Fig. 4

Taxonomic annotation of longitudinal case studies of shotgun-sequenced Staphylococcus species. Shotgun-sequenced Staphylococcus species were analysed in 13 longitudinal case studies together with healthy controls. The individual case studies were grouped together with follow-up samples 1 month and 3 months later (where available) and with or without healthy household controls at the time of initial sampling and 1 month later for one case study. The x-axis shows the proportional abundance of the top 25 species with a minimum abundance of 0.1% across the patient samples, which covers 97.85% of all Staphylococcus reads within the longitudinal cohort. The matching species of the healthy controls are presented at the bottom of Additional file 4: Figure S4 for comparisons. aGPA, active granulomatosis with polyangiitis (GPA); inGPA, inactive GPA; HC, unrelated healthy controls, HHC, healthy household controls