Study participants provided infant stool samples collected at regularly scheduled maternal postnatal follow-up visits (six weeks post partum). Stool was aliquoted in sterile tubes and frozen at −80°C within 24 hours of receipt. Samples were thawed and DNA was extracted using the Zymo DNA extraction kit (Zymo Research). Quantity and purity of the DNA were determined by OD260/280 nanodrop measurement. Reliability and stability of these methods were described by Wu et al 27 (link). Illumina tag sequencing of the 16S rRNA gene V4–V5 hypervariable region was performed at the Marine Biological Laboratories (MBL) in Woods Hole, MA using established methods 28 (link),29 (link). Details of sequencing methods, quality control and filtering, and statistical modeling are presented in the Supplement (see eMethods).