gms | German Medical Science

Culture-based approaches are inadequate to completely understand the interactions of the host and the microbiome, and culture independent molecular assays are more efficient in describing microbial communities [1]. After omitting the paradigm that the healthy lung is sterile, it is now believed that the lung microbiome as a poly-microorganism unit contributes to pathogenesis of various diseases. Most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. Recently, the mycobiome has gained attention and lower respiratory tract (LRT) diseases (e.g. chronic obstructive pulmonary disease, cystic fibrosis) and other diseases or conditions (e.g. HIV infection, lung transplantation, treatment at intensive care units) have been investigated with regard to possible involvement of mycobiome in development or progression of diseases. It has been shown that diversities of mycobiome in the LRT vary in different populations and conditions and links to different stages of diseases have been proposed. However, most of studies are based on sputum samples and contamination by mycobiota of the oral cavity can not be excluded. As shown by Ghannoum et al. [2] the oral cavity of 20 healthy non smoking adults contained various fungal genera (74 culturable and 11 non-culturable) detected by next generation sequencing (NGS) in oral washes. The total number of culturable species detected was 101, with each individual having between 9–23 species. Candida spp. was detected in 75%, Cladosposporium spp. in 60%, Aspergillus spp. and Fusarium spp in 35% and 30% of individuals. C. albicans was the most frequently identified species and was detected in 40% of all investigated subjects. Therefore, mycobiota studies investigating the lower respiratory tract by sampling sputum or by passing the oral cavity with endotracheal/endobronchial catheters or bronchoscopes should be interpreted with caution. Thorough description of sampling techniques and presentation of clinical data including underlying disease and treatments as well as prudent selection of comparators (i.e. healthy adults) are necessary for rational assessment of mycobiota data.