Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts

Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557.


Background: Oral manifestations are common in Crohn's disease (CD). Here we characterized the subgingival microbiota in pediatric patients with CD initiating therapy and after 8 weeks to identify microbial community features associated with CD and therapy.

Methods: Pediatric patients with CD were recruited from The Children's Hospital of Pennsylvania. Healthy control subjects were recruited from primary care or orthopedics clinic. Subgingival plaque samples were collected at initiation of therapy and after 8 weeks. Treatment exposures included 5-ASAs, immunomodulators, steroids, and infliximab. The microbiota was characterized by 16S rRNA gene sequencing. The study was repeated in separate discovery (35 CD, 43 healthy) and validation cohorts (43 CD, 31 healthy).

Results: Most subjects in both cohorts demonstrated clinical response after 8 weeks of therapy (discovery cohort 88%, validation cohort 79%). At week 0, both antibiotic exposure and disease state were associated with differences in bacterial community composition. Seventeen genera were identified in the discovery cohort as candidate biomarkers, of which 11 were confirmed in the validation cohort. Capnocytophaga, Rothia, and TM7 were more abundant in CD relative to healthy controls. Other bacteria were reduced in abundance with antibiotic exposure among CD subjects. CD-associated genera were not enriched compared with healthy controls after 8 weeks of therapy.

Conclusions: Subgingival microbial community structure differed with CD and antibiotic use. Results in the discovery cohort were replicated in a separate validation cohort. Several potentially pathogenic bacterial lineages were associated with CD but were not diminished in abundance by antibiotic treatment, suggesting targets for additional surveillance.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Anti-Bacterial Agents / therapeutic use*
  • Anti-Inflammatory Agents / therapeutic use
  • Capnocytophaga
  • Case-Control Studies
  • Child
  • Child, Preschool
  • Crohn Disease / complications*
  • Crohn Disease / drug therapy
  • Crohn Disease / microbiology
  • Female
  • Gastrointestinal Agents / therapeutic use
  • Gingiva / microbiology*
  • Gingiva / pathology
  • Gingival Diseases / drug therapy
  • Gingival Diseases / microbiology*
  • Humans
  • Immunologic Factors / therapeutic use
  • Infliximab / therapeutic use
  • Longitudinal Studies
  • Male
  • Mesalamine / therapeutic use
  • Microbiota / drug effects*
  • Microbiota / genetics
  • RNA, Ribosomal, 16S
  • Steroids / therapeutic use
  • Young Adult


  • Anti-Bacterial Agents
  • Anti-Inflammatory Agents
  • Gastrointestinal Agents
  • Immunologic Factors
  • RNA, Ribosomal, 16S
  • Steroids
  • Mesalamine
  • Infliximab

Supplementary concepts

  • Pediatric Crohn's disease