Mycobiome in the Lower Respiratory Tract – A Clinical Perspective

Abstract

Recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the 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, also the mycobiome has gained attention. Lower respiratory tract (LRT) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., HIV infection, lung transplantation, and 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. It has been proposed that the mycobiome diversity associated with LRT can vary with different stages of diseases. Overall, Candida was the dominant fungal genus in LRT samples. In this review, we summarize the recent findings regarding the human LRT mycobiome from a clinical perspective focussing on characterization of investigated patient groups and healthy controls as well as sampling techniques. From these data, clinical implications for further studies or routine practice are drawn. To obtain clinically relevant answers efforts should be enhanced to collect well characterized and described patient groups as well as healthy individuals for comparative data analysis and to apply thorough sampling techniques. We need to proceed with elucidation of the role of mycobiota in healthy LRT and LRT diseases to hopefully improve patient care.

Geographic variation in the aetiology, epidemiology and microbiology of bronchiectasis

“…While culture based detection of airway bacteria is routinely used in bronchiectasis, next-generation sequencing (NGS) approaches are being used in research as a faster and more robust alternative for identifying airway pathogens [65,66,102]. Such culture-independent sequencing methodologies have been applied in bronchiectasis and identify a greater degree of airway microbial diversity (Table 1) [103,104]. These methods are not yet appropriate for clinical use because of the challenges in bioinformatic analysis and standardisation.…”

“…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.…”

Microbiota Core in Central Lung Cancer with Streptococcal Enrichment as a Possible Diagnostic Marker

“…In terms of taxonomy, affected bronchi from patients had an enrichment of the Basidiomycota phylum with higher populations of Malassezia genus, whereas the enriched taxon in healthy individuals was the Ascomycota phylum and the genera Candida and Saccharomyces, as previously described [41,52]. Although the public databases are increasing exponentially, it is important to note that a major limitation to describing the mycobiome is the lack of available taxonomic records.…”

Analysis of airway microbiota in adults from a Brazilian cystic fibrosis center

“…The follow-up time of this study-approximately 1 yearmay have contributed to the lack of greater baseline data for the longitudinal analysis. Another possible explanation for the low correlation between the microbiome of CF sputum samples and the clinical course of the disease was the fact that the disease is driven by mucosal events that may be reflected slightly on the sputum, or that the activity of the microbiome changes independently from the bacterial load, being affected by other events, such as the expression of virulence factors, for example [39].…”