Colonization, succession and evolution of the earliest human gastrointestinal microbiome. gut metagenome

Differences in microbial colonization of the gut triggered by earliest exposure have been linked to adverse health effects later in life. At present, the transfer of microbiota from mother to infant, its role in early colonization and subsequent effects on the host remain unresolved because of the lack of data reflecting earliest microbial exposure. Here, we recruited 12 mother-neonate pairs, 4 neonates each born vaginally, by caesarean section and born by caesarean section and small for gestational age. We collected stool and a vaginal swab from mothers one hour prior to delivery, as well as stool from their respective neonates during the first 24 hours, and after 3 and 5 days in order to obtain whole metagenome random shotgun sequence data for a total of 51 samples. We additionally collected stool samples from neonates at days 28, 150 and 1 year after birth for 16S and 18S rRNA gene amplicon sequencing analyses.