Microbiota, diet and medication in human gut disorders

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Date
2017
Authors
Clooney, Adam G.
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University College Cork
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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.
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Keywords
Microbiome , Inflammatory bowel disease , Proton pump inhibitor , Microbiota
Citation
Clooney, A. 2017. Microbiota, diet and medication in human gut disorders. PhD Thesis, University College Cork.