Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

Contributed by James J. Collins, November 15, 2015 (sent for review August 18, 2015; reviewed by David J. Beebe and Rustem F. Ismagilov)
December 14, 2015
113 (1) E7-E15

Significance

The main advance of this study is the development of a microengineered model of human intestinal inflammation and bacterial overgrowth that permits analysis of individual contributors to the pathophysiology of intestinal diseases, such as ileus and inflammatory bowel disease, over a period of weeks in vitro. By studying living human intestinal epithelium, with or without vascular and lymphatic endothelium, immune cells, and mechanical deformation, as well as living microbiome and pathogenic microbes, we identified previously unknown contributions of specific cytokines, mechanical motions, and microbiome to intestinal inflammation, bacterial overgrowth, and control of barrier function. We provide proof-of-principle to show that the microfluidic gut-on-a-chip device can be used to create human intestinal disease models and gain new insights into gut pathophysiology.

Abstract

A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. By ceasing peristalsis-like motions while maintaining luminal flow, lack of epithelial deformation was shown to trigger bacterial overgrowth similar to that observed in patients with ileus and inflammatory bowel disease. Analysis of intestinal inflammation on-chip revealed that immune cells and lipopolysaccharide endotoxin together stimulate epithelial cells to produce four proinflammatory cytokines (IL-8, IL-6, IL-1β, and TNF-α) that are necessary and sufficient to induce villus injury and compromise intestinal barrier function. Thus, this human gut-on-a-chip can be used to analyze contributions of microbiome to intestinal pathophysiology and dissect disease mechanisms in a controlled manner that is not possible using existing in vitro systems or animal models.

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Data Availability

Data deposition: Human Gene 1.0 ST Array mRNA data of Caco-2 cells cultured in various conditions were deposited to the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE65790).

Acknowledgments

We thank Sri Kosuri (Wyss Institute) for providing GFP-labeled E. coli strain; Jehyuk Lee and Carolina Lucchesi (Wyss Institute) for help with the qPCR analysis; and Eunyoung Chun (Harvard T. H. Chan School of Public Health) for assistance with flow cytometry and helpful discussions. This work was supported by the Defense Advanced Research Projects Agency (Cooperative Agreement W911NF-12-2-0036), Food and Drug Administration (Grant HHSF223201310079C), and the Wyss Institute for Biologically Inspired Engineering at Harvard University.

Supporting Information

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Supporting Information
pnas.1522193112.sm01.avi
pnas.1522193112.sm02.avi
pnas.1522193112.sm03.avi

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 113 | No. 1
January 5, 2016
PubMed: 26668389

Classifications

Data Availability

Data deposition: Human Gene 1.0 ST Array mRNA data of Caco-2 cells cultured in various conditions were deposited to the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE65790).

Submission history

Published online: December 14, 2015
Published in issue: January 5, 2016

Keywords

  1. microbiome
  2. gut-on-a-chip
  3. intestine
  4. inflammatory bowel disease
  5. mechanical

Acknowledgments

We thank Sri Kosuri (Wyss Institute) for providing GFP-labeled E. coli strain; Jehyuk Lee and Carolina Lucchesi (Wyss Institute) for help with the qPCR analysis; and Eunyoung Chun (Harvard T. H. Chan School of Public Health) for assistance with flow cytometry and helpful discussions. This work was supported by the Defense Advanced Research Projects Agency (Cooperative Agreement W911NF-12-2-0036), Food and Drug Administration (Grant HHSF223201310079C), and the Wyss Institute for Biologically Inspired Engineering at Harvard University.

Authors

Affiliations

Hyun Jung Kim
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115;
Present address: Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712.
Hu Li
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115;
Present address: Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905.
James J. Collins3 [email protected]
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115;
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139;
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139;
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142;
Harvard-Massachusetts Institute of Technology Program in Health Sciences and Technology, Cambridge, MA 02139;
Donald E. Ingber3 [email protected]
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115;
Vascular Biology Program, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115;
Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138

Notes

3
To whom correspondence may be addressed. Email: [email protected] or [email protected].
Author contributions: H.J.K., J.J.C., and D.E.I. designed research; H.J.K. performed research; H.J.K., H.L., J.J.C., and D.E.I. analyzed data; and H.J.K. and D.E.I. wrote the paper.
Reviewers: D.J.B., University of Wisconsin–Madison; and R.F.I., California Institute of Technology.

Competing Interests

Conflict of interest statement: D.E.I. is a founder of Emulate Inc., holds equity in the company, and chairs its Scientific Advisory Board.

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    Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip
    Proceedings of the National Academy of Sciences
    • Vol. 113
    • No. 1
    • pp. 1-E104

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