Research Article

Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis

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Science  08 Mar 2019:
Vol. 363, Issue 6431, eaat4042
DOI: 10.1126/science.aat4042

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Hooking into antigen transfer

Segmented filamentous bacteria (SFB) are anaerobic, spore-forming, clostridia-like organisms that are important immune modulators in the mammalian gut. For some reason, SFB do not provoke inflammatory responses. Ladinsky et al. probed the mechanistic basis of this soothing effect in mice. SFB attach tightly to intestinal epithelial cells via a hook-like structure. Bacterial material is extruded from the hook and enters the host cell by endocytosis. An extruded SFB protein called P3340 is shuttled by the host protein cell division control protein 42 homolog (CDC42) through the endosomelysosome vesicular pathway to the basolateral side of the intestinal epithelial cell. Here, it prompts an immunomodulatory SFB-specific CD4 T helper 17 cell response, possibly via intestinal macrophages.

Science, this issue p. eaat4042

Structured Abstract


Although commensal microbes populate our barrier surfaces without causing obvious disease, they nonetheless modulate host physiology and immunity. Commensal bacteria can regulate host T cell differentiation and function, and a large fraction of mucosal tissue-resident T cells are thought to recognize commensal antigens, which triggers the T cells’ participation in the maintenance of mucosal homeostasis. Therefore, the mechanisms by which commensal antigens or other microbiota-derived immune mediators are acquired and processed to activate specific types of host T cells are of substantial interest. Understanding commensal-host communication and commensal antigen acquisition is crucial for understanding the mechanisms of tissue homeostasis and for the design of alternative strategies for specific regulation of mucosal health and pathologies.


Host-microbe interactions at the cellular level have been almost exclusively studied in the context of invasive pathogens. Our study explored whether noninvasive commensal microbes may possess previously unappreciated modes of antigen acquisition or communication with the host for maintenance of mucosal T cell homeostasis.


We examined the interaction of segmented filamentous bacteria (SFB), well-characterized T helper 17 (TH17) cell–inducing epithelium-associated commensal microbes, with intestinal epithelial cells (IECs) by means of electron tomography. SFB were not phagocytosed by IECs and did not penetrate the IEC cytosol. SFB and IEC communicated through the generation of endocytic vesicles at the tip of the SFB-IEC synapse. The vesicles were released into the host IEC and contained an SFB cell wall–associated protein, which is a known immunodominant T cell antigen for the generation of mucosal TH17 cells. Endocytic vesicles were present in virtually every SFB-IEC synapse in healthy animals, suggesting a highly dynamic process that occurs at steady state. SFB antigenic proteins were transferred through this process inside IECs and shuttled throughout the IEC endosomal-lysosomal network. Mechanistically, the endocytic process was clathrin-independent but dependent on dynamin and the actin regulator cell division control protein 42 homolog (CDC42). Chemical inhibition of CDC42 activity in vivo led to disruption of the endocytosis. Genetic deletion of CDC42 in IECs resulted in disruption of endocytosis induced by SFB, loss of transfer of antigenic proteins inside IECs, and substantial decrease in the activation of SFB-specific CD4 T cells and SFB-induced TH17 cell differentiation. An examination of a few other epithelium-associated or TH17 cell–inducing intestinal microbes showed dissimilar interactions with IECs, and therefore, SFB currently are the first and only example of this process.


Our results reveal a mechanism of interaction between a commensal microbe and the host that directs transfer of microbial proteins inside host cells. They also describe a previously unappreciated pathway for antigen acquisition from luminal commensal bacteria through IECs. Our results underscore that the study of the interactions of key individual commensal microbes with the host may uncover unappreciated biological pathways. Targeting such pathways may allow for ways to specifically regulate commensal versus pathogenic interactions, regulate the immunomodulatory effects of individual members of the gut microbiota, or design alternative strategies for mucosal vaccination.

SFB use microbial adhesion-triggered endocytosis (MATE) to transfer T cell antigens into IECs and modulate host T cell homeostasis.

SFB interaction with IEC triggers formation of endocytic vesicles that contain proteins from the SFB cell wall. The vesicles enter host IEC through clathrin-independent and dynamin-dependent endocytosis. SFB proteins are shuttled through the IEC endosomal-lysosomal network and induce activation of lamina propria antigen-specific TH17 cells. MATE, transfer of SFB antigenic proteins, and TH17 activation depend on the actin cytoskeleton regulator protein CDC42.


Commensal bacteria influence host physiology, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB) are transferred into intestinal epithelial cells (IECs) through adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. This process transfers microbial cell wall–associated proteins, including an antigen that stimulates mucosal T helper 17 (TH17) cell differentiation, into the cytosol of IECs in a cell division control protein 42 homolog (CDC42)–dependent manner. Removal of CDC42 activity in vivo led to disruption of endocytosis induced by SFB and decreased epithelial antigen acquisition, with consequent loss of mucosal TH17 cells. Our findings demonstrate direct communication between a resident gut microbe and the host and show that under physiological conditions, IECs acquire antigens from commensal bacteria for generation of T cell responses to the resident microbiota.

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