Antibiotic resistance in the gut microbiota

Show simple item record

dc.contributor.advisor Cotter, Paul D. en
dc.contributor.advisor Stanton, Catherine en
dc.contributor.advisor Ross, R. Paul en
dc.contributor.advisor Fitzgerald, Gerald F. en
dc.contributor.author Fouhy, Fiona
dc.date.accessioned 2017-01-06T12:39:38Z
dc.date.issued 2014
dc.date.submitted 2014
dc.identifier.citation Fouhy F. M. 2014. Antibiotic resistance in the gut microbiota. PhD Thesis, University College Cork. en
dc.identifier.endpage 437 en
dc.identifier.uri http://hdl.handle.net/10468/3440
dc.description.abstract Antibiotic resistance is an increasing threat to our ability to treat infectious diseases. Thus, understanding the effects of antibiotics on the gut microbiota, as well as the potential for such populations to act as a reservoir for resistance genes, is imperative. This thesis set out to investigate the gut microbiota of antibiotic treated infants compared to untreated controls using high-throughput DNA sequencing. The results demonstrated the significant effects of antibiotic treatment, resulting in increased proportions of Proteobacteria and decreased proportions of Bifidobacterium. The species diversity of bifidobacteria was also reduced. This thesis also highlights the ability of the human gut microbiota to act as an antibiotic resistance reservoir. Using metagenomic DNA extracted from faecal samples from adult males, PCR was employed to demonstrate the prevalence and diversity of aminoglycoside and β-lactam resistance genes in the adult gut microbiota and highlighted the merits of the approach adopted. Using infant faecal samples, we constructed and screened a second fosmid metagenomic bank for the same families of resistance genes and demonstrated that the infant gut microbiota is also a reservoir for resistance genes. Using in silico analysis we highlighted the existence of putative aminoglycoside and β-lactam resistance determinants within the genomes of Bifidobacterium species. In the case of the β- lactamases, these appear to be mis-annotated. However, through homologous recombination-mediated insertional inactivation, we have demonstrated that the putative aminoglycoside resistance proteins do contribute to resistance. In additional studies, we investigated the effects of short bowel syndrome on infant gut microbiota, the immune system and bile acid metabolism. We also sequenced the microbiota of the human vermiform appendix, highlighting its complexity. Finally, this thesis demonstrated the strain specific nature of 2 different probiotic CLA-producing Bifidobacterium breve on the murine gut microbiota. en
dc.description.sponsorship Irish Research Council (EMBARK initiative); Teagasc (Walsh Fellowship) en
dc.format.mimetype application/pdf en
dc.language English en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2014, Fiona Mary Fouhy. en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Bifidobacterium en
dc.subject Antibiotics en
dc.subject High throughput sequencing en
dc.subject Gut microbiota en
dc.subject Infant en
dc.subject Antibiotic resistance en
dc.subject Metagenomics en
dc.title Antibiotic resistance in the gut microbiota en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD (Science) en
dc.internal.availability Full text available en
dc.description.version Accepted Version
dc.contributor.funder Irish Research Council en
dc.contributor.funder Teagasc en
dc.description.status Not peer reviewed en
dc.internal.school Microbiology en
dc.internal.school Teagasc 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 Not applicable en
dc.thesis.opt-out false
dc.check.chapterOfThesis Chapters 5, Appendix 2 and Appendix 3
dc.check.embargoformat Both hard copy thesis and e-thesis en
ucc.workflow.supervisor g.fitzgerald@ucc.ie
dc.internal.conferring Summer 2015 en


Files in this item

This item appears in the following Collection(s)

Show simple item record

© 2014, Fiona Mary Fouhy. Except where otherwise noted, this item's license is described as © 2014, Fiona Mary Fouhy.
This website uses cookies. By using this website, you consent to the use of cookies in accordance with the UCC Privacy and Cookies Statement. For more information about cookies and how you can disable them, visit our Privacy and Cookies statement