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
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. doi: 10.3389/fcimb.2024.1435745
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
Reliability of intestinal ultrasound for evaluating Crohn’s disease activity using point-of-care and central reading
Goodsall, Thomas M., An, Yoon-Kyo, Andrews, Jane M., Begun, Jakob, Friedman, Antony B., Lee, Andrew, Lewindon, Peter J., Spizzo, Paul, Rodgers, Nick, Taylor, Kirstin M., White, Lauren S., Wilkens, Rune, Wright, Emily K., Zou, Lily, Maguire, Bryan R., Parker, Claire E., Rémillard, Julie, Novak, Kerri L., Panaccione, Remo, Feagan, Brian G., Jairath, Vipul, Ma, Christopher and Bryant, Robert V. (2024). Reliability of intestinal ultrasound for evaluating Crohn’s disease activity using point-of-care and central reading. Clinical Gastroenterology and Hepatology. doi: 10.1016/j.cgh.2024.08.007
2024
Journal Article
A truncation mutant of adenomatous polyposis coli impairs apical cell extrusion through elevated epithelial tissue tension
Gan, Wan J., Giri, Rabina, Begun, Jakob, Abud, Helen E., Hardeman, Edna C., Gunning, Peter W., Yap, Alpha S. and Noordstra, Ivar (2024). A truncation mutant of adenomatous polyposis coli impairs apical cell extrusion through elevated epithelial tissue tension. Cytoskeleton. doi: 10.1002/cm.21893
2024
Journal Article
Impact of a Patient Support Program on time to discontinuation of adalimumab in Australian adult patients with immunemediated inflammatory diseases-an observational study
Jones, Graeme, Calao, Miriam, Begun, Jakob, Sin, Shirley, Kouhkamari, Mahsa H., Young, Elisa, Fernández-Peñas, Pablo, Watts, Alan and Östör, Andrew J. (2024). Impact of a Patient Support Program on time to discontinuation of adalimumab in Australian adult patients with immunemediated inflammatory diseases-an observational study. PLoS One, 19 (6 June) e0300624. doi: 10.1371/journal.pone.0300624
2024
Journal Article
High technical success rate of endoscopic balloon dilatation reduces surgical requirement for patients with stricturing Crohn’s disease
Lim, Emily, Thai, Maxter, An, Yoon-Kyo, Hendy, Peter, Alchlaihawi, Mahmoud, Leong, Rupert, Connor, Susan, Ng, Watson, Gu, Bonita, Thin, Lena, Sparrow, Miles, Gilmore, Robert, Taylor, Kirstin, Sallis, Olivia, Andrews, Jane M., Daker, Charlotte, Gearry, Richard B., Wark, Gabrielle, Ghaly, Simon, Begun, Matt, Krishnaprasad, Krupa, Wu, Tianhong, Ruddick-Collins, Leonie, Schreiber, Veronika, Okano, Satomi, Radford-Smith, Graham, Schulberg, Julien, van Langenberg, Daniel and Begun, Jakob (2024). High technical success rate of endoscopic balloon dilatation reduces surgical requirement for patients with stricturing Crohn’s disease. GastroHep, 2024 (1) 3686618, 1-10. doi: 10.1155/2024/3686618
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. doi: 10.1093/ibd/izae121
2024
Conference Publication
Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis
Khoo, Emi, Amiss, Anna, Ding, Nik S., Bryant, Robert V., Mohsen, Waled, Connor, Susan J., Leong, Rupert, Croft, Anthony, Lynch, Kate D., Sparrow, Miles, De Cruz, Peter, An, Yoon-Kyo, Holtmann, Gerald J. and Begun, Jakob (2024). Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis. Digestive Disease Week (DDW) 2024, Washington, DC, United States, 18-21 May 2024. Philadelphia, PA, United States: Elsevier. doi: 10.1016/s0016-5085(24)00988-0
2024
Conference Publication
A Cost-effective Inflammatory Bowel Disease Flare Management Pathway Utilising Rapid Access Intestinal Ultrasound And Nurse-led Triage To Achieve Hospital Avoidance With High Patient Satisfaction
Fernandes, Richard G., Khoo, Emi, Harris, Heidi Jensen, Gilmore, Robert, Khaing, Myat Myat, Begun, Jakob and An, Yoon-Kyo (2024). A Cost-effective Inflammatory Bowel Disease Flare Management Pathway Utilising Rapid Access Intestinal Ultrasound And Nurse-led Triage To Achieve Hospital Avoidance With High Patient Satisfaction. Digestive Disease Week (DDW) 2024, Chicago, IL United States, 18-21 May 2024. Philadelphia, PA United States: Elsevier BV. doi: 10.1016/s0016-5085(24)01652-4
2024
Conference Publication
Variation In Outcomes In Inflammatory Bowel Disease At Ten Australasian Centres - Crohn's Colitis Cure (CCC) Data Insights Program
McNamara, Jack, Wilson, William E., Pipicella, Joseph L., Ghaly, Simon, Gearry, Richard, Begun, Jakob, Ng, Watson, Lynch, Kate D., Lawrance, Ian C., Schultz, Michael, Walker, Gareth J., Radford-Smith, Graham L., Andrews, Jane M. and Connor, Susan J. (2024). Variation In Outcomes In Inflammatory Bowel Disease At Ten Australasian Centres - Crohn's Colitis Cure (CCC) Data Insights Program. Digestive Disease Week (DDW) 2024, Chicago, IL United States, 18-21 May 2024. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(24)02405-3
2024
Conference Publication
The Real-world Use Of Five-aminosalicylate (5ASA) Treatment For Ulcerative Colitis In Australia And New Zealand: Crohn's Colitis Cure (CCC) Data Insight's Program
Pipicella, Joseph L., McNamara, Jack, Wilson, William E., Lynch, Kate D., Walker, Gareth J., Begun, Jakob, Lawrance, Ian C., Ghaly, Simon, Radford-Smith, Graham L., Williams, Astrid-Jane, Gearry, Richard, Schultz, Michael, Brett, Laurel, Andrews, Jane M. and Connor, Susan J. (2024). The Real-world Use Of Five-aminosalicylate (5ASA) Treatment For Ulcerative Colitis In Australia And New Zealand: Crohn's Colitis Cure (CCC) Data Insight's Program. Digestive Disease Week (DDW) 2024, Chicago, IL United States, 18-21 May 2024. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(24)03792-2
2024
Conference Publication
Dose Escalated Infliximab In Inflammatory Bowel Disease - Crohn's Colitis Cure (CCC) Data Insights Program
Alshiwanna, Basheer, McNamara, Jack, Wilson, William E., Pipicella, Joseph L., Ghaly, Simon, Gearry, Richard, Begun, Jakob, Williams, Astrid-Jane, Lynch, Kate D., Lawrance, Ian C., Schultz, Michael, Walker, Gareth J., Radford-Smith, Graham L., Connor, Susan J. and Andrews, Jane M. (2024). Dose Escalated Infliximab In Inflammatory Bowel Disease - Crohn's Colitis Cure (CCC) Data Insights Program. Digestive Disease Week (DDW) 2024, Chicago, IL United States, 18-21 May 2024. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(24)03074-9
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.e5. doi: 10.1016/j.cgh.2024.04.019
2024
Conference Publication
Dose Escalated Ustekinumab In Inflammatory Bowel Disease - Crohn's Colitis Cure (CCC) Data Insights Program
Barnett, Meghan I., McNamara, Jack, Wilson, William E., Pipicella, Joseph L., Ghaly, Simon, Gearry, Richard, Begun, Jakob, Williams, Astrid-Jane, Lynch, Kate D., Lawrance, Ian C., Schultz, Michael, Walker, Gareth J., Radford-Smith, Graham L., Connor, Susan J. and Andrews, Jane M. (2024). Dose Escalated Ustekinumab In Inflammatory Bowel Disease - Crohn's Colitis Cure (CCC) Data Insights Program. Digestive Disease Week (DDW) 2024, Chicago, IL United States, 18-21 May 2024. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(24)03072-5
2024
Journal Article
Systematic review: defining, diagnosing and monitoring small bowel strictures in Crohn's disease on intestinal ultrasound
Lu, Cathy, Rosentreter, Ryan, Delisle, Maxime, White, Mattie, Parker, Claire E., Premji, Zahra, Wilson, Stephanie R., Baker, Mark E., Bhatnagar, Gauraang, Begun, Jakob, Bruining, David H., Bryant, Robert, Christensen, Britt, Feagan, Brian G., Fletcher, Joel G., Jairath, Vipul, Knudsen, John, Kucharzik, Torsten, Maaser, Christian, Maconi, Giovanni, Novak, Kerri, Rimola, Jordi, Taylor, Stuart A., Wilkens, Rune, Rieder, Florian and The Stenosis Therapy and Anti‐Fibrotic Research (STAR) consortium (2024). Systematic review: defining, diagnosing and monitoring small bowel strictures in Crohn's disease on intestinal ultrasound. Alimentary Pharmacology and Therapeutics, 59 (8), 928-940. doi: 10.1111/apt.17918
2024
Journal Article
Vedolizumab and ustekinumab levels in pregnant women with inflammatory bowel disease and infants exposed in-utero
Prentice, Ralley, Flanagan, Emma, Wright, Emily K., Gibson, Peter R., Rosella, Sam, Rosella, Ourania, Begun, Jakob, An, Yoon-Kyo, Lawrance, Ian C., Kamm, Michael A., Sparrow, Miles, Goldberg, Rimma, Prideaux, Lani, Vogrin, Sara, Kiburg, Katerina V., Ross, Alyson L., Burns, Megan and Bell, Sally J. (2024). Vedolizumab and ustekinumab levels in pregnant women with inflammatory bowel disease and infants exposed in-utero. Clinical Gastroenterology and Hepatology. doi: 10.1016/j.cgh.2024.02.025
2024
Conference Publication
Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis
Khoo, E., Amiss, A., Ding, J. N., Bryant, R., Mohsen, W., Connor, S., Leung, R., Croft, A., Lynch, K., Sparrow, M., De Cruz, P., An, Y. K., Holtmann, G. and Begun, J. (2024). Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis. 19th Congress of ECCO, Stockholm, Sweden, 21-24 February 2024. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjad212.0984
2024
Conference Publication
Upadacitinib is safe and effective in Ulcerative Colitis patients with prior exposure to Tofacitinib
Gilmore, R., Fernandes, R., Hartley, I., Arzivian, A., Leong, R., Andrew, B., Vasudevan, A., Greeve, T., Moore, G., Kim, S., Lightowler, D., Singh, A., Mahy, G., Mithanthaya, A., Venugpal, K., Han, S., Bryant, R., West, J., Segal, J., Christensen, B., Ding, N. J., An, Y. K. and Begun, J. (2024). Upadacitinib is safe and effective in Ulcerative Colitis patients with prior exposure to Tofacitinib. 19th Congress of ECCO, Stockholm, Sweden, 21-24 February 2024. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjad212.1194
2024
Conference Publication
Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis
Khoo, E., Amiss, A., Ding, J. N., Bryant, R., Mohsen, W., Connor, S., Leung, R., Croft, A., Lynch, K., Sparrow, M., De Cruz, P., An, Y. K., Holtmann, G. and Begun, J. (2024). Tofacitinib demonstrates preliminary efficacy in induction of remission in chronic pouchitis. 19th Congress of ECCO, Stockholm, Sweden, 21-24 February 2024. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjad212.0984
2024
Conference Publication
Risk of infection after acute severe ulcerative colitis in East Asia and Australia/New Zealand: AOCC and ANZIBDC collaboration study
Kim, S. J., Kim, D. H., Park, S. H., Kim, K. O., Lee, Y. J., Song, E. M., Kim, E. S., Lee, H. S., An, Y. K., Begun, J., Ruddick-Collins, L., Fernandes, R., Liu, J., Cao, Q., Kobayashi, T. and Wei, S. C. (2024). Risk of infection after acute severe ulcerative colitis in East Asia and Australia/New Zealand: AOCC and ANZIBDC collaboration study. 19th Congress of ECCO, Stockholm, Sweden, 21-24 February 2024. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjad212.0892
Funding
Current funding
Past 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
-
Doctor Philosophy
Reducing post-operative Crohn's disease recurrence
Principal Advisor
Other advisors: Professor David Clark
-
Doctor Philosophy
A randomised, open-label, non-inferiority study of upadacitinib compared with oral prednisolone
Principal Advisor
-
Doctor Philosophy
Microbial Regulation of Host Inflammatory Pathways in Inflammatory Bowel Disease
Principal Advisor
Other advisors: Professor Mark Morrison, Dr Anuj Sehgal
-
Doctor Philosophy
Study of TOfacitinib for the treatment of chronic Pouchitis
Principal Advisor
Other advisors: Professor Gerald Holtmann
-
Doctor Philosophy
Study of TOfacitinib for the treatment of chronic Pouchitis
Principal Advisor
Other advisors: Professor Gerald Holtmann
-
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, 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, Associate Professor Amirali Popat
-
Doctor Philosophy
Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics
Associate Advisor
Other advisors: Dr Md Moniruzzaman, Associate Professor Amirali Popat
-
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
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
-
2017
Master Philosophy
Delivery of Interleukin-22 using Mesoporous Silica Nanoparticles for the Treatment of Murine Colitis
Principal Advisor
Other advisors: Associate 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, Dr 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: