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Associate Professor Jakob Begun
Associate Professor

Jakob Begun

Email: 

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

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

209 works between 1996 and 2025

121 - 140 of 209 works

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

A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy

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

Gut microbiota shape the inflammatory response in mice with an epithelial defect

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

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

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

Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease

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

Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study

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

Switching Australian patients with moderate to severe inflammatory bowel disease from originator to biosimilar infliximab: a multicentre, parallel cohort study

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

One‐pot synthesis of pH‐responsive eudragit‐mesoporous silica nanocomposites enable colonic delivery of glucocorticoids for the treatment of inflammatory bowel disease

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

Monitoring inflammatory bowel disease in pregnancy using gastrointestinal ultrasonography

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.

Curdlan-induced villous permeability, luminal pathobiont translocation to the ileal crypts, ileitis and arthritis are mitigated by clostridia in colonised germ-free SKG mice

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

Vedolizumab for ulcerative colitis: Real world outcomes from a multicenter observational cohort of Australia and Oxford

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

Practical management of inflammatory bowel disease patients during the COVID-19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty

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

The future of faecal microbiota transplantation in gastrointestinal illness

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

Aeromedical retrievals for gastrointestinal disorders in rural and remote Australia: the need for improved access to specialist advice

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

Australian consensus statements for the regulation, production and use of faecal microbiota transplantation in clinical practice

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

Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease

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

Infliximab, adalimumab and vedolizumab concentrations across pregnancy and vedolizumab concentrations in infants following intrauterine exposure

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

Secreted microbial metabolites modulate gut immunity and inflammatory tone

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

MHC class II antigen presentation by the intestinal epithelium initiates graft-versus-host disease and is influenced by the microbiota

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

Malnutrition and quality of life among adult inflammatory bowel disease patients

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

Faecal calprotectin testing for identifying patients with organic gastrointestinal disease: systematic review and meta‐analysis

Funding

Current funding

  • 2024 - 2026
    Gut Health anti-inflammatory potential of Yumbah abalone and mussels
    Marine Bioproducts Cooperative Research Centre
    Open grant
  • 2024 - 2027
    Harnessing microbial immunomodulatory function to improve treatment of inflammatory bowel diseases
    NHMRC IDEAS Grants
    Open grant
  • 2023 - 2028
    Immunity, Infection and Inflammation Program at MRI-UQ
    Mater Foundation
    Open grant
  • 2023 - 2025
    Understanding the regulation and function of OTUD3, a novel ulcerative colitis gene
    The Gutsy Group Inflammatory Bowel Disease Research Grants
    Open grant

Past funding

  • 2023 - 2025
    Epithelial tissue mechanics: a new key to relapse in chronic inflammatory bowel disease
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2021 - 2024
    Drugs from Bugs: Developing New Inflammatory Bowel Disease Drugs from Gut Bacteria-Derived Bioactives
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2020 - 2021
    Functionally characterizing IBD dysbiosis and harnessing gut bioactives to suppress IL-23 driven inflammation
    The Global Grants for Gut Health
    Open grant
  • 2019
    Improving IBD treatment through harnessing the microbiome and improving outcomes in young adults with IBD
    Ferguson Foundation (Reginald Ferguson)
    Open grant
  • 2018 - 2020
    Mater Health Services IBD Biobank
    Research Donation Generic
    Open grant
  • 2018 - 2022
    The regulatory role of Clec12A in antigen presentation and inflammatory disease (NHMRC Project Grant led by Monash University)
    Monash University
    Open grant
  • 2017 - 2020
    Invention of a Genetic Toolkit for Immunomodulatory Gut Bacteria to Expedite the Development of New Crohn's Disease Therapeutics
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2017
    Identification of novel genetic causes of ulcerative colitis to inform individualised treatment
    Sylvia and Charles Viertel Charitable Foundation
    Open grant
  • 2015 - 2016
    Improving IBD treatment through an understanding of genetics and obstacles to adolescent care
    Ferguson Foundation (Reginald Ferguson)
    Open grant
  • 2014 - 2015
    Towards an oral IL-22 agonist for ulcerative colitis
    Ferring Research Institute
    Open grant

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

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:

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