Birth mode was significantly associated with the microbiome in months 3–6 by 16S rRNA gene sequencing and in all time points up to month 14 by metagenomic sequencing (see Supplementary Table 1). Curves show LOESS fit for the data per category, and shaded areas show permutation-based 95% confidence intervals for the fit. a, Longitudinal development of the Bacteroides genus as determined by 16S rRNA gene sequencing (n = 11,717). b, Longitudinal development of the six most abundant species within the Bacteroides genera as determined by metagenomic sequencing (n = 10,867). Grid overlay added to aid visual interpretation. c, NMDS ordination plots showing the mean centroid of each birth mode group stratified by Bacteroides positive or negative based on detection 16S rRNA gene sequencing. Plots include only the first sample obtained from a patient within a given time point for months 3–6, 7–10 and 11–14 (n = 2,257). Centroid size based on number of samples and the bars represent the ±95% confidence interval. d, Longitudinal development of the alpha diversity (richness and Shannon’s diversity) with birth mode further stratified according to Bacteroides positive or negative (n = 11,717). e, Longitudinal development of the microbiome maturation based on the microbiota age and MAZ score against the age of the infant at sampling (n = 11,717). Birth mode was further stratified according to Bacteroides positive or negative.