IHMRI affiliation

Theme:Chronic Conditions and Lifestyle

Research focus

  • Gut microbiome
  • Bowel diseases
  • Medical microbiology


Publications and funding

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  • CIA, Philanthropic, Host-microbe interactions in Crohn’s disease, ($277,000) 2019-2020
  • CIA, Gastroenterological Society of Australia, Genetic-microbiome interactions in primary sclerosing cholangitis-IBD, ($50,000) 2019
  • CI, Gastroenterological Society of Australia, Australian IBD Microbiome (AIM), ($50,000) 2019
  • Chief Investigator, Gastroenterological Society of Australia Collaboration grant ($50, 000) 2018
  • IBD Sydney+ Consortia member, Gastroenterological Society of Australia grant ($50, 001) 2018
  • Chief Investigator, South Western Sydney Local Health District Academic Unit Enhancement grant entitled ‘Gut and the microbiome: Role in health and disease’ ($1,050,000), 2018
  • Chief Investigator, ANU Major Equipment Grant ($100,000), 2018
  • Philanthropic funding, Canberra Hospital Foundation ($277, 000), 2018
  • Chief Investigator, Gastroenterological Society of Australia/Takeda 180 Research grant ($25, 000), 2017
  • NHMRC Peter Doherty Biomedical Early Career Research Fellowship (2015 – 2018), ($309,436)


  • B Nanayakkara, CL O’Brien, DM Gordon (2018). The diversity and distribution of Klebsiella capsules in f. coli and their association with E. coli isolated from Australian water blooms. Environ Microbial Rep. Nov 8.
  • G Le Baul, CL O’Brien (lead co-author), P Pavli, M Roy, P Seksik, X Treton, S Nancey, N Bamich, M Bezault, C Auzolle, D Cazal-Hatem, J Vialal, M Allez, JP Hugot, A Dumay (2018). Prevalence of Yersinia species in the ileum of Crohn’s disease patients and controls. Front Microbial, Sep 21; 8:336.
  • CL O’Brien, CJ Kiely, P Pavli (2018). The microbiome of Crohn’s disease aphthous ulcers. Gut Pathogens, Oct 10.
  • CJ Kiely, P Pav1i, CL O’Brien (2018). Inflammation and changes in the IBD microbiome over time. Gut Microbes. Mar 15:1-25.
  • OVA, Dixit, CL O’Brien, P Pavli, DM Gordon (2018). Within-host evolution versus immigration as a detenninant of Escherichia coli diversity in the human gastrointestinal tract. Environ Microbial. Mar;20(3):993-1001.
  • DM Gordon, S Geyik, 0 Clermont, CL O’Brien, S Huang, C Abayasekara, A Rajesh, K Kennedy, P Pavli, C Rodriguez, BD Johnston, JR Johnson, J Decousser, E Denamur (2017). Pandemic or epidemic? Fine-scale Structure in a cosmopolitan Escherichia coli lineage responsible for extra-intestinal infection. mSphere. May 31;2(3).
  • CL O’Brien, MA Bringer, KE Holt, DM Gordon, AL Dubois, N Bamich, A Darfeuille­Michaud, P Pavli (2016). Comparative genomics of Crohn’s disease-associated adherent-invasive Escherichia coli. Gut. Aug;66(8):1382-1389. lnvited by the Chief Editor of Gut to submit a video abstract for the journal’s website.
  • DM Gordon, CL O’Brien, P Pavli (2015). Escherichia.coli diversity in the lower intestinal tract of humans. Environ Microbial Rep. Aug;7(4):642-8
  • MD Slyton, N Herawati, CL O’Brien, and DM Gordon (2015). Host litter associated dynamics affect Escherichia coli abundance and adhesion genotype in rats. Environ Microbiol Rep. Jun;7(3):583-9.
  • CL OBrien, P Pavli, DM Gordon, GE Allison (2015). Detection of bacterial DNA in lymph nodes of Crohn’s disease patients using high-throughput sequencing. Gut. Oct;63(10):1596-606


  • Member, Gastroenterological Society of Australia Research Workshop Organising Committee (2018-)
  • ‘Local Champion’ Crohn’s and Colitis Australia
  • ANU Medical School custodian for the Network of Early Career Teachers and Academic
  • University House Early Career Academic Fellow, ANU (2016 – 2019)
  • Member, Sydney+ Inflammatory Bowel Disease (IBD) Consortium
  • Member, CSIRO’s Scientists In Schools program (2008-2019)