Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes

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dc.contributor.advisor Hill, Colin en
dc.contributor.advisor Sleator, Roy D. en
dc.contributor.advisor Marchesi, Julian R. en
dc.contributor.author Culligan, Eamonn P. en
dc.date.accessioned 2015-01-19T09:49:42Z
dc.date.available 2015-01-19T09:49:42Z
dc.date.issued 2014
dc.date.submitted 2014
dc.identifier.citation Culligan, E. P. 2014. Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes. PhD Thesis, University College Cork. en
dc.identifier.endpage 286
dc.identifier.uri http://hdl.handle.net/10468/1758
dc.description.abstract The ability to adapt to and respond to increases in external osmolarity is an important characteristic that enables bacteria to survive and proliferate in different environmental niches. When challenged with increased osmolarity, due to sodium chloride (NaCl) for example, bacteria elicit a phased response; firstly via uptake of potassium (K+), which is known as the primary response. This primary response is followed by the secondary response which is characterised by the synthesis or uptake of compatible solutes (osmoprotectants). The overall osmotic stress response is much broader however, involving many diverse cellular systems and processes. These ancillary mechanisms are arguably more interesting and give a more complete view of the osmotic stress response. The aim of this thesis was to identify novel genetic loci from the human gut microbiota that confer increased tolerance to osmotic stress using a functional metagenomic approach. Functional metagenomics is a powerful tool that enables the identification of novel genes from as yet uncultured bacteria from diverse environments through cloning, heterologous expression and phenotypic identification of a desired trait. Functional metagenomics does not rely on any previous sequence information to known genes and can therefore enable the discovery of completely novel genes and assign functions to new or known genes. Using a functional metagenomic approach, we have assigned a novel function to previously annotated genes; murB, mazG and galE, as well as a putative brp/blh family beta-carotene 15,15’-monooxygenase. Finally, we report the identification of a completely novel salt tolerance determinant with no current known homologues in the databases. Overall the genes identified originate from diverse taxonomic and phylogenetic groups commonly found in the human gastrointestinal (GI) tract, such as Collinsella and Eggerthella, Akkermansia and Bacteroides from the phyla Actinobacteria, Verrucomicrobia and Bacteroidetes, respectively. In addition, a number of the genes appear to have been acquired via lateral gene transfer and/or encoded on a prophage. To our knowledge, this thesis represents the first investigation to identify novel genes from the human gut microbiota involved in the bacterial osmotic stress response. en
dc.description.sponsorship Science Foundation Ireland (SFI Grant 07/CE/B1368) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2014. Eamonn P. Culligan en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Microbiology en
dc.subject Metagenomics en
dc.subject Functional metagenomics en
dc.subject Gut microbiota en
dc.subject Human gut microbiome en
dc.subject Bacterial stress response en
dc.subject Bacterial salt tolerance en
dc.subject Novel gene discovery en
dc.title Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes 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.check.info No embargo required en
dc.description.version Accepted Version
dc.contributor.funder Science Foundation Ireland en
dc.description.status Not peer reviewed en
dc.internal.school Alimentary Pharmabotic Centre en
dc.internal.school Microbiology en
dc.check.type No Embargo Required
dc.check.reason No embargo required en
dc.check.opt-out Not applicable en
dc.thesis.opt-out false
dc.check.embargoformat Not applicable en
ucc.workflow.supervisor c.hill@ucc.ie
dc.internal.conferring Summer Conferring 2014


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© 2014. Eamonn P. Culligan Except where otherwise noted, this item's license is described as © 2014. Eamonn P. Culligan
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