Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids

Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.

Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.