Mother and infant microbiomes during the perinatal period: compositional analyses, identification of strain transfer events and implications for pregnancy outcomes

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dc.contributor.advisorCotter, Paul
dc.contributor.advisorvan Sinderen, Douwe
dc.contributor.advisorexternalFeehily, Conor
dc.contributor.advisorexternalWalsh, Calum
dc.contributor.authorNori, Sai Ravi Chandraen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderMarie Sklodowska-Curie granten
dc.date.accessioned2025-05-13T15:33:28Z
dc.date.available2025-05-13T15:33:28Z
dc.date.issued2025
dc.date.submitted2025
dc.description.abstractDuring the perinatal period, the transfer of microbial communities from mother to infant is critical in shaping the infant’s early-life microbiome and broader health outcomes. While it is well established that maternal sources such as the gut, breastmilk, and vaginal tract each contribute to the neonate’s microbiota, fewer studies have examined the fine-scale strain-level differences that can govern colonisation success or influence pregnancy outcomes. This thesis addresses that gap by adopting metagenomic approaches to identify and compare specific bacterial strains across mother-infant pairs, offering novel perspectives on how functional traits may underpin microbe-host interaction and vertical transmission. Chapter 2 highlights how computational choices can markedly affect the reconstruction of metagenome-assembled genomes (MAGs) and, in turn, our interpretations of microbial sharing events. Comparing different binning tools demonstrates that method selection shapes both the number and quality of MAGs recovered, including the detection of critical genes like 16S rRNA and antimicrobial resistance determinants. These findings underscore the necessity of rigorous bioinformatic pipelines for accurately tracing maternal strains into infants. Chapter 3 highlights how functional traits, particularly genes involved in human milk oligosaccharide (HMO) metabolism may confer a competitive advantage in the HMO-rich infant gut. Such insights illuminate why some maternal strains flourish in early infancy even when they are not dominant in the maternal microbiome. Chapters 4 and 5 focus on the maternal vaginal microbiome, a niche strongly linked to pregnancy outcomes but relatively understudied at the microbial strain level. Investigating Lactobacillus strains and their genetic variation reveals that even minor within-species distinctions correlate with gestational duration, offering novel insights on how vaginal microbiome composition may influence pregnancy risks. Taken together, these results underscore the critical importance of examining microbial communities at the strain level to gain a more refined view of mother-infant transmission. Ultimately, these findings open avenues for targeted investigation to understand the mechanisms governing maternal/infant microbial interaction and to tailor interventions for improved health outcomes during the perinatal period.
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationNori, N. S. R. C. 2025. Mother and infant microbiomes during the perinatal period: compositional analyses, identification of strain transfer events and implications for pregnancy outcomes. PhD Thesis, University College Cork.
dc.identifier.endpage179
dc.identifier.urihttps://hdl.handle.net/10468/17479
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/NSF Student Mobility Programme/18/CRT/6214 (S3)/IE/18/CRT/6214 Supplement/
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-DP/945385/EU/Doctorate School in Integrated Genomics Research/INTEGRATE
dc.rights© 2025, Sai Nori.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectGut microbiome
dc.subjectMother-infant
dc.subjectVaginal microbiome
dc.subjectStrain-level resolution
dc.subjectMetagenomics
dc.titleMother and infant microbiomes during the perinatal period: compositional analyses, identification of strain transfer events and implications for pregnancy outcomes
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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