Spatial meta-omics of the inflamed human gastrointestinal mucosal niche

Cerk, Klara (2026) Spatial meta-omics of the inflamed human gastrointestinal mucosal niche. Doctoral thesis, University of East Anglia.

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Abstract

Inflammatory bowel disease (IBD) is associated with complex interactions between host genetics, environmental exposures and alterations in intestinal microbiome. Despite growing evidence implicating the microbiome in disease pathogenesis and progression, current understanding remains limited by methodological constraints and reliance on single-omics approaches, in particular faecal metagenomics.

Methodological optimisation is a prerequisite for translational microbiome research. In particularly sample collection, preservation, DNA/RNA extraction, and sequencing which can surpass biological variations in producing observed microbiota profiles. As a result, this has major effects for translational microbiota research, where it is crucial to obtain reproducible results to enable comparison among different studies and to establish clinically interpretable data.

Most gut microbiome studies rely on faecal samples since they are non-invasive and accessible. However, microbes present in faeces and those associated with the intestinal mucosa occupy distinct ecological niches and may differ substantially in composition and function, and mediate direct host-microbe interactions. Studying mucosal biopsies is hindered by extremely low microbial-to-host DNA ratios and bacterial enrichment is a necessity. With successful bacterial enrichment, another major challenge can be tackled, which is diversity of disease-associated strains that are genetically similar, but phenotypically distinct.

This PhD aimed to develop and apply systems-level methodologies to investigate host-microbe interactions at the intestinal mucosal interface, to identify disease-associated strains and compare them with faecal microbiome data to provide insights into IBD.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User:	Chris White
Date Deposited:	09 Sep 2026 07:28
Last Modified:	09 Sep 2026 07:28
URI:	https://ueaeprints.uea.ac.uk/id/eprint/104476
DOI:

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