatments and the disease is steadily increasing in its prevalence, especially in young people in which symptoms tend to be much more severe. There is no cure for IBD, and treatment options are often ineffective because we still do not know the underlying cause of the disease. Advancements in this area will only come if we have a better understanding of the pathogenesis of IBD.
IBD occurs when the immune system fails to tolerate harmless gut bacteria, but the cause is currently unknown. We investigate the immunology underlying IBD in a physiologically relevant human setting. Our group consists of mucosal immunologists, colorectal surgeons and bioinformaticians. Our research utilises human intestinal tissue freshly discarded from surgery, and we have pioneered immune cell isolation protocols allowing us to carry out functional assays. We have used high parameter flow cytometry and imaging mass cytometry to define the immune cell profile of tissue affected by IBD and revealed that certain subsets of dendritic cells play a role in mediating IBD. We have also interrogated these tissues for viral signatures in order to determine if IBD, like other autoimmune diseases, is linked to viral infection.
Understanding the underlying mechanisms that cause IBD in humans will pave the way for more effective treatment strategies and a cure.

Professor Andrew Harman (left) and Dr Kirstie Bertram (right) discussing their research with IBD sufferer Maddie Millard (centre,) giving her hope for a better future.

Professors Andrew Harman and Scott Byrne in theatre with collaborating colorectal surgeons Associate Professor James Toh (left) and Dr Nimalan Pathma-Nathan (right).
Recent Achievements
- Interrogation of RNAseq and spatial transcriptomic data to link viral gene signatures to Crohn’s Disease
- Defining a link between a new dendritic cell population and Crohn’s Disease
- Generation of a high parameter flow cytometry panels to accurately define human intestinal tissue immune cell populations.
Recent publications
Defining the landscape of human epidermal mononuclear phagocytes. Immunity 2023. PMID: 36921567.
March 2023
An in situ analysis pipeline for initial host - pathogen interactions reveals signatures of human colorectal HIV transmission. Cell Reports 2022. PMID: 36130503.
September 2022
OMIP-096: A 24-color flow cytometry panel to identify and characterize CD4+ and CD8+ tissue-resident T cells in human skin, intestinal, and type II mucosal tissue. Cytometry A 2023. PMID: 37772977.
September 2023
OMIP 082: A 25-color phenotyping to define human innate lymphoid cells, natural killer cells, mucosal-associated invariant T cells, and γδ T cells from freshly isolated human intestinal tissue. Cytometry A 2022. PMID: 35018731.
March 2022
Optimal isolation protocols for examining and interrogating mononuclear phagocytes from human intestinal tissue. Frontiers in Immunology 2021. PMID: 34566985.
September 2021
| NAME | ROLE |
| Andrew Harman | Group Leader |
| Scott Byrne | Group Leader |
| Kirstie Bertram | Senior Research Fellow |
| James Toh | Colorectal Surgeon |
| Nimalan Pathma-Nathan | Colorectal Surgeon |
| Thomas O’Neil | Postdoc |
| Erica Vine | Postdoc |
| Anja Skilton | PhD student |
