The lung mycobiome in the next-generation sequencing era

Geographic variation in the aetiology, epidemiology and microbiology of bronchiectasis

“…Culture-based identification, part of the routine diagnostic microbiology work up in bronchiectasis is inefficient for fungal detection because most fungal species do not grow on common laboratory media [124]. To overcome this, work employing next-generation sequencing (NGS) such as targeted amplicon sequencing and whole-genome shotgun metagenomics may reveal the true diversity of fungal microorganisms within the microbiome that may colonise and contribute to pulmonary pathology in bronchiectasis and as such should be a focus for future work [103,104,125]. Figure 3 summarises the 'microbiome' in bronchiectasis that consists of the 'bacteriome' , 'virome' and 'mycobiome' where based on country, the predominant organism has been identified and geographical differences outlined between Europe, the US and the Asia-Pacific.…”

Legionella pneumophilainfection and antibiotic treatment engenders a highly disturbed pulmonary microbiome with decreased microbial diversity

“…The fungal microbiome fraction was mainly composed of species belonging to the phyla Basidiomycota, and Ascomycota ( Figure 3A ). These two phyla are reported to be the most abundant ones in the human respiratory tract [6]. The major taxa that we identified during the entire sampling period were unclassified species belonging to Agaricomycetes (16-50%), Ascomycota (20-44%), Agaricales (10-18%) and Basidiomycota (8-16%).…”

“…The healthy lung mycobiome is mainly composed of environmental fungi belonging to the phyla Ascomycota and Basidiomycota such as Davidiellaceae, Eurotium Eremothecium , and Cladosporium , while during disease a higher abundance of pathogenic species belonging to the genera Aspergillus , Malassezia or Candida are present [6]. Commensal fungi, like bacteria, seem to participate in immune system stimulation, inflammatory response and protection against pathogens [5, 6]. In contrast to the lung micro- and mycobiome that starts to be investigated better, the presence of eukaryotes, archaea and viruses among the lung microbiota has been very little investigated like for most other body habitats.…”

Anatomical Uniqueness of the Mucosal Immune System (GALT, NALT, iBALT) for the Induction and Regulation of Mucosal Immunity and Tolerance

“…The mucosal lining the upper and lower respiratory tracts is constantly exposed to inhaled antigens and has endogenous microbial communities [172], although the density of the respiratory microbiota is dramatically less than that in the gut, and the species that compose these communities are also different [173]. As a result, MALTs that trigger local immune responses are present in the upper respiratory tract and nasal passages as well as in the lower respiratory tract and lung.…”