Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease

Aims: To identify specific gut bacteria associated with coeliac disease (CD) at diagnosis and after treatment with a gluten-free diet (GFD) in a paediatric population. Methods: 30 and 18 faecal samples from untreated and treated CD patients and 25 and 8 biopsy samples from untreated and treated CD patients, respectively, were analysed. In addition, 30 faecal and 8 biopsy samples from control children were evaluated for comparative purposes. Gut bacterial groups were quantified by real-time PCR. Results: Bacteroides and Clostridium leptum groups were more abundant in faeces and biopsies of CD patients than in controls regardless of the stage of the disease. E coli and Staphylococcus counts were also higher in faeces and biopsies of non-treated CD patients than in those of controls, but their levels were normalised after treatment with a GFD. Bifidobacterium levels were lower in faeces of both groups of CD patients and in biopsies of untreated CD patients compared to controls. Similar bacterial groups were related to CD in biopsies and faeces, indicating that faecal microbiota partly reflects that of the small intestine in CD patients, and could constitute a convenient biological index of this disorder. Conclusions: Duodenal and faecal microbiota is unbalanced in children with untreated CD and only partially restored after long-term treatment with a GFD, constituting a novel factor linked to this disorder.