Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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 Siblings(NTs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Autism Spectrum Disorders Children (ASD Children)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Autism Spectrum Disorders Children (ASD Children) refers to children who show repetitive behaviours and sensory hyper-sensibility.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1646
- Group 1 sample size Number of subjects in the case (exposed) group
- 2154
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, sequence read depth, Confounders controlled for: "genetic ancestry of the individuals" 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.genetic ancestry of the individuals
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Data 3, 5
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children and Neurotypical Siblings..
Abundance in Group 1: increased abundance in Autism Spectrum Disorders Children (ASD Children)
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 3, 5
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children and Neurotypical Siblings..
Abundance in Group 1: decreased abundance in Autism Spectrum Disorders Children (ASD Children)
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subset of Neurotypical Siblings(NTs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subset of Autism Spectrum Disorders Children (ASD Children)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subset of Autism Spectrum Disorders Children (ASD Children) refers to a part of the ASD children(out of the 2154 in the study) who show repetitive behaviours and sensory hyper-sensibility.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 241
- Group 1 sample size Number of subjects in the case (exposed) group
- 291
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 3C, Supplementary Data 14
Description: Differentially abundant taxa in oral samples between Subset of Autism Spectrum Disorders children and Subset of Neurotypical Siblings
Abundance in Group 1: increased abundance in Subset of Autism Spectrum Disorders Children (ASD Children)
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 3C, Supplementary Data 14
Description: Differentially abundant taxa in oral samples between Subset of Autism Spectrum Disorders children and Subset of Neurotypical Siblings
Abundance in Group 1: decreased abundance in Subset of Autism Spectrum Disorders Children (ASD Children)
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Microbial Load
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Microbial Load
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Microbial Load is linked to poor oral hygiene and compromised oral health. It was found in both ASDs and NTs.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
Signature 1
Source: Fig. 2E, Supplementary Data 7
Description: Differentially abundant taxa in oral samples between High microbial load and low microbial load.
Abundance in Group 1: increased abundance in High Microbial Load
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 2E, Supplementary Data 7
Description: Differentially abundant taxa in oral samples between High microbial load and low microbial load.
Abundance in Group 1: decreased abundance in High Microbial Load
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cognitive impairment Abnormality of cognition,Cognitive abnormality,Cognitive defects,Cognitive deficits,Cognitive impairment,Intellectual impairment,cognitive impairment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Intelligence Quotients(Low IQ ≤70)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Intelligence Quotients(High IQ > 85)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 413
- Group 1 sample size Number of subjects in the case (exposed) group
- 784
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.2
Signature 1
Source: Fig. 3C, Supplementary Data 13
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ
Abundance in Group 1: increased abundance in High Intelligence Quotients(High IQ > 85)
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 3C, Supplementary Data 13
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ
Abundance in Group 1: decreased abundance in High Intelligence Quotients(High IQ > 85)
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Intelligence Quotients(Low IQ ≤70) by diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Intelligence Quotients(High IQ > 85) by diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Intelligence Quotients(High IQ) was estimated from parent-reported data by an algorithm developed to estimate with high accuracy cognitive levels in large cohorts of ASD children. High IQ refers to intelligent quotients greater than 85. This was adjusted for picky factor(diet).
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- diet, age, sex
Signature 1
Source: Fig. 3C
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ after adjusting for diet.
Abundance in Group 1: increased abundance in High Intelligence Quotients(High IQ > 85) by diet
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 3C, Supplementary Data 18
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Low IQ and High IQ after adjusting for diet.
Abundance in Group 1: decreased abundance in High Intelligence Quotients(High IQ > 85) by diet
Revision editor(s): KateRasheed
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cognitive function measurement Cognitive function measurement,cognitive function measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower Social Communication Questionnaire (Low SCQ) scale scale
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Upper Social Communication Questionnaire (Upper SCQ) scale
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Upper Social Communication Questionnaire (SCQ) scale is an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities. It reads greater than 95 interval.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Signature 1
Source: Supplementary Data 11
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower SCQ and Upper SCQ scale
Abundance in Group 1: increased abundance in Upper Social Communication Questionnaire (Upper SCQ) scale
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 11
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower SCQ and Upper SCQ scale
Abundance in Group 1: decreased abundance in Upper Social Communication Questionnaire (Upper SCQ) scale
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Developmental Coordination Disorder Questionnaires (DCDQ) scale
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Developmental Coordination Disorder Questionnaires (DCDQ) scale
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Developmental Coordination Disorder Questionnaires (DCDQ) scale refers to an ASD screening measures used to explore phenotypic aspects capable of explaining the observed differences in cognitive abilities.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data 12
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower DCDQ and Upper DCDQ scale
Abundance in Group 1: increased abundance in High Developmental Coordination Disorder Questionnaires (DCDQ) scale
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 12
Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower DCDQ and Upper DCDQ scale
Abundance in Group 1: decreased abundance in High Developmental Coordination Disorder Questionnaires (DCDQ) scale
Revision editor(s): KateRasheed
