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

Jianbo Zhang; Yu Ja Huang; Jun Young Yoon; John Kemmitt; Charles Wright; Kirsten Schneider; Pierre Sphabmixay; Victor Hernandez-Gordillo; Steven J. Holcomb; Brij Bhushan; Gar Rohatgi; Kyle Benton; David Carpenter; Jemila C. Kester; George Eng; David T. Breault; Omer Yilmaz; Mao Taketani; Christopher A. Voigt; Rebecca L. Carrier; David L. Trumper; Linda G. Griffith

doi:10.1016/j.medj.2020.07.001

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

Jianbo Zhang, Yu Ja Huang, Jun Young Yoon, John Kemmitt, Charles Wright, Kirsten Schneider, Pierre Sphabmixay, Victor Hernandez-Gordillo, Steven J. Holcomb, Brij Bhushan, Gar Rohatgi, Kyle Benton, David Carpenter, Jemila C. Kester, George Eng, David T. Breault, Omer Yilmaz, Mao Taketani, Christopher A. Voigt, Rebecca L. CarrierDavid L. Trumper, Linda G. Griffith

Department of Mechanical Engineering

Research output: Contribution to journal › Article › peer-review

35 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	74-98.e9
Journal	Med
Volume	2
Issue number	1
DOIs	https://doi.org/10.1016/j.medj.2020.07.001
Publication status	Published - 2021 Jan 15

Bibliographical note

Funding Information:
This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program . This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109 . We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer.

Funding Information:
This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program. This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109. We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer. Hardware Design, Testing, & Troubleshooting, Y.-J.H. J.Y.Y. D.L.T. L.G.G. J.K. B.B. G.R. K.B. D.C. S.J.H. J.C.K. and J.Z.; Bacterial Culture, J.Z. Y.-J.H. M.T. and C.A.V.; Experimental Design, J.Z. Y.-J.H. L.G.G. and D.L.T.; Experiment Execution, J.Z. Y.-J.H. C.W. K.S. and J.K.; Computational Modeling, P.S.; Cell Culture, Y.-J.H. C.W. K.S. V.H.-G. J.Z. D.T.B. G.E. and O.Y.; Data Analysis, J.Z. Y.-J.H. L.G.G. and D.L.T.; Configuration of Figures & Tables, J.Z. and Y.-J.H.; Writing, J.Z. Y.J.H. L.G.G. and D.L.T.; Supervision & Fund Acquisition, L.G.G. D.L.T. R.L.C. and D.T.B. All of the authors commented on and approved the manuscript. A provisional patent was filed.

Publisher Copyright:
© 2020 The Authors

All Science Journal Classification (ASJC) codes

Medicine(all)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.medj.2020.07.001

Cite this

Zhang, J., Huang, Y. J., Yoon, J. Y., Kemmitt, J., Wright, C., Schneider, K., Sphabmixay, P., Hernandez-Gordillo, V., Holcomb, S. J., Bhushan, B., Rohatgi, G., Benton, K., Carpenter, D., Kester, J. C., Eng, G., Breault, D. T., Yilmaz, O., Taketani, M., Voigt, C. A., ... Griffith, L. G. (2021). Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture. Med, 2(1), 74-98.e9. https://doi.org/10.1016/j.medj.2020.07.001

@article{1624370e60894241830900b75a278ed1,

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

abstract = "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.",

author = "Jianbo Zhang and Huang, {Yu Ja} and Yoon, {Jun Young} and John Kemmitt and Charles Wright and Kirsten Schneider and Pierre Sphabmixay and Victor Hernandez-Gordillo and Holcomb, {Steven J.} and Brij Bhushan and Gar Rohatgi and Kyle Benton and David Carpenter and Kester, {Jemila C.} and George Eng and Breault, {David T.} and Omer Yilmaz and Mao Taketani and Voigt, {Christopher A.} and Carrier, {Rebecca L.} and Trumper, {David L.} and Griffith, {Linda G.}",

note = "Funding Information: This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program . This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109 . We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer. Funding Information: This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program. This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109. We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer. Hardware Design, Testing, & Troubleshooting, Y.-J.H. J.Y.Y. D.L.T. L.G.G. J.K. B.B. G.R. K.B. D.C. S.J.H. J.C.K. and J.Z.; Bacterial Culture, J.Z. Y.-J.H. M.T. and C.A.V.; Experimental Design, J.Z. Y.-J.H. L.G.G. and D.L.T.; Experiment Execution, J.Z. Y.-J.H. C.W. K.S. and J.K.; Computational Modeling, P.S.; Cell Culture, Y.-J.H. C.W. K.S. V.H.-G. J.Z. D.T.B. G.E. and O.Y.; Data Analysis, J.Z. Y.-J.H. L.G.G. and D.L.T.; Configuration of Figures & Tables, J.Z. and Y.-J.H.; Writing, J.Z. Y.J.H. L.G.G. and D.L.T.; Supervision & Fund Acquisition, L.G.G. D.L.T. R.L.C. and D.T.B. All of the authors commented on and approved the manuscript. A provisional patent was filed. Publisher Copyright: {\textcopyright} 2020 The Authors",

year = "2021",

month = jan,

day = "15",

doi = "10.1016/j.medj.2020.07.001",

language = "English",

volume = "2",

pages = "74--98.e9",

journal = "Med",

issn = "2666-6359",

publisher = "Cell Press",

number = "1",

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Zhang, J, Huang, YJ, Yoon, JY, Kemmitt, J, Wright, C, Schneider, K, Sphabmixay, P, Hernandez-Gordillo, V, Holcomb, SJ, Bhushan, B, Rohatgi, G, Benton, K, Carpenter, D, Kester, JC, Eng, G, Breault, DT, Yilmaz, O, Taketani, M, Voigt, CA, Carrier, RL, Trumper, DL & Griffith, LG 2021, 'Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture', Med, vol. 2, no. 1, pp. 74-98.e9. https://doi.org/10.1016/j.medj.2020.07.001

TY - JOUR

T1 - Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture

AU - Zhang, Jianbo

AU - Huang, Yu Ja

AU - Yoon, Jun Young

AU - Kemmitt, John

AU - Wright, Charles

AU - Schneider, Kirsten

AU - Sphabmixay, Pierre

AU - Hernandez-Gordillo, Victor

AU - Holcomb, Steven J.

AU - Bhushan, Brij

AU - Rohatgi, Gar

AU - Benton, Kyle

AU - Carpenter, David

AU - Kester, Jemila C.

AU - Eng, George

AU - Breault, David T.

AU - Yilmaz, Omer

AU - Taketani, Mao

AU - Voigt, Christopher A.

AU - Carrier, Rebecca L.

AU - Trumper, David L.

AU - Griffith, Linda G.

N1 - Funding Information: This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program . This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109 . We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer. Funding Information: This study was supported by the NIH R01EB021908 and the Boehringer Ingelheim SHINE Program. This work was supported in part by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109. We are grateful for S. Levine and D. Ma at the Massachusetts Institute of Technology (MIT) BioMicro Center for their help with the RNA-seq data analysis. We thank B. Joughin for helpful discussions and S. Manalis and the MIT 20.330 students for the inspiration to analyze diffusion and reaction in the mucus layer. Hardware Design, Testing, & Troubleshooting, Y.-J.H. J.Y.Y. D.L.T. L.G.G. J.K. B.B. G.R. K.B. D.C. S.J.H. J.C.K. and J.Z.; Bacterial Culture, J.Z. Y.-J.H. M.T. and C.A.V.; Experimental Design, J.Z. Y.-J.H. L.G.G. and D.L.T.; Experiment Execution, J.Z. Y.-J.H. C.W. K.S. and J.K.; Computational Modeling, P.S.; Cell Culture, Y.-J.H. C.W. K.S. V.H.-G. J.Z. D.T.B. G.E. and O.Y.; Data Analysis, J.Z. Y.-J.H. L.G.G. and D.L.T.; Configuration of Figures & Tables, J.Z. and Y.-J.H.; Writing, J.Z. Y.J.H. L.G.G. and D.L.T.; Supervision & Fund Acquisition, L.G.G. D.L.T. R.L.C. and D.T.B. All of the authors commented on and approved the manuscript. A provisional patent was filed. Publisher Copyright: © 2020 The Authors

PY - 2021/1/15

Y1 - 2021/1/15

N2 - 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.

AB - 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.

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U2 - 10.1016/j.medj.2020.07.001

DO - 10.1016/j.medj.2020.07.001

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SP - 74-98.e9

JO - Med

JF - Med

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ER -

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

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

UN SDGs

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