Longitudinal Analysis of Gut Microbiome among healthy women

We conducted metagenomic sequencing of the human gut microbiome among healthy premenopausal women aged 16 to 40 enrolled at the Massachusetts General Hospital. Participants started OC use between January 2015 and August 2018. They provided blood and stool samples at three time points: baseline prior to initiation of OC use, one, and six months after initiation of OC use. Participants self-collected stool samples using a collection vial containing RNA stabilizer RNAlater. Stool samples were handled at ambient temperature and shipped overnight to MGH. Upon arrival, samples were stored in -80 C freezers immediately. The stool self-collection method has previously been validated in the Human Microbiome Project, PMID: 22699610. DNA was extracted from the stool samples preserved in RNAlater. Metagenomic sequencing was performed at the MGH NextGen Sequencing Core. We used the Illumina HiSeq2500 pair-ended platform for the whole metagenome shotgun sequencing. Raw pair-ended sequencing reads were processed using the KneadData pipeline to trim short reads and remove sequences of human origin.