Metagenomic analyses of the intestinal microbiome from neonates in the MIS BAIR trial

Metagenomic shotgun sequencing was done on stool samples from a subset of 393 participants from The Melbourne Infant Study: BCG for Allergy and Infection Reduction (MIS BAIR). In this randomised trial, 1272 healthy infants were recruited antenatally to investigate whether Bacille Calmette-Guérin (BCG) immunisation given in the first 10 days of life protects against childhood infection, allergy and asthma. Stool samples were collected 5 to 7 days after birth and stool microbiome composition was investigated in different context (e.g. abundance of genetic antibiotic resistance, influence of BCG on the composition, association with vaccine responses, association with eczema prevalence and allergies, etc.).