Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Kang DW, Park JG, Ilhan ZE, Wallstrom G, Labaer J, Adams JB, Krajmalnik-Brown R
Journal
PloS one
Year
2013
High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.
Experiment 1
Subjects
- Location of subjects
- 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 children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with Autism Spectrum Disorder (ASD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with ASD were assessed with the Autism Diagnostics Interview – Revised (ADI- Revised), Autism Diagnostics Observation Schedule (ADOS), Autism Treatment Evaluation Checklist (ATEC), and Pervasive Developmental Disorder Behavior Inventory (PDD-BI) to ensure that they had a diagnosis of autism.
- 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
- 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
- 16S
- 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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- T-Test
- 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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table S7
Description: Genera presenting significant difference between neurotypical and autistic children by two-tailed Student’s t-test results
Abundance in Group 1: increased abundance in Children with Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae | ||
| Eggerthella |
Revision editor(s): AlishaM
Signature 2
Source: Figure S7
Description: Genera presenting significant difference between neurotypical and autistic children by two-tailed Student’s t-test results
Abundance in Group 1: decreased abundance in Children with Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Coprococcus | ||
| Incertae Sedis XIIIncertae Sedis XII | ||
| Fusibacter | ||
| Desulfovibrionaceae | ||
| Desulfovibrio | ||
| Staphylococcaceae | ||
| Staphylococcus |
Revision editor(s): AlishaM
Experiment 2
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 4, Table S8
Description: Genera presenting significant difference between neurotypical and autistic children by nonparametric ranksum test (two-tailed Mann-Whitney test)
Abundance in Group 1: increased abundance in Children with Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Lactobacillus | ||
| Eubacteriaceae | ||
| Eubacterium | ||
| Coriobacteriaceae | ||
| Eggerthella |
Revision editor(s): AlishaM
Signature 2
Source: Table 4, Table S8
Description: Genera presenting significant difference between neurotypical and autistic children by nonparametric ranksum test (two-tailed Mann-Whitney test)
Abundance in Group 1: decreased abundance in Children with Autism Spectrum Disorder (ASD)
Revision editor(s): AlishaM
Experiment 3
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 5
Description: Permutation-based test on univariate regression model with the autistic status and top 10 genera generating the highest AUC.
Abundance in Group 1: increased abundance in Children with Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriaceae | ||
| Eubacterium |
Revision editor(s): AlishaM
Signature 2
Source: Table 5
Description: Permutation-based test on univariate regression model with the autistic status and top 10 genera generating the highest AUC.
Abundance in Group 1: decreased abundance in Children with Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Prevotellaceae | ||
| Prevotella | ||
| Lachnospiraceae | ||
| Coprococcus | ||
| Alcaligenaceae | ||
| Sutterella | ||
| Paraprevotella |
Revision editor(s): AlishaM
Experiment 4
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "gender" 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.gender, Confounders controlled for: "dietary intakes" 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.dietary intakes, Confounders controlled for: "GI problems" 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.GI problems, Confounders controlled for: "autism severity indices" 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.autism severity indices
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
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