Fig. 1

Detection of S. lugdunensis and S. aureus in the nose of study participants by cultivation or metagenome analysis. A Culture outcome for S. lugdunensis and S. aureus in the nasal samples and abundance of metagenome reads for the two species. For each time point and each proband, the culture results for S. lugdunensis (circles filled in grey) and S. aureus (circles filled in yellow) are shown (the initially culture-negative group of probands I–J, which was negative for S. lugdunensis at the first time point, is separated by two dashed lines). A negative culture outcome is indicated by empty circles. For time points 18 and 23 months, also the relative DNA abundances (= rel. proportions of reads specifically for S. lugdunensis and S. aureus) in the metagenomes are indicated by color-coded squares. The color intensity indicates the relative DNA abundance compared to the corresponding median value of DNA abundance (see legend on the right). B Relative proportions (in percent) of S. lugdunensis or S. aureus metagenome reads in microbiomes with positive or negative culture outcomes. Left: relative proportions of S. lugdunensis reads versus culture outcome. The median percentage for culture-positive samples: 0.33%; the median percentage for culture-negative samples: 0.09% (Mann-Whitney test, p = 0.0159). Right: relative proportions of S. aureus reads versus culture outcome. Median percentage for culture-positive samples: 47.27%; median percentage for culture-negative samples: 1.34% (Mann-Whitney test, p = 0.0072). Relative read proportions are shown on the y-axes in the log scale. Medians are indicated by horizontal lines with 95% confidence intervals