The physiological cross-talk between the liver and ileum in healthy ageing

Thesis

The gut microbiome is a complex community of microorganisms that supports metabolism and immunity. The terminal ileum (TI) - a key site of nutrient absorption in the small intestine - harbours bacteria that facilitate lipid uptake, mediate the development of immunity and regulate gut-liver communication. The liver and TI are linked through bile acid homeostasis, which are produced in the liver emulsify fats in the TI before being recirculated. However, the full extent of microbial modulation of host transcription along this axis is unclear. This thesis aims to define ileal microbiota-mediated gene expression in the TI and liver. We tested how microbial absence impacted transcription using RNA-seq of specific pathogen free (SPF) and germ free (GF) mice. We identified widespread changes in transcription in both the ileum and liver in GF mice relative to SPF mice, features that were associated with innate and adaptive immunity, and lipid metabolic pathways. To assess if specific taxa or diversity drive these effects, we used the 12-member MM12 consortium to determine if it restored host transcription to SPF levels. Transcriptional profiles across tissues of MM12 mice were more similar to GF mice, suggesting regulation of gene expression is governed by specific taxa and community complexity. To examine potential ileal microbial drivers of gene expression, we used shotgun metagenomics, qPCR and metagenome-scale metabolic modelling. The MM12 community mirrored SPF at phylum level, where divergence at lower taxonomic ranks was reflected in predicted metabolic output of these communities. The MM12 were predicted to specialise in energy-yielding metabolites via fibre fermentation, where the SPF exhibited a broader repertoire. Correlating metabolite flux predictions with host gene expression revealed various small molecules as potential mediators of lipid metabolism, immunity and cellular regulation. We further used this framework in the context of ageing, where the microbiome has been implicated in tissue decline. RNA-seq of 52 week-old mice versus 12 week-old mice showed increased immune activation and evidence for modified lipid processing in both tissues which correlated with predicted metabolites. These results support that the ileal microbiome contributes to metabolic and immune processes along the gut-liver axis and our approach provides a platform to study functional host-microbe interactions.

Authors: Halkhoree, AC

• DOI: 10.5287/ora-4rbjra8nx
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: computational biology; omics; gnotobiotics; microbiome; bioinformatics; host-microbe interactions; gut-liver axis; transcriptomics; immunology; metagenome scale metabolic modelling; metagenomics
• Subjects: Immunology; Microbiology