Functional genomics of commensal Lactobacilli

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dc.contributor.advisor O'Toole, Paul W. en
dc.contributor.advisor Ross, R. Paul en
dc.contributor.author O'Donnell, Michelle M.
dc.date.accessioned 2014-05-12T15:19:46Z
dc.date.issued 2014
dc.date.submitted 2014
dc.identifier.citation O'Donnell, M. M. 2014. Functional genomics of commensal Lactobacilli. PhD Thesis, University College Cork. en
dc.identifier.endpage 328
dc.identifier.uri http://hdl.handle.net/10468/1558
dc.description.abstract Catabolic flexibility affords a bacterium the ability to utilise different sugar sources as carbon for energy. This is important for commensal lactobacilli like Lactobacillus ruminis which can be exposed to a variety of carbohydrates in vivo. However, little is known about the fermentation capabilities, metabolic pathways, genetic diversity or potential survival mechanisms used by L. ruminis in vivo. A combination of in vitro and in silico techniques was used to identify the catabolic pathways of L. ruminis. I also compared 16 L. ruminis strains using a panel of biochemical and survival assays, genetically, whole genome sequencing and RNA sequencing. Multi locus sequence typing revealed that strains clustered according to their host sources. Transcriptome analysis by RNAseq of two motile strains under three growth conditions, including swarming, identified the up-regulation of carbohydrate-related genes under swarming conditions. This suggests that carbohydrate flexibility may have an uncharacterised role in L. ruminis swarming. Following on from the assessment of L. ruminis catabolic flexibility, the porcine diet was supplemented with galactooligosaccharides or L. ruminis ATCC 25644 plus galactooligosaccharides. Supplementation of the porcine diet with galactooligosaccharide had no effect on microbiota diversity. In contrast, the L. ruminis plus galactooligosaccharide treatment significantly reduced the microbiota diversity. Diet is a major factor that affects the diversity of the gut microbiota. In order to get a more thorough understanding of diet and gut health in animals such as racehorses and domesticated herbivores, I determined the core microbiota of animals consuming different feeds. Interestingly, the gut microbiota diversity correlated with the host phylogeny of the animal. The genome of Lactobacillus equi (2.19 Mb), isolated from a healthy Irish thoroughbred was also sequenced and annotated, and comprised 2,263 predicted genes. The large repertoire of predicted carbohydrate-related genes may offer L. equi an advantage in the complex and harsh hindgut environment. In summary, this thesis uses functional genomics to assess the effect that carbohydrates have on commensal lactobacilli and the microbiota as a whole. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2014, Michelle M. O' Donnell en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Lactobacillus en
dc.subject Lactobacillus ruminis en
dc.subject Diet en
dc.subject Microbiota en
dc.subject Catabolic flexibility en
dc.subject Lactobacillus salivarius clade en
dc.title Functional genomics of commensal Lactobacilli 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 Science Foundation Ireland en
dc.contributor.funder Teagasc
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 No en
dc.thesis.opt-out false
dc.check.chapterOfThesis 4,5,6
dc.check.embargoformat Both hard copy thesis and e-thesis en
ucc.workflow.supervisor pwotoole@ucc.ie
dc.internal.conferring Summer Conferring 2014
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Principal Investigator Programme (PI)/07/IN.1/B1780/IE/Functional genomics of two commensal lactobacilli from humans and animals/


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© 2014, Michelle M. O' Donnell Except where otherwise noted, this item's license is described as © 2014, Michelle M. O' Donnell
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