Human bifidobacterial isolates with a focus on glycan degradation and bacteriocin production by Bifidobacterium pseudocatenulatum

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dc.check.date2029-12-31
dc.check.infoControlled Access
dc.contributor.advisorvan Sinderen, Douwe
dc.contributor.advisorCotter, Paul
dc.contributor.authorSanchez Gallardo, Rocio
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderH2020 Marie Skłodowska-Curie Actions
dc.date.accessioned2024-10-01T14:26:45Z
dc.date.available2024-10-01T14:26:45Z
dc.date.issued2023
dc.date.submitted2023
dc.descriptionControlled Access
dc.description.abstractBifidobacteria are commensal bacteria which inhabit the gastrointestinal tract of humans and other mammals, and to which various probiotic or health-promoting benefits have been attributed. Bifidobacterial strains can metabolize both host- and diet-derived glycans, and these metabolic abilities are critical for their establishment in the gut. Bifidobacteria are among the first colonisers of the neonatal gut, partially due to their ability to digest human milk oligosaccharides (HMOs), present in human milk. Members of the species Bifidobacterium breve, Bifidobacterium bifidum and Bifidobacterium longum are commonly isolated from infant faecal samples and are among the most abundant species found in early life. As the infant changes its diet during weaning the microbiota evolves and therefore the bifidobacterial abundance, prevalence and composition will be subject to change. Infant-associated species become less abundant and other species such as Bifidobacterium adolescentis start to play a more prominent role as they are capable of digesting dietary plant-glycans, therefore being adult-associated strains. Some studies have indicated that Bifidobacterium pseudocatenulatum is a bifidobacterial species that remains constant across the lifetime of a person. Thus, it is expected of this species possesses an extensive enzymatic machinery to adapt to dietary changes. Chapter II of this thesis focuses on the isolation and genomic characterisation of bifidobacterial strains from breast milk. Optimization of a cultivation protocol allowed the recovery of viable Bifidobacterium from frozen human milk samples. Furthermore, the genomic characterization allowed a preliminary analysis of the potential of these strains as probiotic. Chapter III of this thesis describes the isolation and characterisation of 36 B. pseudocatenulatum strains from mother-infant dyads. Following an initial comparative genomic analysis of all strains we focussed on a selection of the B. pseudocatenulatum strains so as to explore their genomic diversity and functionality. Growth abilities of these strains on more than 30 carbohydrate substrates facilitated the correlation between the presence of specific GH-encoding genes and their ability to degrade certain glycans. A large proportion of the genomic diversity observed in these strains was shown to correspond to the presence of prophage-like elements. Chapter IV details the metabolism of LNT in the species B. pseudocatenulatum. Using a combination of transcriptomic and molecular biology techniques, the enzymatic machinery responsible for the degradation of LNT in B. pseudocatenulatum was elucidated. Furthermore, genes were identified that were shown to be responsible for certain B. pseudocatenulatum strains to degrade particular fucosylated HMOs, believed to be important for infant health. Chapter V focussed on the extracellular degradation of particular plant-glycans, in particular xylan and starch, by specific strains of B. pseudocatenulatum. The extracellular enzymes responsible for the degradation of these complex carbohydrates were identified and characterised in this set of novel strains. Furthermore, the distribution across the species of homologs of these key genes was analysed. Chapter VI describes the identification and characterisation of a gene cluster responsible for the production of a novel antimicrobial peptide, designated Pseudocin 196, by B. pseudocatenulatum MM0196. Pseudocin 196 was purified and tested for its antimicrobial activity against a range of bacteria. Pseudocin 196 is the first reported bacteriocin produced by a B. pseudocatenulatum species of human origin and was shown to inhibit clinically relevant pathogens. The work presented in this thesis expands the knowledge of Bifidobacterium pseudocatenulatum taxon, being in particular focussed on various genomic and metabolic capabilities of this species. The findings of this thesis have generated insights into the physiological and ecological roles played by this bacterial species as a common member of the human microbiome. Understanding the symbiotic relationship between this bacterial species and its human host may generate rational approaches through the development of novel functional food products that help to support and maintain the gut homeostasis.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationSanchez Gallardo , R. 2023. Human bifidobacterial isolates with a focus on glycan degradation and bacteriocin production by Bifidobacterium pseudocatenulatum. PhD Thesis, University College Cork.
dc.identifier.endpage395
dc.identifier.urihttps://hdl.handle.net/10468/16475
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Spokes Programme::Fixed Call/16/SP/3827/IE/Determinants of Mother-to-Infant Transfer of Microbiota/
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/754535/EU/APC Postdoctoral EXcellence Programme/APEX
dc.rights© 2023, Rocio Sanchez Gallardo.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectBifidobacteria
dc.subjectCarbohydrate metabolism
dc.subjectBacteriocin
dc.subjectInfant microbiota
dc.subjectProbiotic bacteria
dc.titleHuman bifidobacterial isolates with a focus on glycan degradation and bacteriocin production by Bifidobacterium pseudocatenulatum
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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