Analysis of the Duodenal Microbiome in Autistic Individuals: Association With Carbohydrate Digestion
Abstract
Objectives: There is evidence that symptoms of maldigestion or malabsorption in autistic individuals are related to changes in the indigenous microbiota. Analysis of colonic bacteria has revealed microbial dysbiosis in children with autism; however, characteristics of the duodenal microbiome are not well described. In the present study the microbiome of the duodenal mucosa of subjects with autism was evaluated for dysbiosis, bacteria overgrowth, and microbiota associated with carbohydrate digestion. The relationship between the duodenal microbiome and disaccharidase activity was analyzed in biopsies from 21 autistic subjects and 19 children without autism. Methods: Microbiota composition was determined by 16S ribosomal RNA gene sequencing, and disaccharidase activity via biochemical assays. Results: Although subjects with autism had a higher frequency of constipation (P < 0.005), there was no difference in disaccharidase activity between groups. In addition, no differences in microbiome diversity (species richness and evenness) were observed. Bacteria belonging to the genus Burkholderia were more abundant in subjects with autism, whereas members of the genus Neisseria were less abundant. At the species level, a relative decrease in abundance of 2 Bacteroides species and Escherichia coli was found in autistic individuals. There was a positive correlation between the abundance of Clostridium species, and disaccharidase activity, in autistic individuals. Conclusions: There are a variety of changes at the genus and species level in duodenal microbiota in children with autism that could be influenced by carbohydrate malabsorption. These observations could be affected by variations in individual diets, but also may represent a more pervasive dysbiosis that results in metabolites that affect the behavior of autistic children.
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An overgrowth of Ralstonia, Burkholderia, and Peptostreptococcus has been observed in patients diagnosed with ASD compared to healthy individuals.
“In addition, an overgrowth of Ralstonia, Burkholderia, and Peptostreptococcus has been observed in patients diagnosed with ASD [112].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [112]
Kushak et al. and Srikantha et al. indicate a possibly greater presence of Neisseria, Devosia, Escherichia, Fusobacterium, Sporobacter, and Subdoligranulum in individuals without ASD.
“Moreover, research studies by Kushak et al. and Srikantha et al. indicate a possibly greater presence of Neisseria, Devosia, Escherichia, Fusobacterium, Sporobacter, and Subdoligranulum in individuals without ASD [52,112].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [112]
Two studies showed increases in alpha diversity and six studies showed no significant changes in alpha diversity.
“Two studies showed increases [31, 33] and six studies showed no significant changes in alpha diversity [36, 42, 43, 48, 50, 54].”
From Gut microbiota changes in children with autism spectrum disorder: a systematic review (2020) · cites this paper as [42]
Among seven papers reporting beta diversity, four showed significant differences in beta diversity between ASD and SIB/HC while the rest did not.
“Among the seven [31, 36, 40–42, 48, 50] papers that reported on beta diversity, four [31, 40, 41, 50] papers showed significant differences in beta diversity between ASD and SIB/HC while the rest did not (Additional file 1: Table S2).”
From Gut microbiota changes in children with autism spectrum disorder: a systematic review (2020) · cites this paper as [42]
These seven Prevotella studies showed either a non-significant result in relative abundance or a lower relative abundance in children classified as ASD versus SIB or HC.
“Instead, these seven studies showed either a non-significant result in relative abundance [41, 48, 50, 52] or a lower relative abundance in children classified as ASD versus SIB or HC [31, 39, 42].”
From Gut microbiota changes in children with autism spectrum disorder: a systematic review (2020) · cites this paper as [42]
The general trend supports no alterations in E. coli for children with ASD in five studies versus one study documenting a decrease in E. coli percentage.
“The general trend, however, supports no alterations in E. coli for children in ASD in five studies [30, 35, 42, 48, 52] vs one study [31] documenting a decrease in E. coli percentage among other microbiota.”
From Gut microbiota changes in children with autism spectrum disorder: a systematic review (2020) · cites this paper as [42]
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- Authors
- Kushak, R. I., Winter, H. S., Buie, T. M., Cox, S. B., Phillips, C. D., & Ward, N. L.
- Affiliations
- Massachusetts General Hospital (US)
- Texas Tech University (US)
- University of Wyoming (US)
- Corresponding author
- Kushak, Rafail I.
- Winter, Harland S.
- Buie, Timothy M.
- Venue
- Journal of Pediatric Gastroenterology and Nutrition
- Publisher
- Wiley
- Published
- 2017-05
- Volume
- 64
- Issue
- 5
- Pages
- e110-e116
- ISSN
- 0277-2116 (ISSN-L)
- 1536-4801
- OpenAlex
- W2547912129
- Cited by
- 92
- References
- 44
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 11 · 2023: 10 · 2022: 10 · 2021: 13 · 2020: 14 · 2019: 11 · 2018: 7 · 2017: 2
- FWCI
- 3.46
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Pediatric Gastroenterology and Nutrition (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Defense (W81XWH‐10‐1‐0477)
- Prometheus
- AstraZeneca
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- autism spectrum disorder, duodenal microbiome, dysbiosis, carbohydrate malabsorption, disaccharidase activity, bacterial overgrowth, constipation, Burkholderia, Neisseria, Bacteroides, Escherichia coli, Clostridium, gut microbiota, children
- MeSH terms
- Gastrointestinal Microbiome, Adolescent, Autistic Disorder, Diet, Digestion, Disaccharidases, Duodenum, Female, Humans, Intestinal Mucosa, Male, Retrospective Studies, Biomarkers, Linear Models, Case-Control Studies, Carbohydrate Metabolism, Microbiota, Dysbiosis
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