Figure 3

Differences in nasal Staphylococcus species composition between sample groups. a Differences in shotgun-sequenced nasal Staphylococcus species composition between sample groups were visualised using non-metric multi-dimensional scaling (NMDS plot) and correspondence analysis (CA plot). The significance of the separation between the different sample groups was further assessed by PERMANOVA test (statistical test for bacterial beta diversity). The overall group comparison was statistically different (P = 0.0031). The individual group comparisons revealed statistical differences in beta diversity between aGPA patients and HC (P = 0.0007) and between aGPA patients and disease controls (P = 0.0023). Beta diversity was also statistically different between the HC and inGPA patients (P = 0.0168) and between HC and HHC (P = 0.0168). b Scatter dot plot presentation of statistically associated S. epidermidis and S. aureus. S. epidermidis was found at statistically higher abundance in the HC group compared with aGPA patients. S. aureus was found at statistically higher abundance in aGPA patients compare to DC patients and the HC groups. c The direction of the Spearman’s correlation coefficient value (positive or negative value on the y-axis) determines whether S. epidermidis and S. aureus are either positively or negatively associated with the different sample groups. aGPA, active granulomatosis with polyangiitis (GPA); inGPA, inactive GPA; DC, disease controls (eosinophilic GPA and microscopic polyangiitis); HC, unrelated healthy controls; HHC, healthy household controls; PERMANOVA, permutational multivariate analysis of variance