The entire dataset formed 18 distinct clusters based on lowest Laplace approximation. a, Heat map showing the relative abundance of the 25 most dominant bacterial species per each DMM cluster. b, Box plots showing the alpha diversity (richness and Shannon’s diversity) for each DMM cluster. The centre line shows the median, the boxes cover the 25th and 75th percentiles, and the whiskers extend to the most extreme data point, which is no more than 1.5 times the length of the box away from the box. Points outside the whiskers represent outlier samples. c, Transition model showing the progression of samples through each DMM cluster per each time point, from months 3 to 46 of life. Dashed boxes show the three phases of microbiome progression (developmental, transitional and stable phase). Solid squares next to the labels denote the significant changes in phyla and Shannon diversity (H') per phase based on multiple linear regression. All phyla and the H' were significant in the developmental phase, two phyla and the H' were significant in the transitional phase, and no phyla or the H' were in the stable phase. Nodes and edges are sized based on the total counts. Nodes are coloured according to DMM cluster number and edges are coloured by the transition frequency. Transitions with less than 2% frequency were omitted from the plot.