Effects of the biotic and abiotic environment on ecology and evolution within novel in vitro and ex vivo models of the human gut microbiome

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dc.check.date2028-05-31
dc.contributor.advisorScanlan, Pauline
dc.contributor.advisorClaesson, Marcus
dc.contributor.authorPennycook, Josephen
dc.contributor.funderScience Foundation Ireland
dc.date.accessioned2025-02-14T09:49:15Z
dc.date.available2025-02-14T09:49:15Z
dc.date.issued2024
dc.date.submitted2024
dc.description.abstractLeveraging the precision and replicability of in vitro and ex vivo models, we investigated the ecology and evolution of the human gut microbiota in a variety of environmental conditions. We developed a novel system for culturing microbiota communities and first used it to study the effects of the biotic and abiotic environment on the relationship between a gut-derived bacteriophage and its host. We found that an interaction between the nutrient medium and the broader community of bacteria led to the extinction of phage populations via competitive exclusion of the host and acidification of the medium. After reviewing the existing body of literature regarding the effects of antibiotic treatment on human gut microbiota, we tested the effects of sub-clinical antibiotic exposure on ex vivo faecal communities. Exposure to sub-clinical concentrations of clindamycin led to less diverse communities, more prevalent antibiotic resistance, and a greatly reduced presence of the Actinobacteria phylum, while exposure to amoxicillin and ciprofloxacin had less clear effects. Metabolic assays revealed that exposure to sub-inhibitory antibiotics promoted faster metabolism in Bifidobacterium, although not a faster growth rate, and also that the presence of an antibiotic often prevented the inhibition of metabolism by other environmental stressors. This work has demonstrated the value of laboratory models in the study of the human gut microbiota, while highlighting the importance of environmental context in understanding the system's ecology and evolution.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationPennycook, J. 2024. Effects of the biotic and abiotic environment on ecology and evolution within novel in vitro and ex vivo models of the human gut microbiome. PhD Thesis, University College Cork.
dc.identifier.endpage445
dc.identifier.urihttps://hdl.handle.net/10468/17038
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres Programme/17/RC-PhD/3478/IE/APC PhD Recruitment Scheme/
dc.rights© 2024, Joseph Pennycook.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectHuman gut microbiome
dc.subjectHuman gut microbiota
dc.subjectMicrobiome
dc.subjectAntibiotics
dc.subjectAntibiotic resistance
dc.subjectAntimicrobial resistance
dc.subjectEcology
dc.subjectEvolution
dc.titleEffects of the biotic and abiotic environment on ecology and evolution within novel in vitro and ex vivo models of the human gut microbiome
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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