Fig. 1: Development of the microbiota community composition for individual niches over time.

Non-metric multidimensional scaling (nMDS) plot (a), based on Bray–Curtis (BC) dissimilarity between samples, visualising the overall gut microbial community composition stratified for each niche per time point. Each data point represents the microbial community composition of one sample. The ellipses represent the standard deviation of data points belonging to each group, with the centre points of the ellipses calculated using the mean of the coordinates per group. The stress of the ordination was 0.18. In panel b the temporal community stability for each niche is shown. As a measure of microbiota stability, we calculated the Bray–Curtis distance between consecutive sample pairs belonging to each individual per time interval, i.e., between week 1 and month 2, between month 2 and month 4, and between month 4 and month 6. Boxplots with medians are shown; the lower and upper hinges correspond to the first and third quartiles (the 25th and 75th percentiles); the upper and lower whiskers extend from the hinge to the largest and smallest value no further than 1.5*IQR from the hinge; outliers are plotted individually. Fec faeces, np nasopharynx, sal saliva. Temporal stability was highest for the saliva samples in early-life, which was later overtaken by a higher stability in consecutive faecal samples (median BC dissimilarity between months 4 and 6 for faecal samples 0.18 versus 0.29 for saliva, Wilcoxon test, p < 0.0001).