Gut Microbiota in Children With Cystic Fibrosis: A Taxonomic and Functional Dysbiosis

• Published in: Scientific reports Vol. 9; no. 1; pp. 18593 - 14
• Main Authors: Coffey, Michael J., Nielsen, Shaun, Wemheuer, Bernd, Kaakoush, Nadeem O., Garg, Millie, Needham, Bronwen, Pickford, Russell, Jaffe, Adam, Thomas, Torsten, Ooi, Chee Y.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.12.2019; Nature Publishing Group
• Subjects: 101/58; 45/91; 692/4020/1503/2745; 692/699/1785/4039; Adolescent; Antioxidants; Antioxidants - metabolism; Biomarkers - metabolism; Case-Control Studies; Child; Child, Preschool; Children; Cross-Sectional Studies; Cystic fibrosis; Cystic Fibrosis - microbiology; Dysbacteriosis; Dysbiosis - microbiology; Fatty Acids, Volatile - metabolism; Feces; Female; Gastrointestinal diseases; Gastrointestinal Microbiome; Genera; Humanities and Social Sciences; Humans; Infant; Inflammation; Intestinal microflora; Intestine; Male; Metabolomics; Microbial activity; Microbiota; multidisciplinary; Prospective Studies; Pyruvate kinase; Pyruvic acid; RNA, Ribosomal, 16S - metabolism; rRNA 16S; Science; Science (multidisciplinary); Taxonomy
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-55028-7

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.