Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture

Background: The gut microbiome plays an important role in human health and disease. Gnotobiotic animal and in vitro cell-based models provide some informative insights into mechanistic crosstalk. However, there is no existing system for a long-term co-culture of a human colonic mucosal barrier with super oxygen-sensitive commensal microbes, hindering the study of human-microbe interactions in a controlled manner. Methods: Here, we investigate the effects of an abundant super oxygen-sensitive commensal anaerobe, Faecalibacterium prausnitzii, on a primary human mucosal barrier using a gut microbiome (GuMI) physiome platform that we designed and fabricated. Findings: Long-term continuous co-culture of F. prausnitzii for 2 days with colon epithelia, enabled by continuous flow of completely anoxic apical media and aerobic basal media, results in a strictly anaerobic apical environment fostering the growth of and butyrate production by F. prausnitzii, while maintaining a stable colon epithelial barrier. We identify elevated differentiation and hypoxia-responsive genes and pathways in the platform compared with conventional aerobic static culture of the colon epithelia, attributable to a combination of anaerobic environment and continuous medium replenishment. Furthermore, we demonstrate the anti-inflammatory effects of F. prausnitzii through histone deacetylase (HDAC) and the Toll-like receptor-TLR-nuclear factor κB (NF-κB) axis. Finally, we identify that butyrate largely contributes to the anti-inflammatory effects by downregulating TLR3 and TLR4. Conclusions: Our results are consistent with some clinical observations regarding F. prausnitzii, thus motivating further studies using this platform with more complex engineered colon tissues for understanding the interaction between the human colonic mucosal barrier and microbiota, pathogens, or engineered bacteria. Funding: US National Institute of Biomedical Imaging and Bioengineering, Boehringer Ingelheim Strategic Hub for Innovative New Therapeutics Concept Exploration (SHINE) Program, US National Institute of Environmental Health Sciences.