Abstract
Saccharibacteria are ultrasmall episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated the tripartite interactions between Saccharibacteria (Nanosynbacter lyticus strain TM7x and other strains), their host/non-host-bacteria, and human oral gingival epithelial cells. Both host and non-host-bacteria strongly induce proinflammatory cytokines in epithelial cells, while Saccharibacteria alone elicits limited immune activation. Remarkably, Saccharibacteria dampened proinflammatory cytokine responses to host/non-host-bacteria during coinfection. Mechanistically, this effect results from Saccharibacteria-mediated clustering and endocytosis of surface TLR2 receptor, ultimately leading to reduce TLR2-mediated cytokine signalling. Sacchribacteria type IV pili appendages facilitate epithelial cell binding and subsequent immune dampening via direct interaction between pili adhesins and TLR2. High resolution imaging shows that Saccharibacteria are internalized by epithelial cells through caveolin-mediated endocytosis, subsequently colocalize with endosome markers, and eventually are trafficked to lysosomes for degradation. Moreover, a subset of the Saccharibacteria survives lysosomal degradation and retains the ability to reinfect host-bacteria, highlighting a mechanism for transient persistence in the oral microbiome and a vital role in human immune and microbiome modulation.
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Material availability
All unique reagents and bacterial strains generated in this study are available from the lead contact upon completion of a Material Transfer Agreement.
Data availability
All the data that support the findings of this study are available within the article and its supplementary files. The raw RNA sequencing data are deposited in GEO under the accession number GSE296366. Source data are provided with this article. Source data are provided with this paper.
Code availability
No custom codes were generated in this study. Source data are provided with this paper.
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Acknowledgements
This research was supported by grants from the a under awards 1R01DE031274 (B.B.) 1R01DE023810 (X.H., J.S.M.) and T90 DE026110-07 (A.S.G.). Forsyth Institute Advanced Microscopy Core Facility supported by NIH 1S10OD034405-01 and Harvard Center for Nanoscale Systems (CNS) facilities. We acknowledge Dr. Ning Yu for providing the HGEPp cell line and Lujia Cen for general lab support. Jennifer Gundrum and Kyle Bredin provided technical support with microscopy and flow cytometry. Dr. Mary Ellen Davey and Dr. Hyun Young Kim provided technical support for using the NanoSight.
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Conceptualization by D.C., X.H., J.S.M., and B.B. Data acquisition by D.C., A.S.G., M.K., A.K., and L.L. Methodology by D.C., A.S.G., M.K., K.A.K., K.S.S., P.D., R.J.L., J.S.M., and B.B. Formal analysis by D.C., K.A.K., K.S.S., P.D., R.J.L., J.S.M., X.H., and B.B. Resources provided by R.J.L., J.S.M., X.H., and B.B. Data Curation by K.A.K., K.S.S., and J.S.M. Original draft written by D.C. and B.B. Review and editing by D.C., A.S.G., K.S.S., R.J.L., JSM, X.H., and B.B. Visualization by D.C. Supervision by B.B.
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Chouhan, D., Grossman, A.S., Kerns, K.A. et al. Ultrasmall oral Saccharibacteria modulate gingival immunoactivation through type IV pili and TLR2-dependent endocytosis. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70546-5
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DOI: https://doi.org/10.1038/s41467-026-70546-5
