Fig. 3

Most of the S. lugdunensis-colonized study participants can be assigned to CST3/5 and CST7. A Nasal microbiome profiles at the genus level. Relative proportions of bacterial genera present in the nasal microbiomes at time points 18 months and 23 months are presented by stacked bar charts. The different bacterial genera are indicated by colours as shown in the legend on the right. The presence of S. lugdunensis reads in the metagenomes is indicated (Slu). The microbiome profiles that could be assigned to the community state types (CST) published by Liu et al. [11] are labeled accordingly. Profiles not fitting to one of these types are designated “nd”. B Clustering of the microbiome genus profiles by principal coordinates analysis. Comparison of the microbiome profiles at genus level by principal coordinates analysis based on evolutionary distances according to Hellinger [18]. The data showed the highest variation along principal component 1 (PC1, 52.6%). Principal component 2 (PC2) represents a variation of 15.0%. The microbiomes are represented by colored circles and numbers correlating with the corresponding metagenome analysis time point (−1, 18 months or −2, 23 months). Clusters representing the two main microbiome types CST3/5 and CST7 are labeled correspondingly. Vectors drawn and labeled in light grey point towards the prevalent genera in the clusters/subclusters. Note that sample K-2 clusters with the CST3/5 microbiomes but is de facto regarded as CST1 because the Staphylococcus proportion is mainly composed of S. aureus