Investigating bifidobacteria-host interactions in the gut using organoid models and network biology approaches

Poletti, Martina (2022) Investigating bifidobacteria-host interactions in the gut using organoid models and network biology approaches. Doctoral thesis, University of East Anglia.

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Abstract

Despite numerous studies indicating that Bifidobacterium species exert beneficial effects a range of diseases, current knowledge about the specific modulating factors is limited. One mechanism is represented by autophagy, mediating key processes in intestinal epithelial cells, and which is often disrupted in gut disorders such as inflammatory bowel disease. In this regard, intestinal organoids represent a useful model to investigate these processes, allowing to study the effect of microbial-derived molecules on host epithelial cell function in a high-throughput and representative manner. The goal of this PhD thesis is to combine experimental and computational approaches, including intestinal organoids and network biology methods, to identify specific mechanisms by which Bifidobacterium-derived metabolites affect intestinal epithelial cell function, exerting a beneficial effect on the host.

To achieve these goals, mouse and human intestinal organoid models were developed, and in parallel with existing colon cancer cell lines, their culture conditions were further characterised to allow their co-culture with Bifidobacterium-derived metabolites. Subsequently, downstream applications were optimised to assess modulation of host intestinal barrier, cytokine release, autophagy, and gene expression changes. Host transcriptomics data from organoids was further integrated with a priori knowledge to build regulatory and molecular interaction networks, whose analysis can reveal specific mechanisms modulated by bifidobacteria.

This work resulted in the development and further characterisation of novel experimental models to investigate apical host-microbe interactions, including organoids with reversed polarity or organoid-derived monolayers. Furthermore, exposure of epithelial cultures to Bifidobacterium strains highlighted the ability of bifidobacterial metabolites to improve intestinal barrier function and modulate autophagy in epithelial cells. Transcriptomics analysis of human colonic organoids exposed to Bifidobacterium metabolites also revealed positive modulation of the immune response, epithelial differentiation and tight junctions through epigenetics mechanisms, and the downregulation of cholesterol biosynthesis.

Overall, this work has increased the understanding of the effects of bifidobacteria on the intestinal epithelium, while showing how a combination of experimental and network biology approaches can be used for these types of studies. Once further validated, results of this thesis will help unravel the beneficial effects of probiotics such as bifidobacteria in the gut, further aiding the development of management strategies for inflammatory diseases of the gut.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	23 May 2023 09:32
Last Modified:	23 May 2023 09:32
URI:	https://ueaeprints.uea.ac.uk/id/eprint/92131
DOI:

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