The development and dynamics of the infant skin microbiome

Serghiou, Iliana Rosa (2024) The development and dynamics of the infant skin microbiome. Doctoral thesis, University of East Anglia.

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Abstract

The skin microbiome is organised into microbial communities across the body, with early life a critical point in ecosystem development. Many factors cause temporal community shifts, sometimes causing perturbations and skin disease; highlighting the key role of skin microbes in health. Sequencing methods have allowed us to explore the skin microbiome however many previous studies have used 16S rRNA gene amplicon sequencing, which has its limitations. Currently, there are open questions on how the whole perinatal skin microbiome interacts and functions, before and after birth.

In this study, I used shotgun metagenomics and a controlled healthy pregnancy and infant cohort (Pregnancy and Early Life (PEARL)) to analyse skin microbiome composition, temporal dynamics (bacteriome focused) and microbiome influencing factors. I compared multi body sites (skin, gut and vaginal) to investigate skin microbiome establishment and microbial sharing over time between mothers and their infants.

To achieve these aims, I first optimised a skin specific bacterial DNA extraction method; addressing the limitations of existing commercial kit protocols for low biomass skin samples. The optimised method was validated on a healthy adult and PEARL study subset and sequenced using Shotgun Metagenomics Sequencing (SMS). The resulting data allowed genus, species and strain level profiling, and generation of Metagenome Assembled Genomes (MAGs) to explore the diversity of genomes to aid future determination of functional capacities.

An optimised bacterial DNA recovery method from skin swabs, yielding high quality DNA suitable for shotgun metagenomics, was presented. Its application to the PEARL subset established a SMS generated baseline composition for a healthy infant skin microbiome, highlighting compositional and diversity changes over time. The infant archaeome was also indicated. Sharing of core genera, and their abundance changes over time, was identified between maternal and infant skin, stool and vaginal sites. Strain sharing of these core genera was also presented between mothers and infants. The maternal skin was the main source of microbial transfer to infant skin. A PEARL MAGs catalogue was generated. This research may help develop novel evidence-based probiotics to treat and prevent the increasing occurrence of early life skin disease.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	10 Nov 2025 10:45
Last Modified:	10 Nov 2025 10:45
URI:	https://ueaeprints.uea.ac.uk/id/eprint/100935
DOI:

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