Dr Claire O'Brien
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.
Biography
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
Publications
- Williams, G, Tapsell, L, O'Brien, C et al. 2021, 'Gut microbiome responses to dietary intake of grain-based fibers with the potential to modulate markers of metabolic disease: A systematic literature review', Nutrition Reviews, vol. 79, no. 11, pp. 1274-1292.
- CamprubÃ-Font, C, Bustamante, P, Vidal, R et al. 2020, 'Study of a classification algorithm for AIEC identification in geographically distinct E. coli strains', Scientific Reports, vol. 10, no. 1, pp. 1-7.
- Nanayakkara, B, O'Brien, C & Gordon, D 2019, 'Diversity and distribution of Klebsiella capsules in Escherichia coli', Environmental Microbiology Reports, vol. 11, no. 2, pp. 107-117.
- Nanayakkara, B, O'Brien, C & Gordon, D 2019, 'Phenotypic characteristics contributing to the enhanced growth of Escherichia coli bloom strains', Environmental Microbiology Reports, vol. 11, no. 6, pp. 817-824.
- O'Brien, C, Kiely, C & Pavli, P 2018, 'The microbiome of Crohn's disease aphthous ulcers 06 Biological Sciences 0605 Microbiology', Gut Pathogens, vol. 10, no. 44, pp. 8pp.
- Baut, G, O'Brien, C, Pavli, P et al 2018, 'Prevalence of YersiniaSpecies in the Ileum of Crohn's Disease Patients and Controls', Frontiers in Cellular and Infection Microbiology, vol. 8, no. 336, pp. 1-9pp.
- Kiely, C, Pavli, P & O'Brien, C 2018, 'The microbiome of translocated bacterial populations in patients with and without inflammatory bowel disease', Internal Medicine Journal, vol. 48, no. 11, pp. 1346-1354pp.
- Kiely, C, Pavli, P & O'Brien, C 2018, 'The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome', Gut Microbes, vol. 9, no. 6, pp. 477-485pp.
- Dixit, O, O'Brien, C, Pavli, P et al. 2018, 'Within�host evolution versus immigration as a determinant of Escherichia coli diversity in the human gastrointestinal tract', Environmental Microbiology, vol. 20, no. 3, pp. 993-1001pp.
- Kiely, C, Pavli, P & O'Brien, C 2017, 'Bacterial RNA in lymph nodes of patients with inflammatory bowel disease', Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, 2017, John Wiley & Sons Ltd., Australia, pp. 118-119.
- O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlights potential treatment strategies [meeting abstract]', 12th Congress of European Crohn's and Colitis Organisation, ECCO 2017, ed. Laurence J Egan, Oxford University Press, United Kingdom, pp. S470-S470.
- Kiely, C, Pavli, P & O'Brien, C 2017, 'Inflammation and changes in the inflammatory bowel disease microbiome over time', Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, 2017, John Wiley & Sons Ltd., Australia, pp. 118-118.
- O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlight novel therapeutic targets', Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, 2017, John Wiley & Sons Ltd., Australia, pp. 119-119.
- O'Brien, C, Bringer, M, Holt, K et al 2017, 'Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli', Gut, vol. 66, no. 8, pp. 1382-1389.
- Gordon, D, Geyik, S, Clermont, O et al 2017, 'Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection', mSphere, vol. 2, no. 3, pp. 15pp..
- O'Brien, C, Gordon, D & Pavli, P 2016, 'Microbial communities of Crohn's disease aphtous ulcers', 11th Annual Congress of the European Crohn's and Colitis Organisation (ECCO), Oxford University Press, United Kingdom, pp. S488-S489.
- O'Brien, C, Gordon, D & Pavli, P 2016, 'Higher frequency of adherent-invasive Escherichia coli within a sub- group of B2 phylogroup strains', 11th Annual Congress of the European Crohn's and Colitis Organisation (ECCO), Oxford University Press, United Kingdom, pp. S489-S490.
- Gordon, D, O'Brien, C & Pavli, P 2015, 'Escherichia coli diversity in the lower intestinal tract of humans', Environmental Microbiology Reports, vol. 7, no. 4, pp. 642-648.
- Leu, A, Pavli, P, Gordon, D et al 2015, 'Relative abundance of Mycobacterium in ovine Johne's disease', Microbiology Australia, vol. 36, no. 1, pp. 32-36.
- Blyton, M, Herawati, N, O'Brien, C et al 2015, 'Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats', Environmental Microbiology Reports, vol. 7, no. 3, pp. 583-589.
- O'Brien, C, Pavli, P, Gordon, D et al 2014, 'Detection of bacterial DNA in lymph nodes of Crohn's disease patients using high throughput sequencing', Gut, vol. 63, no. 10, pp. 1596-1606.
- O'Brien, C, Allison, G, Grimpen, F et al 2013, 'Impact of Colonoscopy Bowel Preparation on Intestinal Microbiota', PLOS ONE (Public Library of Science), vol. 8, no. 5.
- O'Brien, C, Allison, G & Pavli, P 2013, 'The more the merrier: Faecalibacterium prausnitzii in Crohn's disease', Journal of Gastroenterology and Hepatology, vol. 28, no. 5, pp. 757-759.
- O'Brien, C & Gordon, D 2011, 'Effect of diet and gut dynamics on the establishment and persistence of Escherichia coli', Microbiology (UK), vol. 157, pp. 1375-1384.
- CL O'Brien, GE Allison, P Pavli, JE Dahlstrom (2011). Molecular profiling of bacterial DNA isolated from formalin-fixed paraffin-embedded tissue: a comparative study (Abstract only). Pathology (2011) 43(S1), pp. S87-S108.
- CL O'Brien, F Grimpen, GE Allison, P Pavli (2010). Effect of colonoscopy bowel preparation on intestinal bacteria. Syntrophy, Vol. 11, 8.
- Clermont, O, Lescat, M, O'Brien, C et al 2008, 'Evidence for a human-specific Escherichia coli clone', Environmental Microbiology, vol. 10, no. 4, pp. 1000-1006.
- Gordon, D & O'Brien, C 2006, 'Bacteriocin diversity and the frequency of multiple bacteriocin production in Escherichia coli', Microbiology (UK), vol. 152, pp. 3239-3244.
Projects and Grants
Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.
- Host-microbe cross-talk in Crohn's disease (Primary Investigator)
- NHMRC Equipment Grant (see 27886) (Primary Investigator)
- Host-microbe interactions in Crohn's disease (Primary Investigator)
- France-Australia Science Innovation Collaboration (FASIC) Program - Early Career Fellowships 2013 (Primary Investigator)
