Abstract
It is impossible to analyze human-specific host–microbiome interactions using animal models and existing in vitro methods fail to support survival of human cells in direct contact with complex living microbiota for extended times. Here we describe a protocol for culturing human organ-on-a-chip (Organ Chip) microfluidic devices lined by human patient-derived primary intestinal epithelium in the presence of a physiologically relevant transluminal hypoxia gradient that enables their coculture with hundreds of different living aerobic and anaerobic bacteria found within the human gut microbiome. This protocol can be adapted to provide different levels of oxygen tension to facilitate coculturing of microbiome from different regions of gastrointestinal tract, and the same system can be applied with any other type of Organ Chip. This method can help to provide further insight into the host–microbiome interactions that contribute to human health and disease, enable discovery of new microbiome-related diagnostics and therapeutics, and provide a novel approach to advanced personalized medicine.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Garrett WS et al (2010) Homeostasis and Inflammation in the Intestine. Cell 140:859–870
Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260
Bein A et al (2018) Microfluidic organ-on-a-chip models of human intestine. Cell Mol Gastroenterol Hepatol 5:659–668
Shah P et al (2016) A microfluidics-based in vitro model of the gastrointestinal human–microbe interface. Nat Commun 7:11535
Jalili-Firoozinezhad S et al (2019) A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng 3:520–531
Kasendra M et al (2018) Development of a primary human small intestine-on-a-chip using biopsy-derived organoids. Sci Rep 8:2871
Sontheimer-Phelps A et al (2020) Human colon-on-a-chip enables continuous in vitro analysis of colon mucus layer accumulation and physiology. Cell Mol Gastroenterol Hepatol 9:507–526
Nikolaev M et al (2020) Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585:574–578
Tovaglieri A et al (2019) Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites. Microbiome 7:43
Kim HJ et al (2016) Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. PNAS 113:E7–E15
Sato T, Clevers H (2013) Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications. Science 340:1190–1194
VanDussen KL et al (2015) Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. Gut 64:911–920
Jalili-Firoozinezhad S et al (2018) Modeling radiation injury-induced cell death and countermeasure drug responses in a human Gut-on-a-Chip. Cell Death Dis 9:223
Acknowledgments
This work was supported by funding from DARPA, FDA, GATES Foundation (all to D.E.I.) and by the Lush Prize (to S.J-F.).
Conflicts of Interest
D.E.I. holds equity in Emulate, Inc., consults for the company, chairs its scientific advisory board, and is a member of its board of directors.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Jalili-Firoozinezhad, S., Bein, A., Gazzaniga, F.S., Fadel, C.W., Novak, R., Ingber, D.E. (2022). Establishment of a Modular Anaerobic Human Intestine Chip. In: Rasponi, M. (eds) Organ-on-a-Chip. Methods in Molecular Biology, vol 2373. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1693-2_5
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1693-2_5
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1692-5
Online ISBN: 978-1-0716-1693-2
eBook Packages: Springer Protocols