Age and environmental exposures influence the fecal bacteriome of young children with cystic fibrosis

Background Mechanisms that facilitate early infection and inflammation in cystic fibrosis (CF) are unclear. We previously showed that young CF children with secondhand smoke exposure (SHSe) have increased susceptibility to respiratory infections. We aimed to define the impact of SHSe and other external factors upon the fecal bacteriome in early CF. Methods Twenty CF infants and children were enrolled, clinical data recorded, and hair nicotine measured as an objective surrogate of SHSe. Fecal samples were collected at clinic visits and bacteriome 16S rRNA gene sequencing performed. Results SHSe was associated with increased alpha diversity and increased relative abundance ofAcinetobacterandAkkermansia, along with decreasedBifidobacteriumandLactobacillus. Recent antibiotic exposure predicted bacterial population structure in children less than 2 years of age and was associated with decreasedBacteroidesrelative abundance. Age was the strongest predictor of overall fecal bacterial composition and positively associated withBlautiaandParabacteroides. Weight for length was negatively associated withStaphylococcusrelative abundance. Conclusions SHSe and other external factors such as antibiotics appear to alter fecal bacterial composition in young CF children, but the strongest predictor of overall composition was age. These findings have implications for understanding the intestinal microbiome in young CF children.