Spatial variability of the microbiome in chronic rhinosinusitis is associated with the patients’ clinical characteristics but not with sinus ostia occlusion

The sinus microbiome in patients with chronic rhinosinusitis (CRS) is considered homogenous across the sinonasal cavity. The middle nasal meatus is the recommended sampling site for 16S rRNA sequencing. However, individuals with unusually high variability between the middle meatus and the sinuses were identified in previous studies. Patients with CRS present various mechanisms of disease evolution. Their sinuses are frequently separated from the middle meatus by pathological changes. This study aimed to identify which factors determine increased microbial heterogeneity between sampling sites in the sinuses. In this cross-sectional study samples for 16S rRNA sequencing were obtained from the middle meatus, the maxillary and frontal sinus in 50 patients with CRS. The microbiome diversity between sampling sites was analyzed in relation to the size of the sinus ostia and clinical metadata. In approximately 15% of study participants, the differences between sampling sites within one patient were greater than between the patient and other individuals. Contrary to a popular hypothesis, obstruction of the sinus ostium resulted in decreased dissimilarity between the sinus and the middle meatus. The dissimilarity between the sampling sites was patient-specific: greater between-sinus differences were associated with greater meatus-sinus differences, regardless of the drainage pathway patency. Decreased spatial variability was observed in patients with nasal polyps and extensive mucosal changes in the sinuses. Researchers and clinicians should be aware that sampling from the middle meatus is not universally representative of the sinus microbiome. The differences between sites cannot be predicted from the patency of communication pathways between them. Importance Chronic rhinosinusitis (CRS) affects up to 10% of the population. The microbiome’s importance for its evolution is a subject of intensive research. It is controversial whether the microbiome within an individual is homogenous and whether sampling from one site is representative. Currently, the middle nasal meatus (the drainage pathway from the maxillary, frontal and anterior ethmoid sinuses) is a recommended sampling site. This study assessed the differences between microbial communities in the middle nasal meatus and the sinuses in 50 patients with CRS. In approximately 15% of patients, we noted significant differences between sampling sites that were not associated with their anatomical separation by pathological tissue. The degree of microbiome variability was associated with the patients’ clinical characteristics and comorbidities. Our results show that sampling limited to one site can result in incorrect therapeutic decisions and erroneous conclusions in future studies. ### Competing Interest Statement The authors have declared no competing interest.