The culturome of the human nose habitats reveals individual bacterial fingerprint patterns

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Abstract

The complex anatomy of the human nose might offer distinct microbial niches. Microbiota composition may affect nose inflammatory diseases andStaphylococcus aureuscarriage. Considering different nasal cavity locations, microbial colonization was analysed across individuals exhibiting chronic nasal inflammatory diseases (n= 18) and those without local inflammation signs (n= 16). Samples were collected systematically during surgery and examined by an extensive culture-based approach and, for a subset, by 16S rRNA gene community profiling. Cultivation yielded 141 taxa with members ofStaphylococcus,CorynebacteriumandPropionibacteriumas most common isolates comprising the nasal core culturome together withFinegoldia magna.Staphylococcus aureuswas most frequently found in association withStaphylococcus epidermidisandPropionibacterium acnes, and the posterior vestibules were redefined asS. aureus' principle habitat. Culturome analysis revealed host-specific bacterial ‘fingerprints’ irrespective of host-driven factors or intranasal sites. Comparisons between cultivable and molecular fingerprints demonstrated that only a small fraction of phylotypes (6.2%) was correlated. While the total number of different phylotypes was higher in the molecular dataset, the total number of identifications down to the species level was higher in the culturomic approach. To determine host-specific microbiomes, the advantages of molecular approaches should be combined with the resolution and reliability of species identification by culturomic analyses.

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