Fig. 2: Ecology and structure of airway microbial communities.

a Mapping of the 50 most abundant OTUs onto 126 novel airway isolates. Isolates are grouped into 16 clusters according to the distance and branching order of their inferred Kegg Ontology (KO) gene content. OTU/isolate nt identity is shown as 95–97% (light blue), 97–99% (medium blue), and 100% (dark blue). The complex relationship between OTUs and isolates reflects multiple copies of the 16S rRNA gene in different taxa, but in general, captures KO phylogenetic structures. b Comparison of abundance (left) and prevalence right) of bacterial OTUs in populations from northern (CELF) and southern (BUS) hemispheres. The species distribution is similar between the CELF and BUS studies. c Comparison of abundance (left) and prevalence right) of bacterial OTUs in the posterior oropharynx (ptOP) and the left lower lobe (LLL) in CELF subjects. The relative abundance of organisms in ptOP is very similar to those in the LLL, although absolute abundance is an order of magnitude lower in the LLL. Lower abundance OTUs in the CELF dataset are more prevalent in the upper than lower airways. d Spearman correlations between the abundance of organisms in the CELF ptOP samples, showing a high degree of positive and negative relationships between OTUs that is the basis of WGCNA network analysis. Common phyla are colour coded at the top of the matrix, and WGCNA modules (named for the most abundant membership) are at the bottom. Network module membership may be dominated by a single phylum (e.g., the Haemophilus or Streptococcus modules) or contain mixed phyla (e.g., the Veillonella module).