Subject Category: Pediatrics

Am J Gastroenterol 2009; 104:3058–3067; doi:10.1038/ajg.2009.524; published online 15 September 2009

Proximal Small Intestinal Microbiota and Identification of Rod-Shaped Bacteria Associated With Childhood Celiac Disease

Gangwei Ou MD, PhD1, Maria Hedberg PhD2, Per Hörstedt PhD3, Vladimir Baranov MD, PhD4, Göte Forsberg MD, PhD5, Mirva Drobni PhD6, Olof Sandström MD, PhD5, Sun Nyunt Wai MD, PhD7, Ingegerd Johansson OD, PhD6, Marie-Louise Hammarström PhD1, Olle Hernell MD, PhD5 and Sten Hammarström PhD1

  1. 1Department of Clinical Microbiology, Immunology, Umeå University, Umeå, Sweden
  2. 2Department of Odontology, Oral Microbiology, Umeå University, Umeå, Sweden
  3. 3Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
  4. 4Department of Clinical Microbiology, Clinical Immunology, Umeå University, Umeå, Sweden
  5. 5Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
  6. 6Department of Odontology, Cariology, Umeå University, Umeå, Sweden
  7. 7Department of Molecular Biology, Umeå University, Umeå, Sweden

Correspondence: Sten Hammarström, Immunology, Umeå University, SE-90185, Umeå, Sweden. E-mail:

Received 18 January 2009; Accepted 28 July 2009; Published online 15 September 2009.





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.



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.



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.



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.