Dr Claire O'Brien

NHMRC Peter Doherty Fellow, Medical School
ANU College of Health and Medicine
T: +61 2 6244 4023

Areas of expertise

  • Bacteriology 060501
  • Microbial Ecology 060504
  • Medical Microbiology 1108
  • Medical Bacteriology 110801
  • Gastroenterology And Hepatology 110307

Research interests

Claire's main research interests are host-microbe interactions in the inflammatory bowel diseases; understanding how perturbations of the gut microbiota relate to health and disease in humans; and the genetics of Escherichia coli.


Dr Claire O’Brien obtained her Bachelor of Science (Biology, First Class) at the Australian National University (ANU) in 2005.  She was awarded an ANU Summer Research, and ANU Honours Scholarship.  For her Honours year she investigated the effect of diet and gut dynamics on the establishment and persistence of Escherichia coli.  Claire undertook her PhD at the Australian National University Medical School under the supervision of Professor Paul Pavli, and invesitigated the role of microbes in Crohn’s disease.  She was awarded her PhD in 2012.  In 2013, Claire was awarded an Australian Academy of Science France-Australia Science Innovation Collaboration (FASIC) Early Career Fellowship.  Claire is currently an NHMRC Peter Doherty Biomedical Research Fellow at the ANU Medical School.  She is an active participant in CSIRO's Scientists and Mathematicians in Schools program, and is a 'local champion' for Crohn's & Colitis Australia.  


Researcher's projects

Host colonisation of microbes in the lower gastrointestinal tract.

Whole genome comparison of E. coli urinary tract infection isolates

Host-microbe interactions over the course of Crohn's disease

Transcriptome analyses of monocyte-derived macrophages from patients with Crohn's disease and their siblings in response to bacterial stimuli

Comparative genome analysis of Crohn's disease-associated adherent, invasive E. coli



Available student projects

Please email me about the possibility of doing Honours, higher degree by research (Masters/PhD), or Medical School research projects.  Collaborative projects are welcome.


Current student projects

Whole genome sequencing of patients with primary sclerosing cholangitis-inflammatory bowel disease and their parents to identify novel mutations

Detection of bacterial RNA in lymph nodes isolated from bowel resections

Whole genome comparisons of E. coli strains isolated from lymph nodes of patients with Crohn's disease

Temporal changes in the mucosal microbiome of patients with Crohn's disease

Monocyte-bacteria interactions in an in vitro transwell system


Past student projects

Diversity of mucosa-associated E. coli along the lower gastrointestinal tract

In silico analysis of the distribution and frequency of bacteriocins in Escherichia coli isolated from Crohn's disease tissues

Antibiotic resistance in Escherichia coli isolated from Crohn's disease patients

Mycobacterium avium subspecies paratuberculosis-specific PCR screening of Crohn's disease mucosa and lymph nodes

The relative abundance of Mycobacterium avium subspecies paratuberculosis (MAP) in Johne's disease

The distribution and role of fimH in host and disease adaptation


Projects and Grants

Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.

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Updated:  13 June 2024 / Responsible Officer:  Director (Research Services Division) / Page Contact:  Researchers