Oral microbiome activity in children with autism spectrum disorder.
Spit bacteria ratios distinguish preschoolers with autism from peers and flag GI co-occurring problems with roughly 80 % accuracy.
01Research in Context
What this study did
Eggleston et al. (2018) collected spit samples from preschoolers with autism, kids with general developmental delay, and neurotypical peers.
Lab tests counted the bacteria living in each saliva sample.
A computer model learned which bacterial ratios matched each group.
What they found
The spit-bacteria pattern correctly flagged autism status about 80 % of the time.
It also spotted which autistic children had tummy problems.
Accuracy stayed between 76 % and 86 % across different comparisons.
How this fits with other research
Cai et al. (2025) later used stool instead of spit and reached even higher accuracy, hinting the mouth may be the easier place to sample.
Mason et al. (2021) used the same spit strategy but tracked RNA molecules; together the papers show saliva can house both microbial and genetic clues.
Kaiser et al. (2022) and Lee et al. (2018) report more bowel disease in autistic youth, backing the idea that mouth bugs reflecting gut trouble matter.
Why it matters
You can’t run a lab in your clinic, but you can note mouth and gut signs. Ask parents about diarrhea, constipation, or reflux during intake. When these complaints show up, share the finding that oral bacteria patterns often line up with GI issues in autism. This gives pediatricians a concrete reason to refer for GI work-ups and may speed overall care.
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02At a glance
03Original abstract
Autism spectrum disorder (ASD) is associated with several oropharyngeal abnormalities, including buccal sensory sensitivity, taste and texture aversions, speech apraxia, and salivary transcriptome alterations. Furthermore, the oropharynx represents the sole entry point to the gastrointestinal (GI) tract. GI disturbances and alterations in the GI microbiome are established features of ASD, and may impact behavior through the "microbial-gut-brain axis." Most studies of the ASD microbiome have used fecal samples. Here, we identified changes in the salivary microbiome of children aged 2-6 years across three developmental profiles: ASD (n = 180), nonautistic developmental delay (DD; n = 60), and typically developing (TD; n = 106) children. After RNA extraction and shotgun sequencing, actively transcribing taxa were quantified and tested for differences between groups and within ASD endophenotypes. A total of 12 taxa were altered between the developmental groups and 28 taxa were identified that distinguished ASD patients with and without GI disturbance, providing further evidence for the role of the gut-brain axis in ASD. Group classification accuracy was visualized with receiver operating characteristic curves and validated using a 50/50 hold-out procedure. Five microbial ratios distinguished ASD from TD participants (79.5% accuracy), three distinguished ASD from DD (76.5%), and three distinguished ASD children with/without GI disturbance (85.7%). Taxonomic pathways were assessed using the Kyoto Encyclopedia of Genes and Genomes microbial database and compared with one-way analysis of variance, revealing significant differences within energy metabolism and lysine degradation. Together, these results indicate that GI microbiome disruption in ASD extends to the oropharynx, and suggests oral microbiome profiling as a potential tool to evaluate ASD status. Autism Res 2018, 11: 1286-1299. © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Previous research suggests that the bacteria living in the human gut may influence autistic behavior. This study examined genetic activity of microbes living in the mouth of over 300 children. The microbes with differences in children with autism were involved in energy processing and showed potential for identifying autism status.
Autism research : official journal of the International Society for Autism Research, 2018 · doi:10.1002/aur.1972