Understanding the gut microbiome; the role of host senescence, sociality, and genetics.

Lee, Chuen Zhang (2025) Understanding the gut microbiome; the role of host senescence, sociality, and genetics. Doctoral thesis, University of East Anglia.

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Abstract

Gut microbiomes (GMs) – microbes living in the intestine – play a central role in host health, survival and evolution, yet what affects their dynamics, and how that impacts host individuals in wild populations remains poorly understood. This thesis investigates host–GM interactions in a natural population of Seychelles warblers, integrating longitudinal sampling, shotgun metagenomics, and host genomic analyses to identify ecological, genetic, and social drivers of GM variation and their consequences for host survival.

I show that both taxonomic and functional GM diversity decline progressively with age, with compositional shifts and an age-related increase in transposase abundance. Host immunogenetics, measured through major histocompatibility complex (MHC) variation, shaped GM structure, revealing trade-offs between microbial defence and microbial metabolic function. Social interactions also influenced the GM: individuals sharing space harboured more similar GMs, and individuals that interact closely (e.g. breeding pairs and helpers) shared more similar anaerobic, but not aerotolerant, taxa. Host inbreeding effects were detectable at both individual and parental levels, correlating with GM taxonomic and functional composition. Genome-wide association analysis further identified nine loci linked to GM composition, the genes these loci encompass implicate host immune and gut physiological pathways shaping the GM. All nine loci were associated with microbial taxa that are related to survival in the warbler, and two loci were directly linked to host survival, demonstrating genomic pathways through which host–GM interactions influence fitness.

Overall, this thesis demonstrates that age, host genetics, and social environment all shape the GM through distinct but interacting mechanisms. By integrating ecological and genomic perspectives, this thesis advances understanding of how GMs are structured in the wild and their potential fitness consequences. More broadly, it emphasises the importance of viewing the hosts and their microbiomes as an interconnected system, with implications for both evolutionary biology and conservation.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	05 Jan 2026 14:42
Last Modified:	05 Jan 2026 14:42
URI:	https://ueaeprints.uea.ac.uk/id/eprint/101517
DOI:

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