The human lung microbiome progressively diminishes in the distal alveolar regions.

Extensive investigations with sequencing methods demonstrate a large and diverse microbiome even in profound areas of the lung. However, there is still substantial lack of cultivation-based evidence and of the viability of the resident microorganisms. We collected human tissue specimens obtained from various regions during lung transplantations and from operations in distal alveolar areas. We characterized the samples by histology and applied sequencing, culture and imaging methods. Sequencing data detected the following trends in the composition of the microbiome: (i) From proximal to distal samples we observed a bacterial shift from Staphylococci, Streptococci and Corynebacteria towards preferentially anaerobically growing bacteria; (ii) we found large variations between individual patients regarding the detected bacterial genera. Culture and imaging methods revealed almost no viable microorganism in the distal alveolar regions in these patients. Bacterial signals detected by sequencing in the lung are likely due to very low numbers of bacteria and/or their remnants.