Sniffing out interspecies interactions in the human nasal microbiota

The human nasal microbiota plays a critical role in modulating colonization and infection by pathobionts such as Staphylococcus aureus and Streptococcus pneumoniae, which are significant contributors to global morbidity and mortality, including antimicrobial-resistant infections. Nasal colonization by these bacteria is a well-established risk factor for invasive disease, yet only subsets of individuals harbor these organisms, suggesting complex host-microbe and microbe-microbe interactions govern colonization dynamics. This study employs human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface to model bacterial colonization under physiologically relevant conditions (34 °C), enabling mechanistic investigation of microbial interactions and epithelial responses. Monocolonization experiments demonstrate that S. aureus, S. pneumoniae, and Dolosigranulum pigrum—a common nasal commensal negatively associated with S. aureus colonization—can establish stable populations within the mucus layer without overt cytotoxicity, except for occasional epithelial irritation by S. aureus. Cytokine profiling reveals both general innate immune activation and species-specific responses, including IL-18 induction by live S. aureus and suppression of CXCL10 by D. pigrum. Using transposon sequencing, D-alanine aminotransferase (dat) was identified as a critical S. aureus fitness factor for nasal colonization, with disruption causing a >3,000-fold colonization defect on HNOs that is chemically complemented by exogenous D-alanine. These findings highlight the importance of bacterial metabolic pathways in colonization fitness within the nasal niche. The HNO model also facilitates testing of multi-species interactions and phage-mediated bacterial killing, offering a promising platform to identify microbial strains, compounds, and phages that could inform novel preventive and therapeutic strategies against nasal pathobiont infections.