Aims To characterise the predominant species of bacterial populations associated with duodenal biopsies of paediatric patients with active and treated coeliac disease.

Methods 20 biopsy specimens from patients with active coeliac disease, 12 from patients with treated coeliac disease, and eight from age-matched controls were evaluated for comparative purposes. Bacteroides, Bifidobacterium and lactic acid bacteria (LAB) populations were analysed by PCR-denaturing gradient gel electrophoresis using group-specific primers.

Results Bacteroides diversity was higher in biopsy specimens from controls than in those from patients with active and treated coeliac disease. Bacteroides distasonis, Bacteroides fragilis/Bacteroides thetaiotaomicron, Bacteroides uniformis and Bacteroides ovatus were more abundant in controls than in patients with coeliac disease (p<0.05). Bacteroides vulgatus was more frequently detected in controls than in patients with treated coeliac disease (p<0.01). Bacteroides dorei was more common in patients with active coeliac disease than in those with treated coeliac disease and control children (p<0.01). Bifidobacterium diversity was higher in patients with coeliac disease than in controls. Bifidobacterium adolescentis and Bifidobacterium animalis subsp lactis were more prevalent in patients with active coeliac disease than in patients with treated coeliac disease and control children. A higher LAB diversity was found in patients with treated coeliac disease and controls than in patients with active coeliac disease. Weissella spp and Lactobacillus fermentum were more frequently detected in patients with treated coeliac disease than in controls and patients with active coeliac disease.

Conclusions Bacteroides, Bifidobacterium and LAB populations in the duodenum of Spanish children with typical coeliac disease (active and treated) and controls differ in diversity and species composition; this could contribute to features of the disease.