Hi @Lena Neufeld, thanks for your question! We assess several complementary readouts from the Organ-chips to verify that the cells are behaving as closely to human in vivo as possible. Specifically, for the Colon Intestine-chip we observe:
- Immunofluorescence staining to verify the presence of cytoskeletal and tight junction markers (ZO-1, E-cadherin, F-actin)
- Apparent permeability assay demonstrating formation of tight barrier
- Bulk RNA-seq analysis can be performed on cells extracted from the Organ-chips, demonstrating closer gene expression to in vivo than organoids
- Multiplex effluent analysis can assess soluble factors excreted from the vascular or epithelial channels
I would also check out this Colon Intestine-Chip publication for more information: https://www.cmghjournal.org/article/S2352-345X(21)00145-4/fulltext
To answer your question on microbiome inclusion, yes it is possible. Here is a study published from the Wyss Institute using Organ-chips to study anaerobic bacteria on intestine: https://www.nature.com/articles/s41551-019-0397-0
Let me know if I answered your full question!