Figure 1.

Establishing the structure and composition of the CF microbiome. (A) A range of respiratory sample types can be assessed, each of which differs with respect to its ease of collection, sensitivity, specificity, and relevance to the lower airways. (B) Samples can be assessed using routine and augmented culture protocols to identify specifically targeted organisms (which allow for pathogen characterization) or an agnostic approach in which next-generation sequencing is used to define the entirety of community constituents. (C) After DNA extraction, microbial communities can be defined based on establishing their gene content either using amplicon (16S ribosomal RNA) amplification or shotgun sequencing (±host DNA depletion strategies) enabling downstream analysis. Figure created with Biorender. Abbreviation: CF, cystic fibrosis.