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The microbiome and innate immunity

Abstract

The intestinal microbiome is a signalling hub that integrates environmental inputs, such as diet, with genetic and immune signals to affect the host's metabolism, immunity and response to infection. The haematopoietic and non-haematopoietic cells of the innate immune system are located strategically at the host–microbiome interface. These cells have the ability to sense microorganisms or their metabolic products and to translate the signals into host physiological responses and the regulation of microbial ecology. Aberrations in the communication between the innate immune system and the gut microbiota might contribute to complex diseases.

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Figure 1: Intestinal epithelial cells orchestrate the host–microbiota interface.
Figure 2: The integration of microbial signals by myeloid cells.
Figure 3: The integration of microbial signals by ILCs.
Figure 4: The hierarchy of anatomy in microbiome–innate-immune-system interactions.
Figure 5: Microbiome–innate-immune-system interactions are involved in multifactorial diseases.

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Acknowledgements

We apologize to those authors whose relevant work could not be included owing to space constraints. We thank the members of the Elinav laboratory for discussions. C.A.T. received a Boehringer Ingelheim Fonds PhD fellowship. N.Z. is supported by the Gilead Sciences International Research Scholars Program in Liver Disease. E.E. is supported by: Y. and R. Ungar; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Gurwin Family Fund for Scientific Research; the Leona M. and Harry B. Helmsley Charitable Trust; the Crown Endowment Fund for Immunological Research; the estate of J. Gitlitz; the estate of L. Hershkovich; the Benoziyo Endowment Fund for the Advancement of Science; the Adelis Foundation; J. L. and V. Schwartz; A. and G. Markovitz; A. and C. Adelson; the French National Center for Scientific Research (CNRS); D. L. Schwarz; the V. R. Schwartz Research Fellow Chair; L. Steinberg; J. N. Halpern; A. Edelheit; grants funded by the European Research Council; a Marie Curie Career Integration Grant; the German–Israeli Foundation for Scientific Research and Development; the Israel Science Foundation; the Minerva Foundation; the Rising Tide Foundation; the Helmholtz Association; and the European Foundation for the Study of Diabetes. E.E. is the incumbent of the Rina Gudinski Career Development Chair.

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Thaiss, C., Zmora, N., Levy, M. et al. The microbiome and innate immunity. Nature 535, 65–74 (2016). https://doi.org/10.1038/nature18847

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