Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease

Am J Gastroenterol. 2009 Dec;104(12):3058-67. doi: 10.1038/ajg.2009.524. Epub 2009 Sep 15.


Objectives: Alterations in the composition of the microbiota in the intestine may promote development of celiac disease (CD). Using scanning electron microscopy (SEM) we previously demonstrated that rod-shaped bacteria were present on the epithelium of proximal small intestine in children with CD but not in controls. In this study we characterize the microbiota of proximal small intestine in children with CD and controls and identify CD-associated rod-shaped bacteria.

Methods: Proximal small intestine biopsies from 45 children with CD and 18 clinical controls were studied. Bacteria were identified by 16S rDNA sequencing in DNA extracted from biopsies washed with buffer containing dithiothreitol to enrich bacteria adhering to the epithelial lining, by culture-based methods and by SEM and transmission electron microscopy.

Results: The normal, mucosa-associated microbiota of proximal small intestine was limited. It was dominated by the genera Streptococcus and Neisseria, and also contained Veillonella, Gemella, Actinomyces, Rothia, and Haemophilus. The proximal small intestine microbiota in biopsies from CD patients collected during 2004-2007 differed only marginally from that of controls, and only one biopsy (4%) had rod-shaped bacteria by SEM (SEM+). In nine frozen SEM+ CD biopsies from the previous study, microbiotas were significantly enriched in Clostridium, Prevotella, and Actinomyces compared with SEM- biopsies. Bacteria of all three genera were isolated from children born during the Swedish CD epidemic. New Clostridium and Prevotella species and Actinomyces graevenitzii were tentatively identified.

Conclusions: Rod-shaped bacteria, probably of the indicated species, constituted a significant fraction of the proximal small intestine microbiota in children born during the Swedish CD epidemic and may have been an important risk factor for CD contributing to the fourfold increase in disease incidence in children below 2 years of age during that time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Biopsy
  • Case-Control Studies
  • Celiac Disease / genetics
  • Celiac Disease / microbiology*
  • Chi-Square Distribution
  • Child
  • Child, Preschool
  • Colony Count, Microbial
  • DNA, Bacterial
  • Female
  • Humans
  • Infant
  • Intestinal Mucosa / microbiology*
  • Intestine, Small / microbiology*
  • Male
  • Microscopy, Electron, Scanning


  • DNA, Bacterial