The mucosal microbiome of inflammatory bowel diseases

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dc.check.date10000-01-01
dc.check.embargoformatE-thesis on CORA onlyen
dc.check.entireThesisEntire Thesis Restricted
dc.check.infoIndefiniteen
dc.check.opt-outYesen
dc.check.reasonReleasing this thesis would cause substantial prejudice to the commercial interests of the sponsor of the postgraduate researchen
dc.contributor.advisorClaesson, Marcusen
dc.contributor.authorRyan, Feargal J.
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderHealth Research Boarden
dc.contributor.funderEuropean Molecular Biology Laboratoryen
dc.contributor.funderIntelligent Systems for Molecular Biologyen
dc.contributor.funderSecond Genome Inc., United Statesen
dc.date.accessioned2017-02-08T09:30:07Z
dc.date.issued2016
dc.date.submitted2016
dc.description.abstractThe human microbiome is the diverse community of micro-organisms that live with humans. The gut microbiome contains the densest collection of microbial cells in the body and has been described as functioning as an organ. Alterations in these microbial communities are associated with disease. This work provides a new methodology for the taxonomic assignment of 16S rRNA gene sequencing data, then utilises this and other cutting edge techniques to elucidate the mucosal associated microbiome in Inflammatory Bowel Disease and finally examines the viability of using mucosal samples for shotgun metagenomics or metatranscriptomics. Taxonomic classification is a corner stone for the characterisation of microbial communities, but currently many studies are limited to genus level classification. Thus, we developed SPINGO, a flexible and stand-alone software dedicated to species level assignment of 16S rRNA gene sequences. SPINGO outperforms other methods in terms of classification accuracy, and is as fast or faster than those that have higher error rates. Crohn’s Disease (CD) and Ulcerative Colitis (UC) are Inflammatory Bowel Diseases (IBD) which cause inflammation along the gastrointestinal tract of millions of people worldwide. By collecting paired colonic pinch biopsies from inflamed and noninflamed tissue from IBD patients and paired healthy biopsies from healthy individuals we reveal a gradient between IBD and healthy controls that is associated with inflammation. Differential abundance analysis reveals a total of 89 taxa in this cohort to be different between CD and UC when compared to healthy controls. Clustering of these samples reveals discrete groups which may provide a frame-work for sub-typing IBD based on the microbiota. Microbiome scientists frequently rely on faecal samples as a proxy for the colonic environment despite numerous studies finding that it is not completely representative. Here we assess the potential of using colonic pinch biopsies for profiling the metagenome and metatranscriptome of the mucosal associated microbiota. We find that current methodologies are not capable of adequately separating microbial and human DNA or RNA resulting in as few as 1 – 2% of microbial reads after sequencing.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Version
dc.format.mimetypeapplication/pdfen
dc.identifier.citationRyan, F. 2016. The mucosal microbiome of inflammatory bowel diseases. PhD Thesis, University College Cork.en
dc.identifier.endpage148en
dc.identifier.urihttps://hdl.handle.net/10468/3566
dc.language.isoenen
dc.publisherUniversity College Corken
dc.rights© 2016, Feargal Ryan.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/en
dc.subjectMicrobiomeen
dc.subjectBioinformaticsen
dc.subjectMetagenomicsen
dc.subjectInflammatory bowel diseaseen
dc.thesis.opt-outtrue
dc.titleThe mucosal microbiome of inflammatory bowel diseasesen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD (Food Science and Technology)en
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