Extended Data Fig. 7: Trends in total microbial loads for all three kingdoms.

a–c, Scatter plots of rDNA-based total abundances of bacteria (a), fungi (b) and archaea (c) against infant day of life (DOL), measured by MK-SpikeSeq in the first phase. The red lines denote the linear regression fit and the 90% confidence bands of the best-fit line of absolute abundances on a logarithmic scale. Spearman correlations show that bacterial and archaeal—but not fungal—loads are positively associated with infant age. Samples with an undetectable kingdom-specific rDNA signal are not plotted. For archaea that show scarce signal in the cohort (c, left), a separate presence–absence plot and Χ² test of binned samples (c, right) also show a positive correlation between archaeal loads and infant age. d, Diagnostics for linear mixed-effects model.