• Research

Multi-omics analysis of intestinal organoids

Using intestinal organoids and multi-omics approaches to analyse intestinal homeostasis, autophagy and the effect of Bifidobacteria.

Project summary.

Led by: Korcsmáros Group

Start date: Sept 2016

Duration: Ongoing

Grants: 2 x BBSRC Doctoral Training Partnership grants



QIB Gut Microbes and Health ISP

Intestinal homeostasis depends on complex interactions between the microbiota, the intestinal epithelium and the host immune system. Dysbiosis of this system can result in multiple gut pathologies, such as inflammatory bowel disease (IBD). Greater understanding of cell-type specific function, regulation, and response to environmental perturbation in the gut will improve our understanding of disease pathomechanisms.

We are combining in silico Systems Biology with experimental data generation and validation to examine host molecular interactions. For the experimental work we are exploiting the small intestinal organoid model to generate ‘omics data. Organoids are 3D structures grown from stem cells recapitulating the normal physiology of organs. They enable the in vitro study of the regulation/dysregulation of epithelial homeostatic functions, cell type-specific functions in health and disease and host-microbiome interactions. The application of in silico networks, using our published databases such as SignaLink and the Autophagy Regulatory Network, will enable contextual and multiscale analysis of the ‘omics data, as well as network analysis and logical modelling.

Currently we are applying this workflow to study Paneth and goblet cell regulatory networks, the effect of autophagy impairment on cell regulation and the impact of Bifidobacteria co-culture on organoid function and cell regulation. By increasing the understanding of the underlying factors playing a role in intestinal dysbiosis and the beneficial effects of commensal bacteria, we hope to pave the way for translational developments in the prevention and treatment of gastrointestinal disease and disturbances.


The human gut commensal Bifidobacteria has been highlighted as a protective agent against a number of health conditions, ranging from pathogen infection to Crohn's disease and asthma. Whilst the specific modulating factors are largely unidentified, evidence suggests that Bifidobacteria can interact with host intestinal cells. Such interactions can alter host molecular pathways leading to modified intestinal cell function.

Bifidobacteria have been shown to activate autophagy by upregulating autophagy genes Atg5, Atg12, Atg16 and by preventing oxidant-induced intestinal epithelial cell death through induction of autophagy. Understanding these effects is likely to be key to understanding the observed benefits of Bifidobacteria.

In this project we are working to investigate the role of Bifidobacteria on the regulation of host autophagy and antimicrobial peptide production in Paneth cells. We are using gut organoids to experimentally characterise the effect of Bifidobacteria on host cell functions as well as to produce ‘omics readouts. The readouts will be generated following fluorescence activated cell sorting, for cell-type resolution.

The ’omics data is applied to in silico networks, generated using published interaction data sources, to enable analysis of regulatory and signalling pathways in the cell types of interest. Comparison of networks generated using naïve organoids and those co-cultured with Bifidobacteria will highlight key pathways and functions modulated by the bacteria.

In particular, we aim to explore the impact of Bifidobacteria on autophagy and antimicrobial peptide production in Paneth cells. Promising targets will be experimentally validated using organoids and Bifidobacteria mutant libraries.


Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn's disease due to autophagy impairment

Jones E, Matthews Z, Gul L, Sudhakar P, Divekar D, Buck J, Jefferson M, Armstrong S, Watson A, Carding S, Mayer U, Powell P, Hautefort I, Wileman T, Korcsmaros T (Preprint bioRxiv 410027)


Tom Wileman

Quadram Institute

Simon Carding

Quadram Institute

Impact statement.

By increasing the understanding of underlying factors involved in intestinal dysbiosis, we hope to pave the way for translational developments in the prevention and treatment of gastrointestinal disease and disturbances.

Through studying the effect of commensal bacteria on organoids, we hope to gain a clearer understanding of host-microbiome interactions and the mechanisms behind the beneficial effects of commensal bacteria. In turn this knowledge could lead to health-promoting advice and improved treatments for gut microbiome dysbiosis and associated diseases.