Changes in the Gut Microbiota of Children with Autism Spectrum Disorder

Autism Res. 2020 Sep;13(9):1614-1625. doi: 10.1002/aur.2358. Epub 2020 Aug 24.


Alterations in the gut microbiota may influence gastrointestinal (GI) dysbiosis frequently reported in individuals with autism spectrum disorder (ASD). In this study, we sequenced the bacterial 16S rRNA gene to evaluate changes in fecal microbiota between 48 children with ASD and 48 healthy children in China. At the phylum level, the number of Firmicutes, Proteobacteria, and Verrucomicrobia decreased in children with ASD, while the Bacteroidetes/Firmicutes was significantly higher in autistic children due to enrichment of Bacteroidetes. At the genus level, the amount of Bacteroides, Prevotella, Lachnospiracea_incertae_sedis, and Megamonas increased, while Clostridium XlVa, Eisenbergiella, Clostridium IV, Flavonifractor, Escherichia/Shigella, Haemophilus, Akkermansia, and Dialister decreased in children with ASD relative to the controls. Significant increase was observed in the number of species synthesizing branched-chain amino acids (BCAAs), like Bacteroides vulgatus and Prevotella copri, while the numbers of Bacteroides fragilis and Akkermansia muciniphila decreased in children with ASD compared to the controls. Most importantly, the highest levels of pathogenic bacteria were different for each child with ASD in this cohort. We found that only one functional module, cellular antigens, was enriched in children with ASD, and other pathways like lysine degradation and tryptophan metabolism were significantly decreased in children with ASD. These findings provide further evidence of altered gut microbiota in Chinese ASD children and may contribute to the treatment of patients with ASD. LAY SUMMARY: This study characterized the gut bacteria composition of 48 children with ASD and 48 neurotypical children in China. The metabolic disruptions caused by altered gut microbiota may contribute significantly to the neurological pathophysiology of ASD, including significant increases in the number of species synthesizing BCAAs, and decreases in the number of probiotic species. These findings suggest that a gut microbiome-associated therapeutic intervention may provide a novel strategy for treating GI symptoms frequently seen in individuals with ASD. Autism Res 2020, 13: 1614-1625. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.

Keywords: Akkermansia; Bacteroides; Prevotella; autism spectrum disorders; children; gut microbiota.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autism Spectrum Disorder / microbiology*
  • Bacteroides / genetics
  • Bacteroides / isolation & purification
  • Case-Control Studies
  • Child
  • Child, Preschool
  • China
  • Female
  • Gastrointestinal Microbiome* / genetics
  • Humans
  • Male
  • Prevotella / genetics
  • Prevotella / isolation & purification
  • RNA, Ribosomal, 16S


  • RNA, Ribosomal, 16S

Supplementary concepts

  • Bacteroides vulgatus
  • Prevotella copri