Overview
Background
Associate Professor Jakob Begun is the IBD Group leader in the Immunity, Infection, and Inflammation Program at Mater Research University of Queensalnd, and has a basic and translational laboratory at the Translational Research Institute in Brisbane. He is an Associate Professor in the University of Queensland Faculty of Medicine. After completing his Bachelor of Science at Cornell University Jakob attended Cambridge University where he completed an MPhil in Biochemistry. He then moved on to Harvard Medical School where he completed his MD and PhD in genetics studying the host pathogen interaction using C. elegans as a model system. He completed his clinical training in internal medicine at Brigham and Women’s hospital and went on to complete general gastroenterology training at Massachusetts General Hospital (MGH) as well as advanced training in the treatment of Inflammatory Bowel Disease (IBD).
Dr Begun first joined Mater Research - University of Queensland in 2014, and at the same time received a clinical staff appointment in Gastroenterology at the Mater Hospital Brisbane. His clinical activities are focussed on the treatment and mangement of patients with IBD. He is the director of the IBD unit at the Mater Hospital Brisbane and at the Mater Young Adult Health Centre Brisbane .In January 2015 he was awarded the University of Queensland Reginald Ferguson Fellowship in Gastroenterology to support his research activity. He leads a basic and translational laboratory at the Translational Research Institute investigating the interaction between the innate immune system and the gut microbiome, as well as genetic contributions to disease. He also performs clinical research examining predictors of response to therapy, minimising barriers of care for adolescents and young adults with IBD, improving outcomes in pregnancy and IBD, and the use of intestinal ultrasound in IBD. He is the chair of the Gastroenterology Society of Australia-IBD Faculty and of the president of the Gastroenterology Network of Intestinal Ultrasound (GENIUS).
Availability
- Associate Professor Jakob Begun is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Bachelor of Biology, Cornell University
- Doctoral Diploma of Medicine, Harvard University
- Doctor of Philosophy of Genetics, Harvard University
- Member, Gastroenterological Society of Australia, Gastroenterological Society of Australia
- Fellow, Royal Australasian College of Physicians, Royal Australasian College of Physicians
Research impacts
Inflammatory bowel disease(IBD) is a complex disease with genetic and environmental triggers. The microbiota is one of the biggest environmental contributors and interest in its impact on human health and disease is a growing. Studies in IBD have led the way in identifying disease associated microbial signals, but has not yet led to any new therapies.
As a clinician-scientist I am driven by my patients’ needs to address all aspects of their disease: including genetic and environmental risk factors, disease monitoring, and developing novel therapeutics. My tranlsational research program contributes to KNOWLEDGE IMPACT by discovering the function of IBD-susceptibility genes and anti-inflammatory bio-actives produced by the gut microbiota. My clinical research program advances HEALTH IMPACT by optimizing patient monitoring through evidence-based use of biochemical tests and imaging technology.
-Knowledge Impact. My research into the interaction between IBD susceptibility genes and bacterial handling has been highly cited, and led to an NHMRC collaborative project grant.
-Health Impact. My research program into advances in patient monitoring has led to the application for faecal calprotectin testing to be covered by the Medicare Benefit Scheme – which will have a direct impact on patient monitoring in the clinic. Additionally my monitoring research into the use of intestinal ultrasound has led to the formation of the Gastroenterology Network of Intestinal Ultrasound and the increase in ultrasound use in IBD patients in Australia.
Works
Search Professor Jakob Begun’s works on UQ eSpace
2026
Journal Article
Examining attitudes to intestinal ultrasound in inflammatory bowel disease: a national survey of Australian gastroenterologists
Chen, Lynna, Ruddick-Collins, Leonie, An, Yoon-Kyo, Baraty, Brandon, Begun, Jakob, Boyapati, Ray K., Bryant, Robert V., Smith, Rebecca L. and Srinivasan, Ashish R. (2026). Examining attitudes to intestinal ultrasound in inflammatory bowel disease: a national survey of Australian gastroenterologists. Therapeutic Advances in Gastroenterology, 19 17562848261432538. doi: 10.1177/17562848261432538
2026
Journal Article
Development of a novel polyleucine-based immunopotentiator for subunit vaccines against Group A Streptococcus
Lu, Lantian, Cruz, Jazmina L. Gonzalez, Giri, Rabina, Zhang, Yuexiao, Bashiri, Sahra, Cadena, Leslie C. Domínguez, Li, Shuhang, Khalil, Zeinab G., Hussein, Waleed M., Wang, Jingwen, Kiong, Jolynn, Lu, Xuehan, Zhang, Jiahui, Lu, Miao, Huang, Wenbin, Kong, Wei Yang, Nahar, Ummey Jannatun, Koirala, Prashamsa, Guo, Zhong, Walden, Patricia, Blumenthal, Antje, Begun, Jakob, Alexandrov, Kirill, Toth, Istvan, Stephenson, Rachel J. and Skwarczynski, Mariusz (2026). Development of a novel polyleucine-based immunopotentiator for subunit vaccines against Group A Streptococcus. Small e11459. doi: 10.1002/smll.202511459
2026
Conference Publication
DEVELOPMENT OF A NEXT GENERATION ENGINEERED LIVE MICROBIOME BIOTHERAPEUTIC, E COLI NISSLE 1917-TTR, FOR ULCERATIVE COLITIS
Horgan, Kevin, Barnett, Jacqueline, Godovannyi, Artem, Usakiewicz, Jacek, Adur, Malavika, Mayer, Emeran, Begun, Jakob and Gibson, Deanna (2026). DEVELOPMENT OF A NEXT GENERATION ENGINEERED LIVE MICROBIOME BIOTHERAPEUTIC, E COLI NISSLE 1917-TTR, FOR ULCERATIVE COLITIS. Crohn's and Colitis Congress, Las Vegas Nv, Jan 22-24, 2026. PHILADELPHIA: W B SAUNDERS CO-ELSEVIER INC.
2026
Journal Article
Pathogenic OTUD3 mutations predispose to ulcerative colitis due to barrier dysfunction
Giri, Rabina, Lee, Minyi, Magor, Graham, Bergot, Anne-Sophie, He, Yaowu, Kryza, Thomas, Khan, Tashbib, Schreiber, Veronika, Gordon, Robert J., Zagani, Rachid, Hasnain, Sumaira Z., Lourie, Rohan, Ewing, Adam, Hooper, John D., Thomas, Ranjeny, Florin, Timothy H., Perkins, Andrew, Gala, Manish and Begun, Jakob (2026). Pathogenic OTUD3 mutations predispose to ulcerative colitis due to barrier dysfunction. Cellular and Molecular Gastroenterology and Hepatology, 20 (2) 101659, 1-20. doi: 10.1016/j.jcmgh.2025.101659
2025
Journal Article
Cost-effective inflammatory bowel disease flare pathway with nurse-led triage and rapid access intestinal ultrasound reduces hospital resource use with high patient satisfaction
Fernandes, Richard Gareth, Khoo, Emi, Jensen Harris, Heidi, Gilmore, Robert, Khaing, Myat Myat, Ennever, Jenny, Mullen, Kaity, Begun, Jakob and An, Yoon-Kyo (2025). Cost-effective inflammatory bowel disease flare pathway with nurse-led triage and rapid access intestinal ultrasound reduces hospital resource use with high patient satisfaction. Journal of Crohn's and Colitis, 19 (12) jjaf221. doi: 10.1093/ecco-jcc/jjaf221
2025
Journal Article
Australian real‐world effectiveness and safety of ustekinumab for the treatment of Crohn's Disease: Results of the AURORA Study, including the ANZIBD Consortium
An, Yoon‐Kyo, Lindsay, Niamh, Allan, Natalie, Khoo, Emi, Fernandes, Richard, Gilmore, Robert, Amiss, Anna, Pham, Hai, Ooi, Soong‐Yuan, Thin, Lena, Lightowler, Daniel, Connor, Susan J., Williams, Astrid, De Cruz, Peter, Li Wai Suen, Christopher F. D., Kariyawasam, Viraj, Mitrev, Nikola, Ghaly, Simon, Andrews, Jane M., Christensen, Britt, Sparrow, Miles P., White, Lauren S., Bryant, Robert, Ding, Nik S., Leong, Rupert W., Van Langenberg, Daniel R., Seltenreich, Hansjoerg, Subramaniam, Kavitha, Radford‐Smith, Graham and Begun, Jakob (2025). Australian real‐world effectiveness and safety of ustekinumab for the treatment of Crohn's Disease: Results of the AURORA Study, including the ANZIBD Consortium. JGH Open, 9 (12) e70322, e70322. doi: 10.1002/jgh3.70322
2025
Journal Article
Patterns and predictors of steroid use in a real-world inflammatory bowel disease cohort
Wu, Rodger, Rivas, Consuelo, Su, Wai Kin, Deschenes, Renée, Wilson, William, Pipicella, Joseph L., Connor, Susan J., Andrews, Jane M., An, Yoon-Kyo, Begun, Jakob, Boyapati, Ray, Dutt, Shoma, Gearry, Richard B, Ghaly, Simon, Haifer, Craig, Lawrance, Ian C, Lynch, Kate, Moore, Gregory, Radford-Smith, Graham, Shahzad, Asif, Schultz, Michael, Su, Heidi, Ng, Watson, Verdon, Christine, Walker, Gareth and Wark, Gabrielle (2025). Patterns and predictors of steroid use in a real-world inflammatory bowel disease cohort. JGH Open, 9 (12) e70308, 1-14. doi: 10.1002/jgh3.70308
2025
Conference Publication
Endotoxemia causes inflammatory bowel diseases-associated anemia and inflammation via TLR4 expressed by CD169+ macrophages
Bisht, Kavita, Zhong, Ruiqing, An, Yoon-Kyo, Shatunova, Svetlana, Wang, Ran, Barbier, Valerie, Tang, Yifu, Giri, Rabina, Amiss, Anna, Alexander, Kylie, Millard, Susan, Pettit, Allison, Winkler, Ingrid, Begun, Jakob and Levesque, Jean-Pierre (2025). Endotoxemia causes inflammatory bowel diseases-associated anemia and inflammation via TLR4 expressed by CD169+ macrophages. 54th Annual Scientific Meeting of the ISEH - International Society for Experimental Hematology, Kumamoto, Japan, 24-27 September 2025. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.exphem.2025.105131
2025
Journal Article
Acute severe ulcerative colitis patients from Asia have lower colectomy risk than patients from Australasia
Fernandes, Richard Gareth, Kim, Dong Hyun, Ruddick-Collins, Leonie, Vasudevan, Abhinav, Brownson, Anthony Robert, Ngoi, Benjamin, Lin, Chun-Chi, Haifer, Craig, Kim, Dae Sung, Swe, Ei, Wright, Emily Kate, Song, Eun Mi, Mahy, Gillian, Moore, Gregory Thomas, Lee, Hyun Seok, Kim, Hyun Soo, Zhang, Jennifer, Yan Mak, Joyce Wing, Lee, Jun, Lynch, Kate, Gazelakis, Kathryn, Rice, Katie, Kim, Kyeong Ok, Liu, Jing, Lilian Bracken, Lucy Mary, Garg, Mayur, Schultz, Michael, Clark, Nicholas, Cao, Qian ... An, Yoon-Kyo (2025). Acute severe ulcerative colitis patients from Asia have lower colectomy risk than patients from Australasia. Clinical Gastroenterology and Hepatology. doi: 10.1016/j.cgh.2025.10.019
2025
Journal Article
Point-of-care intestinal ultrasound impacts inflammatory bowel disease care and reduces the need for additional investigations
Tan, Wei-Lian, Khoo, Emi, Khaing, Myat-Myat, Barr, Emily, Fernandes, Richard G., Pham, Hai, An, Yoon-Kyo and Begun, Jakob (2025). Point-of-care intestinal ultrasound impacts inflammatory bowel disease care and reduces the need for additional investigations. Journal of Gastroenterology and Hepatology, 40 (10), 2472-2481. doi: 10.1111/jgh.70019
2025
Journal Article
Pro-inflammatory macrophages transporting gut-derived bacterial DNA drive autoimmune arthritis in spondyloarthropathy
Cai, Benjamin, Giri, Rabina, Cameron, Amy J., Rahman, M. Arifur, Small, Annabelle, Altmann, Christopher, Lim, Yenkai, Rehaume, Linda M., Morrison, Mark, Wechalekar, Mihir D., Begun, Jakob, Bergot, Anne-Sophie and Thomas, Ranjeny (2025). Pro-inflammatory macrophages transporting gut-derived bacterial DNA drive autoimmune arthritis in spondyloarthropathy. JCI Insight, 10 (17) e188028, 1-19. doi: 10.1172/jci.insight.188028
2025
Conference Publication
Inflammatory bowel disease flares are associated with elevated pathogen prevalence as identified via the MetaPanel metagenomic diagnostic assay
Krause, Lutz, Boyd, Joel, Cooper, Martha, Pribyl, Alena, An, Yoon-Kyo, Begun, Jakob and Cuive, Paraic O. (2025). Inflammatory bowel disease flares are associated with elevated pathogen prevalence as identified via the MetaPanel metagenomic diagnostic assay. HOBOKEN: WILEY.
2025
Journal Article
IBD 2024: charting a new course in IBD Proceedings of the Takeda Symposium 22–23 November 2024 W Hotel, Brisbane, Queensland, Australia
Mahadevan, Uma, Jairath, Vipul, Begun, Jakob, Pudipeddi, Aviv, Garg, Mayur, De Cruz, Peter, Li Wai Suen, Christopher F. D., Choy, Matthew C., Con, Danny, Vaughan, Rose, Chetwood, John D., Clark, David A., Haifer, Craig, Sparrow, Miles P., Leong, Rupert and Mountifield, Réme (2025). IBD 2024: charting a new course in IBD Proceedings of the Takeda Symposium 22–23 November 2024 W Hotel, Brisbane, Queensland, Australia. Journal of Gastroenterology and Hepatology, 40 (S3), 3-22. doi: 10.1111/jgh.70020
2025
Conference Publication
The burden of viral respiratory infections in immunosuppressed inflammatory bowel disease patients
Huynh, David, Khoo, Emi, Anandan, Aathavan Shanmuga and Begun, Jakob (2025). The burden of viral respiratory infections in immunosuppressed inflammatory bowel disease patients. HOBOKEN: WILEY.
2025
Conference Publication
Early faecal calprotectin predicts clinical outcomes in acute severe ulcerative colitis: Results from PREDICT-UC
Suen, Christopher F. D. Li Wai, Choy, Matthew C., Con, Danny, Driver, Kate, Bruen, Dylan, Glason, Joshua, Bonelli, Fabrizio, Bittar, Intissar, Boyd, Kristy, Pena, Raquel, Burrell, Kathryn, Rosella, Ourania, Proud, David, Brouwer, Richard, Gorelik, Alexandra, Liew, Danny, Connell, William, Wright, Emily K., Taylor, Kirstin, Pudipeddi, Aviv, Sawers, Michelle, Christensen, Britt, Ng, Watson, Begun, Jakob, Radford-Smith, Graham, Garg, Mayur, Martin, Neal, van Langenberg, Daniel R., Ding, Nik S. ... De Cruz, Peter (2025). Early faecal calprotectin predicts clinical outcomes in acute severe ulcerative colitis: Results from PREDICT-UC. HOBOKEN: WILEY.
2025
Conference Publication
Comparative accuracy and reliability of handheld versus cart-based ultrasound in assessing inflammatory bowel disease activity
Khaing, Myat Myat, Fernandes, Richard, An, Yoon-Kyo, Baraty, Brandon, Bryant, Robert V., Ghaly, Simon, Smith, Rebecca, Srinivasan, Ashish, Hay, Karen and Begun, Jakob (2025). Comparative accuracy and reliability of handheld versus cart-based ultrasound in assessing inflammatory bowel disease activity. HOBOKEN: WILEY.
2025
Conference Publication
Early serum and faecal infliximab levels predict outcomes after infliximab rescue in acute severe ulcerative colitis: Results from the PREDICT-UC randomised controlled trial
Suen, Christopher F. D. Li Wai, Choy, Matthew C., Con, Danny, Cheng, Kaylene, Nigro, Julie, Breheney, Kerry, Boyd, Kristy, Pena, Raquel, Burrell, Kathryn, Rosella, Ourania, Proud, David, Brouwer, Richard, Gorelik, Alexandra, Liew, Danny, Connell, William, Wright, Emily K., Taylor, Kirstin, Pudipeddi, Aviv, Sawers, Michelle, Christensen, Britt, Ng, Watson, Begun, Jakob, Radford-Smith, Graham L., Garg, Mayur, Martin, Neal, van Langenberg, Daniel R., Ding, Nik S., Beswick, Lauren, Leong, Rupert W. ... De Cruz, Peter (2025). Early serum and faecal infliximab levels predict outcomes after infliximab rescue in acute severe ulcerative colitis: Results from the PREDICT-UC randomised controlled trial. HOBOKEN: WILEY.
2025
Conference Publication
Australian multicentre real-world experience of upadacitinib induction therapy for moderate to severe Crohn's disease
Yeo, Jeremy, Gilmore, Robert, Pham, Lily, Fernandes, Richard, Nguyen, Andrew, Vasudevan, Abhinav, Parkash, Nikita, Moore, Gregory, Christmas, Michael, White, Lauren, Subhaharan, Deloshaan, Mohsen, Waled, Ramaswamy, Pradeep Kakkadasam, Massouridis, Benjamin, Sparrow, Miles P., Ding, John, Lin, Alan, Clark, Nicholas, An, Yoon and Begun, Jakob (2025). Australian multicentre real-world experience of upadacitinib induction therapy for moderate to severe Crohn's disease. HOBOKEN: WILEY.
2025
Conference Publication
Complete disease clearance as a novel composite endpoint to predict long-term relapse in vedolizumab-treated patients with ulcerative colitis: A post-hoc analysis from the VIEWS randomised controlled trial
Pudipeddi, Aviv, Paramsothy, Sudarshan, Kariyawasam, Viraj, Paramsothy, Ramesh, Ghaly, Simon, Haifer, Craig, An, Yoon-Kyo, Begun, Jakob, Connor, Susan J., Corte, Crispin, Ward, Mark G., De Cruz, Peter, Fung, Caroline, Redmond, Diane, Chan, Webber, Mourad, Fadi, Kermeen, Melissa and Leong, Rupert W. (2025). Complete disease clearance as a novel composite endpoint to predict long-term relapse in vedolizumab-treated patients with ulcerative colitis: A post-hoc analysis from the VIEWS randomised controlled trial. HOBOKEN: WILEY.
2025
Journal Article
Upadacitinib induction is effective and safe in ulcerative colitis patients including those with prior exposure to tofacitinib: a multicenter real-world cohort study
Gilmore, Robert, Fernandes, Richard, Hartley, Imogen, Arzivian, Arteen, Leong, Rupert, Andrew, Bridgette, Vasudevan, Abhinav, Greeve, Tessa, Moore, Gregory Thomas, Kim, Steven, Lightowler, Daniel, Singh, Abhey, Mahy, Gillian, Mithanthaya, Aditya, Venugopaul, Kannan, Han, Sangwoo, Bryant, Robert, West, Jack, Segal, Jonathan, Christensen, Britt, Corte, Crispin, Ding, Nik, An, Yoon-Kyo and Begun, Jakob (2025). Upadacitinib induction is effective and safe in ulcerative colitis patients including those with prior exposure to tofacitinib: a multicenter real-world cohort study. Intestinal Research, 23 (3), 347-357. doi: 10.5217/ir.2024.00127
Funding
Current funding
Supervision
Availability
- Associate Professor Jakob Begun is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
Supervision history
Current supervision
-
Doctor Philosophy
Study of TOfacitinib for the treatment of chronic Pouchitis
Principal Advisor
Other advisors: Professor Gerald Holtmann
-
Doctor Philosophy
Reducing post-operative Crohn's disease recurrence
Principal Advisor
Other advisors: Professor David Clark, Dr Rabina Giri
-
Doctor Philosophy
Novel and real-world use of Janus Kinase inhibitors for the management of Inflammatory Bowel Disease
Principal Advisor
-
Master Philosophy
Investigating the Role of JAK Inhibitors in Epithelial and Fibrotic Responses in Inflammatory BowelDisease
Associate Advisor
Other advisors: Dr Rabina Giri
-
Doctor Philosophy
Investigating immunomodulatory function of gut microbiome and FXR pathway in IBD
Associate Advisor
Other advisors: Dr Rabina Giri
-
Doctor Philosophy
Disrupting Immune Responses to Reverse Fibrosis
Associate Advisor
Other advisors: Dr Rabina Giri, Honorary Professor Sumaira Hasnain
-
Doctor Philosophy
Bacteria x Archaea Interactions in Crohn's disease
Associate Advisor
Other advisors: Professor Mark Morrison
-
Doctor Philosophy
Medicinal chemistry of new Nature-inspired treatments for Inflammatory Bowel Disease (IBD)
Associate Advisor
Other advisors: Dr Angela Salim, Professor Rob Capon
Completed supervision
-
2024
Doctor Philosophy
Drugs from Bugs: Harnessing the host-microbe interactions that modulate the immune responses in Inflammatory Bowel Disease
Principal Advisor
Other advisors: Dr Angela Salim, Professor Mark Morrison
-
2024
Doctor Philosophy
Australia Ustekinumab Real-world Observational Research (AURORA)
Principal Advisor
-
2017
Master Philosophy
Delivery of Interleukin-22 using Mesoporous Silica Nanoparticles for the Treatment of Murine Colitis
Principal Advisor
Other advisors: Professor Amirali Popat
-
2026
Doctor Philosophy
Metal-organic frameworks as oral delivery carriers for management of Inflammatory Bowel Disease
Associate Advisor
Other advisors: Dr Rabina Giri, Professor Amirali Popat
-
2024
Doctor Philosophy
Defining the Role of the Mucosa-Associated Microbiota in Digestive Health and Disease Using Novel ex-vivo Combinations of Microbe Culture with Metagenomics
Associate Advisor
Other advisors: Professor Mark Morrison
-
2023
Doctor Philosophy
Structure-function relationships of the mucosa-associated microbiota in Crohn's disease
Associate Advisor
Other advisors: Professor Gerald Holtmann, Professor Mark Morrison
-
2023
Doctor Philosophy
Mindfulness Based Cognitive Therapy for Youth with Inflammatory Bowel Disease and Depression: Understanding Mindfulness in the Context of Depression and Inflammation
Associate Advisor
Other advisors: Professor Steve Kisely
-
2022
Master Philosophy
Targeting Intestinal Epithelial Cell-Derived Interleukin-23 (p19) To Improve Intestinal Barrier Integrity in Inflammatory Bowel Disease
Associate Advisor
Other advisors: Dr Ran Wang, Honorary Professor Sumaira Hasnain
-
2021
Doctor Philosophy
Exploring the gut-liver axis and immunity in paracetamol-induced toxicity
Associate Advisor
Other advisors: Dr Ran Wang
-
2019
Doctor Philosophy
Investigation of Wnt pathway inhibition on host cell control of Listeria monocytogenes infection
Associate Advisor
Other advisors: Professor Antje Blumenthal
Media
Enquiries
Contact Associate Professor Jakob Begun directly for media enquiries about:
- adolescent
- autophagy
- Crohn's disease
- Inflammatory Bowel Disease
- ulcerative colitis
Need help?
For help with finding experts, story ideas and media enquiries, contact our Media team: