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Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn’s-Like Microbiota Disturbances

Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM, University Bordeaux, U1045, F-33000 Bordeaux, France
CRCM Pédiatrique, CHU Bordeaux, CIC 1401, F-33000 Bordeaux, France
Fédération Hospitalo-Universitaire FHU, ACRONIM, F-33000 Bordeaux, France
Bordeaux Bioinformatics Center, University Bordeaux, F-33000 Bordeaux, France
Laboratoire Bordelais de Recherche en Informatique, CNRS, University Bordeaux, UMR 5800, F-33400 Talence, France
Service de Rhumatologie, CHU Bordeaux, F-33000 Bordeaux, France
INSERM, MRGM, University Bordeaux, U1211, F-33000 Bordeaux, France
PGTB, University Bordeaux, F-33000 Bordeaux, France
BIOGECO, INRA, University Bordeaux, F-33610 Cestas, France
INRA—Bordeaux Aquitaine Centre, University Bordeaux, USC EA 3671, Infections Humaines à Mycoplasmes et à Chlamydiae, CHU Bordeaux, F-33000 Bordeaux, France
BaRITOn, INSERM, University Bordeaux, UMR1053, CHU Bordeaux, F-33000 Bordeaux, France
Authors to whom correspondence should be addressed.
These authors contributed equally as co-first authors.
J. Clin. Med. 2019, 8(5), 645;
Received: 6 April 2019 / Revised: 29 April 2019 / Accepted: 6 May 2019 / Published: 10 May 2019
(This article belongs to the Special Issue Diagnosis and Treatment of Small Bowel Disorders)
PDF [17522 KB, uploaded 10 May 2019]


Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic inflammation and microbiota disturbances. The link between gut inflammation and microbiota dysbiosis is still poorly understood. The main objective of this study was to assess gut microbiota composition in CF children depending on their intestinal inflammation. We collected fecal samples from 20 children with CF. Fecal calprotectin levels were measured and fecal microbiota was analyzed by 16S rRNA sequencing. We observed intestinal inflammation was associated with microbiota disturbances characterized mainly by increased abundances of Staphylococcus, Streptococcus, and Veillonella dispar, along with decreased abundances of Bacteroides, Bifidobacterium adolescentis, and Faecalibacterium prausnitzii. Those changes exhibited similarities with that of Crohn’s disease (CD), as evidenced by the elevated CD Microbial-Dysbiosis index that we applied for the first time in CF. Furthermore, the significant over-representation of Streptococcus in children with intestinal inflammation appears to be specific to CF and raises the issue of gut–lung axis involvement. Taken together, our results provide new arguments to link gut microbiota and intestinal inflammation in CF and suggest the key role of the gut–lung axis in the CF evolution. View Full-Text
Keywords: cystic fibrosis; gut microbiota; intestinal inflammation; fecal calprotectin; dysbiosis index cystic fibrosis; gut microbiota; intestinal inflammation; fecal calprotectin; dysbiosis index

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Enaud, R.; Hooks, K.B.; Barre, A.; Barnetche, T.; Hubert, C.; Massot, M.; Bazin, T.; Clouzeau, H.; Bui, S.; Fayon, M.; Berger, P.; Lehours, P.; Bébéar, C.; Nikolski, M.; Lamireau, T.; Delhaes, L.; Schaeverbeke, T. Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn’s-Like Microbiota Disturbances. J. Clin. Med. 2019, 8, 645.

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