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Exploring the gut microbiome of children from Cape Town communities
Thesis (PhD)--Stellenbosch University, 2021.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2021
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| _version_ | 1867614029836451840 |
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| access_status_str | Open Access |
| author | Van Zyl, Kristien Nel |
| author2 | Newton-Foot, Mae |
| author_browse | Newton-Foot, Mae Van Zyl, Kristien Nel |
| author_facet | Newton-Foot, Mae Van Zyl, Kristien Nel |
| author_sort | Van Zyl, Kristien Nel |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2021. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/124220 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:45:32.686Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/124220 Exploring the gut microbiome of children from Cape Town communities Van Zyl, Kristien Nel Newton-Foot, Mae Whitelaw, Andrew Christopher Stellenbosch University. Faculty of Science. Dept. Department of Pathology. Medical Microbiology. Microbiomes -- Cape Town (South Africa) Multidrug-resistant tuberculosis -- Cape Town (South Africa) Microbial metabolites -- Cape Town (South Africa) UCTD Thesis (PhD)--Stellenbosch University, 2021. ENGLISH ABSTRACT: Despite the increase in microbiome investigations in the last decade, descriptions of the microbiota remain limited in developing countries, particularly in children. Little is known about the gut microbiota of young children in South Africa and there is a need for investigations of the composition and diversity of microbiota and the influence of demographic, clinical, and environmental factors on the microbiota in this setting. This study formed part of the ongoing Tuberculosis child multidrug-resistant preventive therapy (TB-CHAMP) clinical trial, which aims to determine the efficacy and safety of levofloxacin preventive therapy in a cohort of children <5 years exposed to multidrug-resistant tuberculosis in the household. This sub-study explored the composition, diversity, and factors influencing the baseline bacterial and fungal gut microbiota of these children, prior to randomisation into treatment or placebo arms. A pilot study was performed to assess the effect of stool sample storage and transport conditions on the microbiota and to develop a practical DNA extraction standard operating procedure for the remainder of the sub-study and future microbiome studies in this setting. Quantitative PCR showed that the gut microbiota was not affected by storage and transport conditions common to this setting. Targeted 16S rRNA and internal transcribed spacer 1 gene sequencing was performed on the Illumina platform to characterise the bacterial and fungal microbiota. The bacterial microbiota of young children from Cape Town communities were shown to be similar to those in children from developing countries and age was the main driver of differences in both bacterial and fungal communities. While the risk for dysbiosis was shown to be low overall, recent antibiotic use and household pollution were associated with reduced bacterial diversity. The inconsistent detection and abundance of fungi even in participants of the same age, highlighted the need for expanded research, including dietary and longitudinal analysis. The need for longitudinal analysis in paediatric populations was further emphasised by a systematic review on the effects of antibiotics on the microbiome, particularly in populations who are at risk for increased antibiotic exposure. The findings also demonstrated the population and target site-specific responses of the microbiome to antibiotics, which underlined the need for individual evaluation of the effect of antibiotics on the gut microbiome. This study set the groundwork for future investigations in the TB-CHAMP cohort, including the temporal development and stability of the gut microbiome in these children, and the impact of levofioxacin preventive therapy on the microbiota and resistance reservoirs in the gut. AFRIKAANSE OPSOMMING: Ondanks die toename in mikrobioomondersoeke in die afgelope dekade, bly beskrywings van die mikrobiota beperk in ontwikkelinde omgewings, veral in kinders. Min is bekend oor die gastrc:—intestinale mikrobiota van jong kinders in Suid-Afrika. Daar is 'n behoefte aan ondersoeke rakende die samestelling en diversiteit van die mikrobiota en die invloed van demografiese-, kliniese-, en omgewingsfaktore op die mikrobiota in hierdie omgewing. Hierdie studie was deel van die "Tuberculosis child multidrug-resistant preventive therapy" (TB-CHAMP) kliniese proefstudie, wat poog om die effektiwiteit en veiligheid van levofloksasien profilakse te bestudeer in 'n kohort van kinders <5 jaar wat blootgestel is aan veelmiddelweerstandige tuberkulose in hul huishouding. Hierdie sub-studie het die samestelling, diversiteit en faktore wat die basislyn bakteriéle en swam gastro-intestinale mikrobiota van hierdie kinders beinvloed, voor randomisering na behandeling of placebo groepe, verken 'n Studie is geloods om die effek van stoor- en vervoertoestande van stoelgangmonsters op die mikrobiota te bepaal en om 'n praktiese DNA ekstraksie standaardwerksprotokol vir die res van die studie, en toekomstige mikrobioom studies in hierdie instelling, te ontwikkel. Kwantitatiewe PKR het gewys dat die gastro-intestinale mikrobiota nie deur stoor- en vervoertoestande wat algemeen in hierdie studie gebruik word, beinvoed word nie. Geteikende 16S rRNA en "internal transcribed spacer 1" geenvolgordebepaling is deur middel van Illumina tegnologie gedoen, om die bakteriéle en swam mikrobiota te karakteriseer. Die bakteriéle mikrobiota van jong kinders vanaf gemeenskappe in Kaapstad is bewys om soortgelyk te wees aan dié van ontwikkelende lande en die hoof drywer van verandering in beide bakterie en swamme was ouderdom. Terwyl die risiko van disbiose oor die algemeen laag was, was onlangse antibiotika verbruik en huishoudelike besoedeling geassosieer met verminderde bakteriéle diversiteit. Die inkonsekwente opsporing en hoeveelheid fungi, selfs in kinders van dieselfde ouderdom, het kollig op die behoefte vir verdere navorsing, insluitend dieetkundige en longitudinale analise, geplaas. Die behoefte aan longitudinale analise in pediatriese bevolkings is verder beklemtoon deur 'n sistematiese oorsig van die effek van antibiotika op die mikrobioom, veral in bevolkings wat 'n hoer risiko vir blootstelling aan antibiotika het Die resultate het 00k die individualteit van die mikrobioomveranderinge in verskillende bevolkings en teikenareas gewys. Dit beklemtoon die behoefte aan individuele ondersoek van die effek van antibiotika op die mikrobioom. Hierdie studie het die grondslag neergelé vir toekomstige ondersoeke in die TB-CHAMP kohort, insluitend die ontwikkeling en stabiliteit van die gastro-intestinale mikrobioom met tyd, en die impak van levofioksasien profilaksis op die mikrobiota en antibiotiese-weerstand-reservoir in die gastrc:-intestinale kanaal. Doctoral 2021-10-28T07:53:18Z 2022-02-22T10:17:12Z 2021-10-28T07:53:18Z 2021-12 Thesis http://hdl.handle.net/10019.1/124220 en_ZA Stellenbosch University xiv, 169 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Microbiomes -- Cape Town (South Africa) Multidrug-resistant tuberculosis -- Cape Town (South Africa) Microbial metabolites -- Cape Town (South Africa) UCTD Van Zyl, Kristien Nel Exploring the gut microbiome of children from Cape Town communities |
| title | Exploring the gut microbiome of children from Cape Town communities |
| title_full | Exploring the gut microbiome of children from Cape Town communities |
| title_fullStr | Exploring the gut microbiome of children from Cape Town communities |
| title_full_unstemmed | Exploring the gut microbiome of children from Cape Town communities |
| title_short | Exploring the gut microbiome of children from Cape Town communities |
| title_sort | exploring the gut microbiome of children from cape town communities |
| topic | Microbiomes -- Cape Town (South Africa) Multidrug-resistant tuberculosis -- Cape Town (South Africa) Microbial metabolites -- Cape Town (South Africa) UCTD |
| url | http://hdl.handle.net/10019.1/124220 |
| work_keys_str_mv | AT vanzylkristiennel exploringthegutmicrobiomeofchildrenfromcapetowncommunities |