Microbiota, diet and medication in human gut disorders

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dc.contributor.advisor Claesson, Marcus en
dc.contributor.advisor Sleator, Roy en
dc.contributor.advisor O'Driscoll, Aisling en
dc.contributor.advisor Shanahan, Fergus en
dc.contributor.author Clooney, Adam G.
dc.date.accessioned 2018-02-13T12:42:33Z
dc.date.issued 2017
dc.date.submitted 2017
dc.identifier.citation Clooney, A. 2017. Microbiota, diet and medication in human gut disorders. PhD Thesis, University College Cork. en
dc.identifier.endpage 197 en
dc.identifier.uri http://hdl.handle.net/10468/5453
dc.description.abstract The microbiota, a community of micro-organisms in a particular environment, have been intensely researched in the past decade and interest appears to continue to increase. The human body is richly populated with bacterial cells (3.8x1013) and alterations in these communities are associated with disease. Microbiota research lacks standardised approaches to experimental design and data analysis due to rapidly evolving techniques and software. We conducted a comparison between various approaches in both amplicon and shotgun metagenomics sequencing using various primer binding regions and next generation sequencers. We found disparities between both 16S rRNA gene variable regions and metagenomic sequencing techniques, the latter of which was due to the taxonomic classifier. We emphasise the requirement for careful study design and caution when comparing microbiota studies. Proton Pump Inhibitors are prescribed to prevent gastric reflux and duodenal ulcers but concern has been raised due to associations with C. difficile infection. We assessed the microbiota of long-term PPI users versus controls, but found no similarities to the microbiota of C. diff infection. However we did uncover microbial alterations including by a decrease in biodiversity and an increase in Holdemania filiformis along with a decrease in Pseudoflabonifractor capillosus in the PPI microbiota. Changes in the gut microbiota have been associated with IBD, although there is disparity between the alterations. We conducted the largest longitudinal IBD microbiota study to date. We compared the microbiota of patients with IBD in both active and inactive disease states to controls. Although we found significant differences in biodiversity and taxonomic composition between patients with IBD and controls, there was a lack of significant change between disease activity states. However, there was a significant decrease in microbiota stability in patients with altering disease activity. Age, diet, medications, resection and geographical location significantly impacted the gut microbiota in both diversity and composition. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2017, Adam Clooney. en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Microbiome en
dc.subject Inflammatory bowel disease en
dc.subject Proton pump inhibitor en
dc.subject Microbiota en
dc.title Microbiota, diet and medication in human gut disorders en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral Degree (Structured) en
dc.type.qualificationname PhD (Science) en
dc.internal.availability Full text not available en
dc.check.info Indefinite en
dc.check.date 10000-01-01
dc.description.version Accepted Version
dc.contributor.funder Science Foundation Ireland en
dc.description.status Not peer reviewed en
dc.internal.school Microbiology en
dc.internal.school Alimentary Pharmabiotic Centre en
dc.check.reason This thesis is due for publication or the author is actively seeking to publish this material en
dc.check.opt-out No en
dc.thesis.opt-out false
dc.check.entireThesis Entire Thesis Restricted
dc.check.embargoformat Both hard copy thesis and e-thesis en
ucc.workflow.supervisor m.claesson@ucc.ie
dc.internal.conferring Spring 2018 en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/ en


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© 2017, Adam Clooney. Except where otherwise noted, this item's license is described as © 2017, Adam Clooney.
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