This study aimed at comparing the differences of the microbiota and metabolome between CD children under GFD (treated celiac disease, T-CD) and non-celiac children (healthy control, HC). The intestinal and faecal microbiota was characterized by culture-independent and -dependent methods whereas metabolomic studies were carried out using gas-chromatography mass spectrometry/solid-phase microextraction BI 10773 nmr (GC-MS/SPME) and 1H nuclear magnetic resonance (NMR) spectroscopy. Results Molecular analysis of the bacterial community of duodenal biopsies and faecal samples The dominant microbiota and specific subgroups (Bifidobacteria and Lactobacillus)

from stool samples and from duodenal biopsies (mucus and mucosa associated bacteria) were analyzed by PCR (Polymerase chain reaction)-DGGE (denaturing gradient gel electrophoresis). Universal primers targeting V6-V8 regions of the 16S rRNA gene were used. Eubacterial AG-881 datasheet profiles from PCR-DGGE analysis of duodenal biopsies of treated celiac disease (T-CD) children showed high richness

with two to eight well resolved and strong bands (Figure 1A). Only the electrophoretic profile of 19 T-CD duodenal biopsy contained one band. Profiles of non-celiac children (HC) had only one to three strong bands. Banding patterns were processed using the Bionumerics software. Pearson correlation coefficients ranged from 4.6 to 99.5%. Except for two duodenal biopsies (33 and 34 HC) which showed high similarity to T-CD samples, all HC banding patterns were grouped together with 98.2% similarity coefficient. The major part of the T-CD samples were grouped together at 95% of the similarity. Overall, DGGE profiles of the PCR amplicons obtained with primers Lac1 and Lac2 had two strong, common and well-resolved bands, and a few bands with low intensity (Figure 1B). High similarity was found among samples belonging to T-CD and HC groups. Most of the T-CD and HC duodenal biopsies were grouped together at ca. 90% of similarity and all samples at 72.9%. Sequencing of the DGGE bands

revealed the common presence of L. plantarum (band a). Although Lac1 and Lac2 primers were commonly used to detect Lactobacillus species [9, 24, 25], human DNA (band these b) was also found. Finally, no PCR amplicons were found by using three different sets of primers targeting the Bifidobacteria group. This suggested that Bifidobacteria were probably absent from duodenal biopsies of both T-CD and HC. Figure 1 Clustering of denaturing gradient gel electrophoresis (DGGE) profiles of biopsies from thirty-four children (1-34). Universal V6-V8 (A) and Lac1/Lac2 Lactobacillus group (B) primers were used. Clustering was carried out using the unweighted pair-group method with the arithmetic average (UPGMA) based on the Pearson correlation coefficient.