Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

39468837

DOI Digital object identifier for electronic documents.

10.1080/19490976.2024.2418984

URI Uniform resource identifier for web resources.

https://doi.org/10.1080/19490976.2024.2418984

Authors

Wan Y., Wong O.W.H., Tun H.M., Su Q., Xu Z., Tang W., Ma S.L., Chan S., Chan F.K.L., Ng S.C.

Journal

Gut microbes

Year

2024

Keywords:

Autism spectrum disorder, bacteria, diagnosis, microbiome

Accumulating evidence suggests that gut microbiota alterations influence brain function and could serve as diagnostic biomarkers and therapeutic targets. The potential of using fecal microbiota signatures to aid autism spectrum disorder (ASD) detection is still not fully explored. Here, we assessed the potential of different levels of microbial markers (taxonomy and genome) in distinguishing children with ASD from age and gender-matched typically developing peers (n = 598, ASD vs TD = 273 vs 325). A combined microbial taxa and metagenome-assembled genome (MAG) markers showed a better performance than either microbial taxa or microbial MAGs alone for detecting ASD. A machine-learning model comprising 5 bacterial taxa and 44 microbial MAG markers (2 viral MAGs and 42 bacterial MAGs) achieved an area under the receiving operator curve (AUROC) of 0.886 in the discovery cohort and 0.734 in an independent validation cohort. Furthermore, the identified biomarkers and predicted ASD risk score also significantly correlated with the core symptoms measured by the Social Responsiveness Scale-2 (SRS-2). The microbiome panel showed a superior classification performance in younger children (≤6 years old) with an AUROC of 0.845 than older children (>6 years). The model was broadly applicable to subjects across genders, with or without gastrointestinal tract symptoms (constipation and diarrhea) and with or without psychiatric comorbidities (attention deficit and hyperactivity disorder and anxiety). This study highlights the potential clinical validity of fecal microbiome to aid in ASD diagnosis and will facilitate studies to understand the association of disturbance of human gut microbiota and ASD symptom severity.

Experiment 1

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Needs review

Curated date: 2025/10/16

Curator: Kyaw

Revision editor(s): Kyaw

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Autism spectrum disorder atypical autism,autism spectrum disease,autism spectrum disorder,Autism Spectrum Disorders,autistic spectrum disorder,CHILD DEVELOPMENT DIS PERVASIVE,Child Development Disorders, Pervasive,Development Disorder, Pervasive,Development Disorders, Pervasive,Disorder, Autism Spectrum,Disorder, Pervasive Development,Disorders, Autism Spectrum,Disorders, Pervasive Development,PDD,PERVASIVE CHILD DEVELOPMENT DIS,Pervasive Child Development Disorders,Pervasive Development Disorder,Pervasive Development Disorders,pervasive developmental disorder - not otherwise specified,pervasive developmental disorders,Spectrum Disorder, Autism,Spectrum Disorders, Autism,Autism spectrum disorder

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Typical Developing (TD) Children

Group 1 name Corresponds to the case (exposed) group for case-control studies: Autism Spectrum Disorder (ASD) Children

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children with a clinician-confirmed diagnosis of ASD based on the DSM-4 or DSM-5 diagnostic criteria.

Group 0 sample size Number of subjects in the control (unexposed) group: 144

Group 1 sample size Number of subjects in the case (exposed) group: 129

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: ANCOM

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.6

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, sex

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Richness Number of species: decreased

Signature 1

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Curated date: 2025/10/16

Curator: Kyaw

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Source: Text

Description: Children with autism spectrum disorder show enrichment of Clostridium and Bacteroides nordii in their gut microbiome compared to typically developing controls.

Abundance in Group 1: increased abundance in Autism Spectrum Disorder (ASD) Children

NCBI	Quality Control	Links
Bacteroides nordii
Clostridium

Revision editor(s): Kyaw

Signature 2

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Curated date: 2025/10/16

Curator: Kyaw

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Source: Text

Description: Children with autism spectrum disorder show depletion of Lactococcus, Schaalia odontolytica, and Gemella morbillorum in their gut microbiome compared to typically developing controls.

Abundance in Group 1: decreased abundance in Autism Spectrum Disorder (ASD) Children

NCBI	Quality Control	Links
Bacteroides uniformis
Blautia wexlerae
Caudoviricetes sp.
Faecalibacterium prausnitzii
Gemella morbillorum
Lachnospiraceae bacterium
Lactococcus
Schaalia odontolytica
Ruminococcus obeum A2–162Ruminococcus obeum A2–162
Bifidobacterium kashiwanohense PV20–2Bifidobacterium kashiwanohense PV20–2
Streptococcus salivarius

Revision editor(s): Kyaw