a, Microbiota alpha diversity (Shannon diversity index) increased over developmental time. The violin plot outlines the kernel probability density; the width of the shaded area represents the proportion of the data shown. Centre line shows median; box limits indicate the 25th and 75th percentiles; whiskers extend 1.5× the interquartile range from the 25th and 75th percentiles; and outliers are represented by dots. The gut microbiotas of babies on day 4 (n = 310 individuals), 7 (n = 532 individuals) and 21 (n = 325 individuals), and in infancy (n = 302 individuals), as well as from matched mothers (n = 175), are plotted. b, c, Stability of the gut microbiota, stratified by inter-individual (day 4, n = 310 individuals; day 7, n = 532 individuals; and day 21, n = 325 individuals) and intra-individual comparisons in sliding time windows (day 4 to 7, n = 274 individuals and day 7 to 21, n = 285 individuals) during the neonatal period (b), in the context of the overall infancy period (c). Microbiota stability measurements from the TEDDY15 study (the earliest measurements on day 90, and at year 3) are plotted in crosses. Solid lines show the median per time window. Shaded areas show the 99% confidence interval, estimated using binomial distribution. Error bars indicate median absolute deviation. The significance of the difference between groups was determined by two-sided Wilcoxon rank-sum test.