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A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip

Nature Biomedical Engineering volume 3, pages 520–531 (2019)Cite this article

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An Author Correction to this article was published on 18 June 2019

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Abstract

The diverse bacterial populations that comprise the commensal microbiome of the human intestine play a central role in health and disease. A method that sustains complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro would thus enable the investigation of host–microbiome interactions. Here, we show the extended coculture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota, using a microfluidic intestine-on-a-chip that permits the control and real-time assessment of physiologically relevant oxygen gradients. When compared to aerobic coculture conditions, the establishment of a transluminal hypoxia gradient in the chip increased intestinal barrier function and sustained a physiologically relevant level of microbial diversity, consisting of over 200 unique operational taxonomic units from 11 different genera and an abundance of obligate anaerobic bacteria, with ratios of Firmicutes and Bacteroidetes similar to those observed in human faeces. The intestine-on-a-chip may serve as a discovery tool for the development of microbiome-related therapeutics, probiotics and nutraceuticals.

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Fig. 1: Oxygen-sensitive human Intestine Chip microfluidic culture device.
Fig. 2: Coculture of human intestinal epithelium and B. fragilis on-chip.
Fig. 3: Analysis of the diversity and relative abundance of microbiota cocultured in Intestine Chips under aerobic and anaerobic conditions.
Fig. 4: Anaerobic conditions in the Intestine Chip enhance the growth of multiple genera compared to the aerobic chip and conventional liquid culture.
Fig. 5: Anaerobic coculture of a gut microbiome obtained from fresh human patient-derived stool with primary human ileal epithelium in the Intestine Chip.

Data availability

The main data supporting the findings of this study are available in the Article and Supplementary Information. The raw data generated in this study are available from the corresponding author on reasonable request.

Change history

  • 18 June 2019

    In the version of this Article originally published, the authors mistakenly cited Fig. 5d in the sentence beginning ‘Importantly, the microbiome cultured in these primary Intestine Chips...’; the correct citation is Supplementary Table 2. This has now been amended.

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Acknowledgements

This research was supported by a US FDA grant (HHSF223201310079C), a DARPA THoR grant (W911NF-16-C-0050), the Bill & Melinda Gates Foundation, the Wyss Institute for Biologically Inspired Engineering at Harvard University and Fundação para a Ciência e a Tecnologia Portugal (project PD/BD/105774/2014 at the Institute for Bioengineering and Biosciences). We thank D. E. Achatz (PreSens GmbH) for providing oxygen-sensing particles and for her expert technical advice and T. Ferrante for his assistance with imaging.

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Author notes

  1. These authors contributed equally: Sasan Jalili-Firoozinezhad, Francesca S. Gazzaniga, Elizabeth L. Calamari.

Authors and Affiliations

  1. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA

    Sasan Jalili-Firoozinezhad, Francesca S. Gazzaniga, Elizabeth L. Calamari, Diogo M. Camacho, Cicely W. Fadel, Amir Bein, Ben Swenor, Bret Nestor, Michael J. Cronce, Alessio Tovaglieri, Oren Levy, Richard Novak & Donald E. Ingber

  2. Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal

    Sasan Jalili-Firoozinezhad & Joaquim M. S. Cabral

  3. Department of Immunology, Harvard Medical School, Boston, MA, USA

    Francesca S. Gazzaniga & Dennis L. Kasper

  4. Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland

    Alessio Tovaglieri

  5. Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA, USA

    Katherine E. Gregory

  6. Department of Pediatrics, Harvard Medical School, Boston, MA, USA

    Katherine E. Gregory & David T. Breault

  7. Department of Endocrinology, Boston Children’s Hospital, Boston, MA, USA

    David T. Breault

  8. Harvard Stem Cell Institute, Cambridge, MA, USA

    David T. Breault

  9. Vascular Biology Program and Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA

    Donald E. Ingber

  10. Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA

    Donald E. Ingber

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Contributions

S.J.-F., F.S.G., E.L.C., J.M.S.C., R.N. and D.E.I. designed the research. S.J.-F., E.L.C., F.S.G., B.N., C.W.F., A.T., A.B., B.S. and M.J.C. performed experiments. S.J.-F., F.S.G., D.M.C., E.L.C., B.N., D.L.K., R.N. and D.E.I. analysed and interpreted the data. K.E.G. helped to prepare infant microbiota. D.T.B. established and prepared human ileal organoids. S.J.-F., F.S.G., E.L.C., D.M.C. and D.E.I. wrote the Article with input from B.N., O.L., J.M.S.C. and R.N. All authors reviewed, discussed and edited the manuscript.

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Correspondence to Donald E. Ingber.

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D.E.I. holds equity in Emulate, Inc., consults for the company and chairs its scientific advisory board.

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Jalili-Firoozinezhad, S., Gazzaniga, F.S., Calamari, E.L. et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng 3, 520–531 (2019). https://doi.org/10.1038/s41551-019-0397-0

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