Extended Data Fig. 1: Overview of total stool microbial shotgun metagenomic sequencing.

a, Percentage of reads mapped to human or microbial genomes or that were unassigned. The types of DNA detected are indicated on the right. b, Correlation between the percentage of human DNA and sampling time after delivery using month-0 samples (n = 20). The percentage of human DNA is shown on the y axis, and the sampling time after delivery is shown on the x axis. The black dashed line shows the linear regression line and the grey-shaded region shows the 95% confidence interval for the slope. Two-sided Spearman’s rank-order correlation method was used to test significance (R represents Spearman’s ρ). c, Taxonomic composition of bacteria at the phylum level. The total read number is shown on the y axis; the x axis shows different samples. d, Bacterial richness. The y axis shows the richness calculated as the number of observed species. e, Bacterial diversity. d, e, A two-sided Wilcoxon rank-sum test was used to test the difference between different age groups (n = 20 infants at three time points). The horizontal lines in the box plots represent the third quartile, median and first quartile; whiskers extend to ±1.5× the interquartile range. The dots represent the outliers.