Respiratory microbiota and lower respiratory tract disease

ABSTRACT

Introduction: The respiratory airways harbor a complex succession of ecological niches with distinct but related bacterial communities. Particular challenges of respiratory microbiome research have led to limited scientific output compared to other human microbiomes.

Areas covered: In this review, we summarize the current state of knowledge of the bacterial respiratory microbiome, with a particular focus on associations between the respiratory microbiome and lower respiratory tract conditions.

Expert commentary: There is growing evidence that the respiratory microbiome is associated with lower respiratory infectious diseases and related conditions. Most respiratory microbiome reports are metataxonomic cross-sectional or case-control studies with relatively small sample sizes. Large, prospective projects with metatranscriptomics or metabolomics approach are needed to unravel the effect of the respiratory microbiome on health-related conditions. Moreover, standardization in sampling, library preparation, sequencing techniques and data analysis should be encouraged.

KEYWORDS:

• Respiratory microbiome
• lower respiratory tract infections
• pneumonia
• bronchiolitis
• asthma
• next-generation sequencing
• 16S rRNA

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Additional information

Funding

This work was supported by the Fundação para a Ciência e a Tecnologia (FCT, Portugal) grant to GHTM - UID/Multi/04413/2013, and by ‘Plan Nacional de I+D+I’ and ‘Instituto de Salud Carlos III- Subdirección General de Evaluación y Fomento de la Investigación Sanitaria’, project PI16/00174, and the European Regional Development Fund (FEDER). ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya.