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

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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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.

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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.

Author information

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.

Competing interests

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

Correspondence to Donald E. Ingber.

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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.