Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection

PLoS One. 2015 Oct 1;10(10):e0137725. doi: 10.1371/journal.pone.0137725. eCollection 2015.


In order to assess potential associations between autism spectrum disorder (ASD) phenotype, functional GI disorders and fecal microbiota, we recruited simplex families, which had only a single ASD proband and neurotypical (NT) siblings, through the Simons Simplex Community at the Interactive Autism Network (SSC@IAN). Fecal samples and metadata related to functional GI disorders and diet were collected from ASD probands and NT siblings of ASD probands (age 7-14). Functional gastrointestinal disorders (FGID) were assessed using the parent-completed ROME III questionnaire for pediatric FGIDs, and problem behaviors were assessed using the Child Behavior Check List (CBCL). Targeted quantitative polymerase chain reaction (qPCR) assays were conducted on selected taxa implicated in ASD, including Sutterella spp., Bacteroidetes spp. and Prevotella spp. Illumina sequencing of the V1V2 and the V1V3 regions of the bacterial 16S rRNA genes from fecal DNA was performed to an average depth of 208,000 and 107,000 high-quality reads respectively. Twenty-five of 59 ASD children and 13 of 44 NT siblings met ROME III criteria for at least one FGID. Functional constipation was more prevalent in ASD (17 of 59) compared to NT siblings (6 of 44, P = 0.035). The mean CBCL scores in NT siblings with FGID, ASD children with FGID and ASD without FGID were comparably higher (58-62 vs. 44, P < 0.0001) when compared to NT children without FGID. There was no significant difference in macronutrient intake between ASD and NT siblings. There was no significant difference in ASD severity scores between ASD children with and without FGID. No significant difference in diversity or overall microbial composition was detected between ASD children with NT siblings. Exploratory analysis of the 16S rRNA sequencing data, however, identified several low abundance taxa binned at the genus level that were associated with ASD and/or first order ASD*FGID interactions (FDR <0.1).

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Autism Spectrum Disorder / microbiology*
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Case-Control Studies
  • Child
  • Diet
  • Feces / microbiology*
  • Female
  • Gastrointestinal Tract / microbiology
  • Humans
  • Male
  • Microbiota*
  • Phenotype
  • RNA, Ribosomal, 16S / genetics
  • Siblings*


  • RNA, Ribosomal, 16S

Associated data

  • BioProject/PRJNA282013

Grants and funding

This work was supported by the Simons Foundation Autism Research Initiative, grant #239729 to E.L. ( The funder had a role in the study design, in that the study participants were from the Simons Simplex Community at the Interactive Autism Network, but otherwise had no role in other aspects of the study design, data collection and analysis, decision to publish or preparation of the manuscript.