Infant cystic fibrosis BAL and stool microbiome

BAL and stool was collected over the first two years of life from infants with cystic fibrosis (CF) in Melbourne, Australia who were treated with ongoing prophylactic amoxicillin/clavulanate to assess microbial maturation over this period. Low biomass BAL samples underwent 16S amplicon sequencing using custom primers for the V1-V2 region (F-27/R-338) and the Illumina MiSeq system. Stool samples underwent Illumina shotgun sequencing via the NovaSeq 6000 system.