Development of the gut microbiota in early life: The impact of cystic fibrosis and antibiotic treatment.

•The microbial community composition of the gut in children with cystic fibrosis is different from that in healthy children, from the first months of life on.•The microbial composition of the gut in children with cystic fibrosis is less stable over time, with a lower abundance of healthy commensals and a higher abundance of potential pathogens, compared to that in healthy children.•Antibiotic use in children with CF is associated with a lower microbial diversity, lower abundance of healthy commensals, and higher abundance of potential pathogens.