Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups

Study information

Needs review

study design

meta-analysis

Citation

PMID PubMed identifier for scientific articles.

36220843

DOI Digital object identifier for electronic documents.

10.1038/s41598-022-21327-9

URI Uniform resource identifier for web resources.

Authors

West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ, Iwai S

Journal

Scientific reports

Year

2022

Observational studies have shown that the composition of the human gut microbiome in children diagnosed with Autism Spectrum Disorder (ASD) differs significantly from that of their neurotypical (NT) counterparts. Thus far, reported ASD-specific microbiome signatures have been inconsistent. To uncover reproducible signatures, we compiled 10 publicly available raw amplicon and metagenomic sequencing datasets alongside new data generated from an internal cohort (the largest ASD cohort to date), unified them with standardized pre-processing methods, and conducted a comprehensive meta-analysis of all taxa and variables detected across multiple studies. By screening metadata to test associations between the microbiome and 52 variables in multiple patient subsets and across multiple datasets, we determined that differentially abundant taxa in ASD versus NT children were dependent upon age, sex, and bowel function, thus marking these variables as potential confounders in case-control ASD studies. Several taxa, including the strains Bacteroides stercoris t__190463 and Clostridium M bolteae t__180407, and the species Granulicatella elegans and Massilioclostridium coli, exhibited differential abundance in ASD compared to NT children only after subjects with bowel dysfunction were removed. Adjusting for age, sex and bowel function resulted in adding or removing significantly differentially abundant taxa in ASD-diagnosed individuals, emphasizing the importance of collecting and controlling for these metadata. We have performed the largest (n = 690) and most comprehensive systematic analysis of ASD gut microbiome data to date. Our study demonstrated the importance of accounting for confounding variables when designing statistical comparative analyses of ASD- and NT-associated gut bacterial profiles. Mitigating these confounders identified robust microbial signatures across cohorts, signifying the importance of accounting for these factors in comparative analyses of ASD and NT-associated gut profiles. Such studies will advance the understanding of different patient groups to deliver appropriate therapeutics by identifying microbiome traits germane to the specific ASD phenotype.

Experiment 1

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Curated date: 2023/11/10

Curator: Chinelsy

Revision editor(s): WikiWorks, Chinelsy, Ese

Subjects

Location of subjects: Canada; China; India; Italy; United States of America

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: neurotypical (NT) 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 diagnosed with Autism spectrum disorder (ASD) (all datasets pooled, no adjustment for bowel function, age, or sex).

Group 0 sample size Number of subjects in the control (unexposed) group: 13

Group 1 sample size Number of subjects in the case (exposed) group: 13

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: PERMANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Signature 1

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Curated date: 2025/03/24

Curator: ChiomaBlessing

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Source: Figure 3 & Table S4

Description: Differentially abundant bacterial taxa identified in Autism Spectrum Disorder (ASD) children compared to Neurotypical (NT) children (all datasets pooled, no adjustment for bowel function, age, or sex).

Abundance in Group 1: increased abundance in autism spectrum disorder (ASD) children

NCBI	Quality Control	Links
Acinetobacter towneri
Aggregatibacter segnis
Delftia
Ligilactobacillus ruminis
Roseomonas

Revision editor(s): ChiomaBlessing, Ese

Experiment 2

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Curated date: 2023/11/13

Curator: Chinelsy

Revision editor(s): WikiWorks, Chinelsy, Anne-mariesharp, Ese

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test: DESeq2

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Experiment 3

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Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

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Curated date: 2023/11/10

Curator: Chinelsy

Revision editor(s): WikiWorks, Chinelsy, Ese

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: neurotypical (NT)

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children with Autism Spectrum Disorder (ASD)

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 20

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V2-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Not specified

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex, Confounders controlled for: "bowel" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.bowel