This PDF file includes:

• fig. S1. Experimental design.
  
• fig. S2. Actual body mass in 69 mice discordant to birth mode during early development.
  
• fig. S3. Percent fat in 24 mice discordant to birth mode at 15 weeks of age.
  
• fig. S4. PCoA of Bray-Curtis distances between fecal communities from weeks 3 to 6 in mice born vaginally or by C-section.
  
• fig. S5. Fecal β diversity in males and females discordant to birth mode at different ages.
  
• fig. S6. Fecal β diversity in mice delivered by C-section or vaginally born controls by gender, at different ages.
  
• fig. S7. Fecal intra– and inter–birth-mode-group UniFrac community distances in male and female mice at different ages.
  
• fig. S8. Fecal intra– and inter–gender-group UniFrac community distances in C-section and vaginally born controls at different ages.
  
• fig. S9. Fecal α diversity in mice discordant to birth mode at different ages.
  
• fig. S10. Rarefaction curves of PD whole tree and observed species α diversity metrics.
  
• fig. S11. LEfSE of communities at weaning (week 3) and young adulthood (week 6) by delivery mode.
  
• fig. S12. Average relative abundance of 24 birth mode LEfSe–discriminant taxa over 3 to 6 weeks of age.
  
• table S1. Number of fecal specimens from mouse lineages differing in birth mode.

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