Abstract
Commensal bacteria within the gut microbiome contribute to development of host tolerance to infection, however, identifying specific microbes responsible for this response is difficult. Here we describe methods for developing microfluidic organ-on-a-chip models of small and large intestine lined with epithelial cells isolated from duodenal, jejunal, ileal, or colon organoids derived from wild type or transgenic mice. To focus on host-microbiome interactions, we carried out studies with the mouse Colon Chip and demonstrated that it can support co-culture with living gut microbiome and enable assessment of effects on epithelial adhesion, tight junctions, barrier function, mucus production, and cytokine release. Moreover, infection of the Colon Chips with the pathogenic bacterium, Salmonella typhimurium, resulted in epithelial detachment, decreased tight junction staining, and increased release of chemokines (CXCL1, CXCL2, and CCL20) that closely mimicked changes previously seen in mice. Symbiosis between microbiome bacteria and the intestinal epithelium was also recapitulated by populating Colon Chips with complex living mouse or human microbiome. By taking advantage of differences in the composition between complex microbiome samples cultured on each chip using 16s sequencing, we were able to identify Enterococcus faecium as a positive contributor to host tolerance, confirming past findings obtained in mouse experiments. Thus, mouse Intestine Chips may represent new experimental in vitro platforms for identifying particular bacterial strains that modulate host response to pathogens, as well as for investigating the cellular and molecular basis of host-microbe interactions.
Highlights
The epithelium lining the intestine is an essential barrier that protects our bodies from the trillions of microbes within the microbiome that resides within its lumen
Organoid culture medium was perfused through both channels and a confluent monolayer was observed covering the porous membrane by 1 week of culture in both wild type (WT) and Kaede chips, and similar results were obtained when we used intestinal epithelial cells isolated from organoids derived from mouse duodenum, jejunum, and ileum (Supplementary Figures S1A–D)
We showed that both complex species-specific microbiota or individual types of bacteria can be cultured in the Colon Chips and that bacterial-specific effects on epithelial cell adhesion, tight junctions, barrier function, mucus production, and cytokine release can be quantified directly
Summary
The epithelium lining the intestine is an essential barrier that protects our bodies from the trillions of microbes within the microbiome that resides within its lumen. The intestinal epithelium regulates this critical barrier by integrating signals from commensal bacteria within the microbiome with cues from immune cells in the lamina propria, such that a state of host tolerance develops which enables host-microbiome symbiosis. Maintaining this state of tolerance in which microbes and the host co-exist without causing damage to each other is essential to protect against a wide variety of diseases. In the present study, we set out to explore if Organ Chip technology could be leveraged to develop an in vitro model of the mouse intestinal barrier in the colon that can be used to study host-microbiome interactions that contribute to tolerance development
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