Fig. 2
Baseline nasal microbiota composition in association with pneumococcal carriage3 outcome. Non-metric multidimensional scaling (NMDS) plot where each point represents the microbial community composition of one sample. Samples (n = 116) were coloured according to carriage3 outcome (red, high-dense carriers, n = 49; blue, non-carriers, n = 40 and orange, low-dense carriers, n = 27). The standard deviation of data points within carriage outcome groups is shown. In addition, the 10 highest ranked operational taxonomic units (OTUs) were simultaneously visualized (triangles). The stress value indicates how well the high-dimensional data are represented in the two-dimensional space; a value of ~0.2 indicates a reasonable representation. P values and effect sizes (R2) describing the strength and the significance of the association between baseline nasal microbiota and pneumococcal carriage outcome were generated using PERMANOVA tests, and are adjusted for the month, presence of any virus at baseline, the interactions between carriage outcome and the vaccination group/presence of any virus at baseline. See Table 1 for details
