
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
2025
Journal Article
SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome
Tillett, Bree J., Dwiyanto, Jacky, Secombe, Kate R., George, Thomas, Zhang, Vivian, Anderson, Dovile, Duggan, Emily, Giri, Rabina, Loo, Dorothy, Stoll, Thomas, Morrison, Mark, Begun, Jakob, Hill, Michelle M., Gurzov, Esteban N., Bell, Kirstine J., Saad, Sonia, Barlow, Christopher K., Creek, Darren J., Chong, Chun Wie, Mariño, Eliana and Hamilton-Williams, Emma E. (2025). SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome. Nature Communications, 16 (1) 2893, 1-20. doi: 10.1038/s41467-025-58319-y
2025
Journal Article
Cannabidiol targets colorectal cancer cells via cannabinoid receptor 2, independent of common mutations
Moniruzzaman, Md, Wong, Kuan Yau, Janjua, Taskeen Iqbal, Martin, Jennifer H., Begun, Jakob and Popat, Amirali (2025). Cannabidiol targets colorectal cancer cells via cannabinoid receptor 2, independent of common mutations. ACS Pharmacology and Translational Science, 8 (2), 543-556. doi: 10.1021/acsptsci.4c00644
2025
Journal Article
Guselkumab in patients with moderately to severely active ulcerative colitis (QUASAR): phase 3 double-blind, randomised, placebo-controlled induction and maintenance studies
Rubin, David T., Allegretti, Jessica R, Panés, Julián, Shipitofsky, Nicole, Yarandi, Shadi S, Huang, Kuan-Hsiang Gary, Germinaro, Matthew, Wilson, Rebbecca, Zhang, Hongyan, Johanns, Jewel, Feagan, Brian G, Hisamatsu, Tadakazu, Lichtenstein, Gary R, Bressler, Brian, Peyrin-Biroulet, Laurent, Sands, Bruce E, Dignass, Axel, Abrahamovych, Orest, Abu-Farsakh, Niazy, Afanasieva, Halyna, Akpinar, Hale, Kharrat, Houssam Al, Altintas, Engin, Altwegg, Romain, Andreev, Pavel, Aomatsu, Kazuki, Araki, Hiroshi, Argollo, Marjorie, Ariel, Federico ... Zureikat, Firas (2025). Guselkumab in patients with moderately to severely active ulcerative colitis (QUASAR): phase 3 double-blind, randomised, placebo-controlled induction and maintenance studies. The Lancet, 405 (10472), 33-49. doi: 10.1016/S0140-6736(24)01927-5
2025
Journal Article
Upadacitinib was administered as a sequential salvage therapy for acute severe ulcerative colitis: a case report
Huynh, David, Khaing, Myat Myat, Fernandes, Richard Gareth, Malloy, Reuben, Lin, Lei, Gilmore, Robert, Walker, Nicole, Khoo, Emi and Begun, Jakob (2025). Upadacitinib was administered as a sequential salvage therapy for acute severe ulcerative colitis: a case report. Case Reports in Gastroenterology, 19 (1), 1-6. doi: 10.1159/000542711
2025
Journal Article
Epidemiology and Treatment Patterns of Fistulizing Crohn's Disease in a Large, Real-World Australasian Cohort
McNamara, Jack, Wilson, William, Pipicella, Joseph L., Ghaly, Simon, Begun, Jakob, Lawrance, Ian C., Gearry, Richard, Andrews, Jane M. and Connor, Susan J. (2025). Epidemiology and Treatment Patterns of Fistulizing Crohn's Disease in a Large, Real-World Australasian Cohort. Gastro Hep Advances, 4 (4) 100594, 100594. doi: 10.1016/j.gastha.2024.100594
2025
Conference Publication
Handheld ultrasound devices are an accurate alternative to cart-based ultrasound for IBD disease activity assessment
Fernandes, R., Swe, E., Khaing, M. M., Gilmore, R., Khoo, E., An, Y. K. and Begun, J. (2025). Handheld ultrasound devices are an accurate alternative to cart-based ultrasound for IBD disease activity assessment. 20th Congress of ECCO, Berlin, Germany, 19-22 February 2025. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjae190.1349
2025
Conference Publication
P0112 Cannabidiol (CBD) targeting of colorectal cancer cells is mutation-independent and via CB2 receptor
Moniruzzaman, M., Janjua, T., Begun, J. and Popat, A. (2025). P0112 Cannabidiol (CBD) targeting of colorectal cancer cells is mutation-independent and via CB2 receptor. 20th Congress of ECCO, Berlin, Germany, 19-22 February 2025. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjae190.0286
2024
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 (2024). 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. doi: 10.5217/ir.2024.00127
2024
Journal Article
Does improving depression symptoms in young adults with inflammatory bowel disease alter their microbiome?
Davies, Julie M., Teh, Jing Jie, Ewais, Tatjana and Begun, Jakob (2024). Does improving depression symptoms in young adults with inflammatory bowel disease alter their microbiome?. Inflammatory Bowel Diseases, 30 (12), 2428-2439. doi: 10.1093/ibd/izae121
2024
Conference Publication
Endotoxemia As Possible Cause of Inflammatory Bowel Diseases-Associated Anemia
Bisht, Kavita, An, Yoon-Kyo, Shatunova, Svetlana, Wang, Ran, Barbier, Valerie, Giri, Rabina, Amiss, Anna, Tang, Yifu, Alexander, Kylie, Millard, Susan, Winkler, Ingrid G., Pettit, Allison, Begun, Jakob and Levesque, Jean-Pierre (2024). Endotoxemia As Possible Cause of Inflammatory Bowel Diseases-Associated Anemia. 66th ASH Annual Meeting, San Diego, CA United States, 7-10 December 2024. Washington, DC United States: American Society of Hematology. doi: 10.1182/blood-2024-193349
2024
Journal Article
Optimizing 5-aminosalicylate for moderate ulcerative colitis: expert recommendations from the Asia-Pacific, Middle East, and Africa Inflammatory Bowel Disease Coalition
Akyüz, Filiz, An, Yoon Kyo, Begun, Jakob, Aniwan, Satimai, Bui, Huu Hoang, Chan, Webber, Choi, Chang Hwan, Chopdat, Nazeer, Connor, Susan J, Desai, Devendra, Flanagan, Emma, Kobayashi, Taku, Lai, Allen Yu-Hung, Leong, Rupert W, Leow, Alex Hwong-Ruey, Leung, Wai Keung, Limsrivilai, Julajak, Muzellina, Virly Nanda, Peddi, Kiran, Ran, Zhihua, Wei, Shu Chen, Sollano, Jose, Teo, Michelle Mui Hian, Wu, Kaichun, Ye, Byong Duk and Ooi, Choon Jin (2024). Optimizing 5-aminosalicylate for moderate ulcerative colitis: expert recommendations from the Asia-Pacific, Middle East, and Africa Inflammatory Bowel Disease Coalition. Intestinal Research, 23 (1), 37-55. doi: 10.5217/ir.2024.00089
2024
Journal Article
Effects of thiopurine withdrawal on vedolizumab-treated patients with ulcerative colitis: a randomized 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 Lan-San, Redmond, Diane, Chan, Webber, Mourad, Fadi, Kermeen, Melissa and Leong, Rupert W. (2024). Effects of thiopurine withdrawal on vedolizumab-treated patients with ulcerative colitis: a randomized controlled trial. Clinical Gastroenterology and Hepatology, 22 (11), 2299-2308. doi: 10.1016/j.cgh.2024.04.019
2024
Journal Article
Intensified versus standard dose infliximab induction therapy for steroid-refractory acute severe ulcerative colitis (PREDICT-UC): an open-label, multicentre, randomised controlled trial
Choy, Matthew C., Li Wai Suen, Christopher F. D., Con, Danny, Boyd, Kristy, Pena, Raquel, Burrell, Kathryn, Rosella, Ourania, Proud, David, Brouwer, Richard, Gorelik, Alexandra, Liew, Danny, Connell, William R., Wright, Emily K., Taylor, Kirstin M., Pudipeddi, Aviv, Sawers, Michelle, Christensen, Britt, Ng, Watson, Begun, Jakob, Radford-Smith, Graham, Garg, Mayur, Martin, Neal, van Langenberg, Daniel R., Ding, Nik S., Beswick, Lauren, Leong, Rupert W., Sparrow, Miles P. and De Cruz, Peter (2024). Intensified versus standard dose infliximab induction therapy for steroid-refractory acute severe ulcerative colitis (PREDICT-UC): an open-label, multicentre, randomised controlled trial. The Lancet Gastroenterology & Hepatology, 9 (11), 981-996. doi: 10.1016/s2468-1253(24)00200-0
2024
Journal Article
Defining mucosal healing in randomized controlled trials of inflammatory bowel disease: a systematic review and future perspective
Parigi, Tommaso Lorenzo, Solitano, Virginia, Armuzzi, Alessandro, Acosta, Manuel Barreiro de, Begun, Jake, Ben-Horin, Shomron, Biedermann, Luc, Colombel, Jean-Frederic, Dignass, Axel, Fumery, Mathurin, Ghosh, Subrata, Kobayashi, Taku, Louis, Edouard, Magro, Fernando, Panaccione, Remo, Rausch, Astrid, Reinisch, Walter, Selinger, Christian, Jairath, Vipul, Danese, Silvio and Peyrin-Biroulet, Laurent (2024). Defining mucosal healing in randomized controlled trials of inflammatory bowel disease: a systematic review and future perspective. United European Gastroenterology Journal, 12 (9), 1266-1279. doi: 10.1002/ueg2.12671
2024
Journal Article
International expert guidance for defining and monitoring small bowel strictures in Crohn's disease on intestinal ultrasound: a consensus statement
Lu, Cathy, Rosentreter, Ryan, Parker, Claire E, Remillard, Julie, Wilson, Stephanie R, Baker, Mark E, Bhatnagar, Gauraang, Begun, Jakob, Bruining, David H, Bryant, Robert V, Christensen, Britt, Feagan, Brian G, Fletcher, Joel G, Gordon, Ilyssa, Henderson, Gaylyn, Jairath, Vipul, Knudsen, John, Kucharzik, Torsten, Lesack, Kyle, Maaser, Christian, Maconi, Giovanni, Novak, Kerri, Rimola, Jordi, Taylor, Stuart A, Wilkens, Rune and Rieder, Florian (2024). International expert guidance for defining and monitoring small bowel strictures in Crohn's disease on intestinal ultrasound: a consensus statement. The Lancet Gastroenterology & Hepatology, 9 (12), 1101-1110. doi: 10.1016/s2468-1253(24)00265-6
2024
Conference Publication
The Efficacy of Maintenance Treatment with Guselkumab in Patients With Moderately to Severely Active Ulcerative Colitis: Phase 3 QUASAR Maintenance Study Results at Week 44 by Biologic/Janus Kinase History
Allegretti, Jessica R., Panés, Julián, Peyrin-Biroulet, Laurent, Sands, Bruce E., Yarandi, Shadi, Huang, Kuan-Hsiang G., Germinaro, Matthew, Zhan, Jia, Zhang, Hongyan, Begun, Jakob, Kierkuś, Jarosław, Kravchenko, Tetiana, Hisamatsu, Tadakazu, Rubin, David T., Bressler, Brian and Dignass, Axel (2024). The Efficacy of Maintenance Treatment with Guselkumab in Patients With Moderately to Severely Active Ulcerative Colitis: Phase 3 QUASAR Maintenance Study Results at Week 44 by Biologic/Janus Kinase History. 2024 ACG Annual Meeting, Philadelphia, PA United States, 25-30 October 2024. Philadelphia, PA United States: Lippincott Williams & Wilkins. doi: 10.14309/01.ajg.0001034328.68326.43
2024
Journal Article
Group B Streptococcus vaginal colonisation throughout pregnancy is associated with decreased Lactobacillus crispatus and increased Lactobacillus iners abundance in the vaginal microbial community
Maidment, Toby I., Pelzer, Elise S., Borg, Danielle J., Cheung, Eddie, Begun, Jake, Nitert, Marloes Dekker, Rae, Kym M., Clifton, Vicki L. and Carey, Alison J. (2024). Group B Streptococcus vaginal colonisation throughout pregnancy is associated with decreased Lactobacillus crispatus and increased Lactobacillus iners abundance in the vaginal microbial community. Frontiers in Cellular and Infection Microbiology, 14 1435745, 1-11. doi: 10.3389/fcimb.2024.1435745
2024
Conference Publication
A cross section of inflammatory bowel disease management in older persons in Australasia: Crohn's Colitis Cure (CCC) data insights program
Seng, Crystal, Su, Wai Kin, Wilson, William, Haifer, Craig, Williams, Astrid-Jane, Forbes, Angela, Lawrance, Ian, Lynch, Kate, Brett, Laurel, Begun, Jakob, Connor, Susan J., Andrews, Jane and Walker, Gareth (2024). A cross section of inflammatory bowel disease management in older persons in Australasia: Crohn's Colitis Cure (CCC) data insights program. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2024, Adelaide, SA Australia, 14-16 September 2024. Richmond, VIC Australia: John Wiley & Sons.
2024
Conference Publication
Efficacy of combination vedolizumab and upadacitinib treatment in refractory inflammatory bowel disease: a case series
Swe, Ei Phyu Phyu, Gilmore, Robert, Murali, Amrutha, Etchegaray, Amirah, Fernandes, Richard, An, Yoon-Kyo and Begun, Jakob (2024). Efficacy of combination vedolizumab and upadacitinib treatment in refractory inflammatory bowel disease: a case series. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2024, Adelaide, SA Australia, 14-16 September 2024. Richmond, VIC Australia: John Wiley & Sons.
2024
Conference Publication
Janus kinase inhibitors for the management of acute severe ulcerative colitis: An Australian multicentre study
Gilmore, Robert, Fernandes, Richard, Subhaharan, Deloshaan, Mohsen, Waled, Thin, Lena, Chin, Simone, Con, Danny, De Cruz, Peter, Demase, Kathryn, Sparrow, Miles P., Lucas, Sarah, Garg, Mayur, Bryant, Robert, Segal, Jonathan, Christensen, Britt, Begun, Jakob and An, Yoon-Kyo (2024). Janus kinase inhibitors for the management of acute severe ulcerative colitis: An Australian multicentre study. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2024, Adelaide, SA Australia, 14-16 September 2024. Richmond, VIC Australia: John Wiley & Sons.
Funding
Current funding
Supervision
Availability
- Associate Professor Jakob Begun is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Supervision history
Current supervision
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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
-
Doctor Philosophy
Microbial Regulation of Host Inflammatory Pathways in Inflammatory Bowel Disease
Principal Advisor
Other advisors: Professor Mark Morrison
-
Doctor Philosophy
Study of TOfacitinib for the treatment of chronic Pouchitis
Principal Advisor
Other advisors: Professor Gerald Holtmann
-
Doctor Philosophy
Medicinal chemistry of new Nature-inspired treatments for Inflammatory Bowel Disease (IBD)
Associate Advisor
Other advisors: Dr Angela Salim, Dr Zeinab Khalil, Professor Rob Capon
-
Doctor Philosophy
Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics
Associate Advisor
Other advisors: Dr Md Moniruzzaman, Professor Amirali Popat
-
Doctor Philosophy
Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics
Associate Advisor
Other advisors: Dr Md Moniruzzaman, Professor Amirali Popat, Dr Rabina Giri
-
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
-
Doctor Philosophy
Investigating immunomodulatory function of gut microbiome and FXR pathway in IBD
Associate Advisor
Other advisors: Dr Rabina Giri
-
Doctor Philosophy
Bacteria x Archaea Interactions in Crohn's disease
Associate Advisor
Other advisors: Professor Mark Morrison
Completed supervision
-
2024
Doctor Philosophy
Australia Ustekinumab Real-world Observational Research (AURORA)
Principal Advisor
-
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
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2017
Master Philosophy
Delivery of Interleukin-22 using Mesoporous Silica Nanoparticles for the Treatment of Murine Colitis
Principal Advisor
Other advisors: 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
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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
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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
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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
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2021
Doctor Philosophy
Exploring the gut-liver axis and immunity in paracetamol-induced toxicity
Associate Advisor
Other advisors: Dr Ran Wang
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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
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