
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
2021
Journal Article
A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy
Sheng, Yong Hua, Giri, Rabina, Davies, Julie, Schreiber, Veronika, Alabbas, Saleh, Movva, Ramya, He, Yaowu, Wu, Andy, Hooper, John, McWhinney, Brett, Oancea, Iulia, Kijanka, Gregor, Hasnain, Sumaira, Lucke, Andrew J., Fairlie, David P., McGuckin, Michael A., Florin, Timothy H. and Begun, Jakob (2021). A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy. Cellular and Molecular Gastroenterology and Hepatology, 11 (1), 33-53. doi: 10.1016/j.jcmgh.2020.05.012
2021
Journal Article
Gut microbiota shape the inflammatory response in mice with an epithelial defect
Wang, Ran, Moniruzzaman, Md, Wong, Kuan Yau, Wiid, Percival, Harding, Alexa, Giri, Rabina, Tong, Wendy Hui, Creagh, Jackie, Begun, Jakob, McGuckin, Michael A. and Hasnain, Sumaira Z. (2021). Gut microbiota shape the inflammatory response in mice with an epithelial defect. Gut microbes, 13 (1), 1-18. doi: 10.1080/19490976.2021.1887720
2021
Journal Article
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
Klionsky, Daniel J., Abdel-Aziz, Amal Kamal, Abdelfatah, Sara, Abdellatif, Mahmoud, Abdoli, Asghar, Abel, Steffen, Abeliovich, Hagai, Abildgaard, Marie H., Abudu, Yakubu Princely, Acevedo-Arozena, Abraham, Adamopoulos, Iannis E., Adeli, Khosrow, Adolph, Timon E., Adornetto, Annagrazia, Aflaki, Elma, Agam, Galila, Agarwal, Anupam, Aggarwal, Bharat B., Agnello, Maria, Agostinis, Patrizia, Agrewala, Javed N., Agrotis, Alexander, Aguilar, Patricia V., Ahmad, S. Tariq, Ahmed, Zubair M., Ahumada-Castro, Ulises, Aits, Sonja, Aizawa, Shu, Akkoc, Yunus ... Tong, Chun-Kit (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy, 17 (1), 1-382. doi: 10.1080/15548627.2020.1797280
2020
Journal Article
Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease
Krishnaprasad, Krupa, Walsh, Alissa, Begun, Jakob, Bell, Sally, Carter, David, Grafton, Rachel, Sechi, Alexandra, Sewell, Karen, McMahon, Anna, Connor, Susan, Radford-Smith, Graham and Andrews, Jane M. (2020). Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease. Scandinavian Journal of Gastroenterology, 55 (12), 1419-1426. doi: 10.1080/00365521.2020.1839960
2020
Journal Article
Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study
Ewais, Tatjana, Begun, Jake, Kenny, Maura, Headey, Alan, Tefay, Merilyn and Kisely, Steve (2020). Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study. BMJ Open, 10 (11) e041140, e041140. doi: 10.1136/bmjopen-2020-041140
2020
Journal Article
Switching Australian patients with moderate to severe inflammatory bowel disease from originator to biosimilar infliximab: a multicentre, parallel cohort study
Haifer, Craig, Srinivasan, Ashish, An, Yoon‐Kyo, Picardo, Sherman, Langenberg, Daniel, Menon, Shankar, Begun, Jakob, Ghaly, Simon and Thin, Lena (2020). Switching Australian patients with moderate to severe inflammatory bowel disease from originator to biosimilar infliximab: a multicentre, parallel cohort study. Medical Journal of Australia, 214 (3) mja2.50824, 128-133. doi: 10.5694/mja2.50824
2020
Journal Article
One‐pot synthesis of pH‐responsive eudragit‐mesoporous silica nanocomposites enable colonic delivery of glucocorticoids for the treatment of inflammatory bowel disease
Qu, Zhi, Wong, Kuan Yau, Moniruzzaman, Md., Begun, Jakob, Santos, Hélder A, Hasnain, Sumaira Z., Kumeria, Tushar, McGuckin, Michael A. and Popat, Amirali (2020). One‐pot synthesis of pH‐responsive eudragit‐mesoporous silica nanocomposites enable colonic delivery of glucocorticoids for the treatment of inflammatory bowel disease. Advanced Therapeutics, 4 (2) 2000165, 2000165. doi: 10.1002/adtp.202000165
2020
Journal Article
Monitoring inflammatory bowel disease in pregnancy using gastrointestinal ultrasonography
Flanagan, Emma, Wright, Emily K., Begun, Jakob, Bryant, Robert V., An, Yoon-Kyo, Ross, Alyson L., Kiburg, Katerina V. and Bell, Sally J. (2020). Monitoring inflammatory bowel disease in pregnancy using gastrointestinal ultrasonography. Journal of Crohn's and Colitis, 14 (10), 1405-1412. doi: 10.1093/ecco-jcc/jjaa082
2020
Conference Publication
Curdlan-induced villous permeability, luminal pathobiont translocation to the ileal crypts, ileitis and arthritis are mitigated by clostridia in colonised germ-free SKG mice
Bergot, Anne-Sophie, Giri, Rabina, Cameron, Amy, Duggan, Emily, Loayza, Jeimy Jimenez, Morrison, Mark, Rehaume, Linda, Begun, Jakob and Thomas, Ranjeny (2020). Curdlan-induced villous permeability, luminal pathobiont translocation to the ileal crypts, ileitis and arthritis are mitigated by clostridia in colonised germ-free SKG mice. Annual Meeting of the American-College-of-Rheumatology (ACR), Virtual, 5-9 November 2020. Hoboken, NJ USA: John Wiley & Sons.
2020
Journal Article
Vedolizumab for ulcerative colitis: Real world outcomes from a multicenter observational cohort of Australia and Oxford
Reddy Pulusu, Samba Siva, Srinivasan, Ashish, Krishnaprasad, Krupa, Cheng, Daniel, Begun, Jakob, Keung, Charlotte, Van Langenberg, Daniel, Thin, Lena, Mogilevski, Tamara, de Cruz, Peter, Radford-Smith, Graham, Flanagan, Emma, Bell, Sally, Kashkooli, Soleiman, Sparrow, Miles, Ghaly, Simon, Bampton, Peter, Sawyer, Elise, Connor, Susan, Rizvi, Quart-Ul-Ain, Andrews, Jane M., Mahy, Gillian, Chivers, Paola, Travis, Simon and CraigLawrance, Ian (2020). Vedolizumab for ulcerative colitis: Real world outcomes from a multicenter observational cohort of Australia and Oxford. World Journal of Gastroenterology, 26 (30), 4428-4441. doi: 10.3748/WJG.V26.I30.4428
2020
Journal Article
Practical management of inflammatory bowel disease patients during the COVID-19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty
Aysha, Al-Ani, Rentsch, Clarissa, Prentice, Ralley, Johnson, Doug, Bryant, Robert V., Ward, Mark G., Costello, Samuel P., Lewindon, Peter, Ghaly, Simon, Connor, Susan J., Begun, Jakob and Christensen, Britt (2020). Practical management of inflammatory bowel disease patients during the COVID-19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty. Internal Medicine Journal, 50 (7), 798-804. doi: 10.1111/imj.14889
2020
Journal Article
The future of faecal microbiota transplantation in gastrointestinal illness
Reed, Hayley and Begun, Jakob (2020). The future of faecal microbiota transplantation in gastrointestinal illness. Microbiology Australia, 41 (2), 70-74. doi: 10.1071/ma20027
2020
Journal Article
Aeromedical retrievals for gastrointestinal disorders in rural and remote Australia: the need for improved access to specialist advice
Gardiner, Fergus W, Bishop, Lara, McMahon, Kathryn, Nwose, Ezekiel U, Connor, Susan, Begun, Jakob and Andrews, Jane M. (2020). Aeromedical retrievals for gastrointestinal disorders in rural and remote Australia: the need for improved access to specialist advice. Internal medicine journal, 50 (5), 619-623. doi: 10.1111/imj.14822
2020
Journal Article
Australian consensus statements for the regulation, production and use of faecal microbiota transplantation in clinical practice
Haifer, Craig, Kelly, Colleen R., Paramsothy, Sudarshan, Andresen, David, Papanicolas, Lito E., McKew, Genevieve L., Borody, Thomas J., Kamm, Michael, Costello, Samuel P., Andrews, Jane M., Begun, Jakob, Chan, Hiu Tat, Connor, Susan, Ghaly, Simon, Johnson, Paul D. R., Lemberg, Daniel A., Paramsothy, Ramesh, Redmond, Andrew, Sheorey, Harsha, van der Poorten, David and Leong, Rupert W. (2020). Australian consensus statements for the regulation, production and use of faecal microbiota transplantation in clinical practice. Gut, 69 (5) 320260, 801-810. doi: 10.1136/gutjnl-2019-320260
2020
Conference Publication
Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease
Giri, R., Shamsunnahar, K., Salim, A., Capon, R., Morrison, M., Cuiv, P. O. and Begun, J. (2020). Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease. 15th Congress of ECCO, Vienna, Austria, 12-15 February 2020. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjz203.035
2020
Journal Article
Infliximab, adalimumab and vedolizumab concentrations across pregnancy and vedolizumab concentrations in infants following intrauterine exposure
Flanagan, Emma, Gibson, Peter R., Wright, Emily K., Moore, Gregory T., Sparrow, Miles P., Connell, William, Kamm, Michael A., Begun, Jakob, Christensen, Britt, De Cruz, Peter, Shelton, Edward, Dowling, Damian, Andrews, Jane M., Brown, Steven J., Niewiadomski, Olga, Ward, Mark G., Rosella, Ourania, Rosella, Gennaro, Kiburg, Katerina V., Ross, Alyson L. and Bell, Sally J. (2020). Infliximab, adalimumab and vedolizumab concentrations across pregnancy and vedolizumab concentrations in infants following intrauterine exposure. Alimentary Pharmacology and Therapeutics, 52 (10), 1551-1562. doi: 10.1111/apt.16102
2019
Other Outputs
Secreted microbial metabolites modulate gut immunity and inflammatory tone
Giri, Rabina, Hoedt, Emily C., Shamsunnahar, Khushi, McGuckin, Michael A., Morrison, Mark, Capon, Robert J., Begun, Jakob and Cuív, Páraic Ó (2019). Secreted microbial metabolites modulate gut immunity and inflammatory tone. doi: 10.1101/2019.12.16.861872
2019
Journal Article
MHC class II antigen presentation by the intestinal epithelium initiates graft-versus-host disease and is influenced by the microbiota
Koyama, Motoko, Mukhopadhyay, Pamela, Schuster, Iona S., Henden, Andrea S., Hülsdünker, Jan, Varelias, Antiopi, Vetizou, Marie, Kuns, Rachel D., Robb, Renee J., Zhang, Ping, Blazar, Bruce B., Thomas, Ranjeny, Begun, Jakob, Waddell, Nicola, Trinchieri, Giorgio, Zeiser, Robert, Clouston, Andrew D., Degli-Esposti, Mariapia A. and Hill, Geoffrey R. (2019). MHC class II antigen presentation by the intestinal epithelium initiates graft-versus-host disease and is influenced by the microbiota. Immunity, 51 (5), 885-898. doi: 10.1016/j.immuni.2019.08.011
2019
Journal Article
Malnutrition and quality of life among adult inflammatory bowel disease patients
Pulley, Jessica, Todd, Alwyn, Flatley, Christopher and Begun, Jakob (2019). Malnutrition and quality of life among adult inflammatory bowel disease patients. JGH Open, 4 (3), 454-460. doi: 10.1002/jgh3.12278
2019
Journal Article
Faecal calprotectin testing for identifying patients with organic gastrointestinal disease: systematic review and meta‐analysis
An, Yoon‐Kyo, Prince, David, Gardiner, Fergus, Neeman, Teresa, Linedale, Ecushla C., Andrews, Jane M., Connor, Susan and Begun, Jakob (2019). Faecal calprotectin testing for identifying patients with organic gastrointestinal disease: systematic review and meta‐analysis. Medical Journal of Australia, 211 (10) mja2.50384, 461-467. doi: 10.5694/mja2.50384
Funding
Current funding
Supervision
Availability
- Associate Professor Jakob Begun is:
- Available for supervision
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Supervision history
Current supervision
-
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
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
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
-
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
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: 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
-
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
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