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Compared to healthy individuals, CD patients seemed to be characterized by higher numbers of Gram-negative bacteria and lower numbers Gram-positive bacteria.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      This study aimed at investigating the microbiota and metabolome of 19 celiac disease children under gluten-free diet (treated celiac disease, T-CD) and 15 non-celiac children (HC). PCR-denaturing gradient gel electrophoresis (DGGE) analyses by universal and group-specific primers were carried out in duodenal biopsies and faecal samples. Based on the number of PCR-DGGE bands, the diversity of\n                      <jats:italic>Eubacteria<\/jats:italic>\n                      was the higher in duodenal biopsies of T-CD than HC children.\n                      <jats:italic>Bifidobacteria<\/jats:italic>\n                      were only found in faecal samples. With a few exceptions, PCR-DGGE profiles of faecal samples for\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      and\n                      <jats:italic>Bifidobacteria<\/jats:italic>\n                      differed between T-CD and HC. As shown by culture-dependent methods, the levels of\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      ,\n                      <jats:italic>Enterococcus<\/jats:italic>\n                      and\n                      <jats:italic>Bifidobacteria<\/jats:italic>\n                      were confirmed to be significantly higher (\n                      <jats:italic>P<\/jats:italic>\n                      = 0.028;\n                      <jats:italic>P<\/jats:italic>\n                      = 0.019; and\n                      <jats:italic>P<\/jats:italic>\n                      = 0.023, respectively) in fecal samples of HC than in T-CD children. On the contrary, cell counts (CFU\/ml) of presumptive\n                      <jats:italic>Bacteroides<\/jats:italic>\n                      ,\n                      <jats:italic>Staphylococcus<\/jats:italic>\n                      ,\n                      <jats:italic>Salmonella<\/jats:italic>\n                      ,\n                      <jats:italic>Shighella<\/jats:italic>\n                      and\n                      <jats:italic>Klebsiella<\/jats:italic>\n                      were significantly higher (\n                      <jats:italic>P<\/jats:italic>\n                      = 0.014) in T-CD compared to HC children.\n                      <jats:italic>Enterococcus faecium<\/jats:italic>\n                      and\n                      <jats:italic>Lactobacillus plantarum<\/jats:italic>\n                      were the species most diffusely identified. This latter species was also found in all duodenal biopsies of T-CD and HC children. Other bacterial species were identified only in T-CD or HC faecal samples. As shown by Randomly Amplified Polymorphic DNA-PCR analysis, the percentage of strains identified as lactobacilli significantly (\n                      <jats:italic>P<\/jats:italic>\n                      = 0.011) differed between T-CD (ca. 26.5%) and HC (ca. 34.6%) groups. The metabolome of T-CD and HC children was studied using faecal and urine samples which were analyzed by gas-chromatography mass spectrometry-solid-phase microextraction and\n                      <jats:sup>1<\/jats:sup>\n                      H-Nuclear Magnetic Resonance. As shown by Canonical Discriminant Analysis of Principal Coordinates, the levels of volatile organic compounds and free amino acids in faecal and\/or urine samples were markedly affected by CD.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>As shown by the parallel microbiology and metabolome approach, the gluten-free diet lasting at least two years did not completely restore the microbiota and, consequently, the metabolome of CD children. Some molecules (e.g., ethyl-acetate and octyl-acetate, some short chain fatty acids and free amino acids, and glutamine) seems to be metabolic signatures of CD.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2180-11-219","type":"journal-article","created":{"date-parts":[[2011,10,4]],"date-time":"2011-10-04T20:26:04Z","timestamp":1317759964000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":280,"title":["Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization"],"prefix":"10.1186","volume":"11","author":[{"given":"Raffaella","family":"Di Cagno","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"De Angelis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilaria","family":"De Pasquale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maurice","family":"Ndagijimana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamela","family":"Vernocchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrizia","family":"Ricciuti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Gagliardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Laghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmine","family":"Crecchio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Elisabetta","family":"Guerzoni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Gobbetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruggiero","family":"Francavilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,10,4]]},"reference":[{"key":"1513_CR1","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1007\/s11894-008-0085-9","volume":"10","author":"J Tye-Din","year":"2008","unstructured":"Tye-Din J, Anderson R: Immunopathogenesis of celiac disease. 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