Abstract
Intestinal dysbiosis has been observed in children with cystic fibrosis (CF), yet the functional consequences are poorly understood. We investigated the functional capacity of intestinal microbiota and inflammation in children with CF. Stool samples were collected from 27 children with CF and 27 age and gender matched healthy controls (HC) (aged 0.8–18 years). Microbial communities were investigated by iTag sequencing of 16S rRNA genes and functional profiles predicted using Tax4Fun. Inflammation was measured by faecal calprotectin and M2-pyruvate kinase. Paediatric CF gastrointestinal microbiota demonstrated lower richness and diversity compared to HC. CF samples exhibited a marked taxonomic and inferred functional dysbiosis when compared to HC. In children with CF, we predicted an enrichment of genes involved in short-chain fatty acid (SCFA), antioxidant and nutrient metabolism (relevant for growth and nutrition) in CF. The notion of pro-inflammatory GI microbiota in children with CF is supported by positive correlations between intestinal inflammatory markers and both genera and functional pathways. We also observed an association between intestinal genera and both growth z-scores and FEV1%. These taxonomic and functional changes provide insights into gastrointestinal disease in children with CF and future gastrointestinal therapeutics for CF should explore the aforementioned pathways and microbial changes.
Highlights
Gastrointestinal (GI) disease in cystic fibrosis (CF) begins in utero, continues throughout childhood and into adulthood[1,2]
We hypothesise that the composition and functional capacity of bacterial communities in the intestine of children with CF are different when compared to healthy controls (HC)
We have demonstrated that the intestines of children with CF exhibit a marked taxonomic and inferred functional dysbiosis when compared to well-matched healthy controls
Summary
Gastrointestinal (GI) disease in cystic fibrosis (CF) begins in utero, continues throughout childhood and into adulthood[1,2]. Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) results in an altered intestinal milieu with proposed disease factors including: (i) reduced bicarbonate secretion and low intestinal pH, (ii) thick and inspissated mucus, (iii) a lack of endogenous pancreatic enzymes, (iv) delayed intestinal transit and (v) possibly an impaired innate immunity[3,4] These mechanisms in combination with an energy- and fat-dense diet[5] and frequent antibiotic usage likely contribute to a dysbiosis of the intestinal bacterial community, which has been observed in CF6–9.
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