Fig. 1: Genomic characteristics of airway mucosal bacteria.

a Culture collection phylogeny based on average nucleotide identities between genomes with 1000 bp fragment length. Putatively novel species are highlighted in red (indicating that it is not related to any species in the TypeMat DB or NCBI Prok DB (P < 0.05) when assessed using MIGA and not assigned to a known species or incongruent species assignment using gtdbtk). Greyed-out isolates are not fully supported by MIGA and gtdbtk. Genome completeness and contamination are displayed as a bar chart. AMR finder was used to identify antimicrobial resistance genes at the protein level (red panel). Virulence factors were identified using the VFDB and Ariba databases and binned into 15 categories (heatmap). The asthma status of the host is indicated in the black asthma/control panel. Cultivation conditions are indicated in green circles for selected growth media, blue rectangles for aerobic, and white rectangles for anaerobic cultivation. Positive Gram staining for GNB, GNC, GPB, GPC, and other Gram staining is shown in black circles. The neuraminidase activity was tested if a blue star was present and was filled for the positive test and white for a negative test. b Taxonomic novelty as calculated by MIGA using TypeMat reference. The scatterplot shows support (P-value, vertical axis) for each taxon relative to complementary hypotheses that this taxon is a previously known one (red markers) or a novel one (cyan markers) at each taxonomic level (horizontal axis). Many of the isolate collections constitute novel species within known genera. c Composition of bacteria isolated and cultivated from five subjects. Counts are shown for all lineages from species level (outer circle) to phylum level (inner circle) in squared brackets. The ETE3 toolkit was used to fetch taxonomic lineages for all genera of cultured isolates¹⁰¹. The number of unique species was summed up and visualised along with their lineages using Krona tools¹⁰².