Identification of host-microbiome interactions in nasal diseases using multiomics integration

Background An imbalance in the nasal microbiome is thought to be closely related to the development of nasal diseases. However, nasal microbiome-host interactions have rarely been studied. Objective The aim of this study was to comprehensively investigate the cross-talk between mucosal gene expression and the microbiota in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and nasal inverted papilloma (NIP). Methods We performed a cross-sectional study of 43 patients with CRSwNP, 27 patients with NIP and 34 controls using 5R 16S rRNA gene sequencing. A total of 40 CRSwNP samples, 20 NIP samples and 20 control samples were analyzed according to host transcriptome. Results This study describes the microbiome characteristics of the specific nasal mucosal microenvironment in patients with CRSwNP and NIP. In CRSwNP and NIP samples, host gene-bacteria interaction analysis revealed multiple host pathways that were associated with the nasal microbiota, mainly including multiple host pathways such as those related to immunity, metabolism, host defense, and cell proliferation. In addition, in both nasal diseases, the shared host pathways that were associated with the nasal microbiota were mainly immune response-related pathways, such as the NF-kappa B signaling pathway. In CRSwNP, disease-specific pathways that were associated with the nasal microbiota were mainly related to host recognition and the immune response, while in NIP, disease-specific pathways were mainly related to cell proliferation. Based on Bayesian network analysis, we found that the abundance of Geobacillus stearothermophilus in nasal polyps was significantly correlated with the NF-kB pathway activation, and we further proved this correlation. Conclusion Our study highlights the complex interplay between the nasal microbiota and host-population patterns, with disease-specific and shared host gene-microbiome associations associated with different features of nasal disease. Our findings may provide new insights into the pathophysiology of nasal diseases and a theoretical basis for future microbiota-based treatment strategies for nasal diseases.