2.2. Stool Sample Collection and Processing 
During the third trimester of pregnancy (weeks 32–38 gestation), 120 participants of the VDAART trial provided a stool sample. Subjects were asked to collect a 0.5 teaspoon-sized sample 1 to 2 days before a study visit and store the sample in a home freezer before transport with a freezer pack to the study site. Stool was not collected if participants had used antibiotics in the previous 7 days. After delivery to the study site, stool samples were immediately stored at −80 °C. Microbiome profiling was performed by sequencing the 16S rRNA hypervariable region 4 (V4 515F/816R region) on the Illumina MiSeq platform at Partners Personalized Medicine (Boston, MA, USA). Of the 120 stool samples collected, 2 with fewer than 1000 reads measured were excluded from the analysis, leaving 118 samples.