Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

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

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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)

NCBI	Quality Control	Links
Abiotrophia defectiva
Actinomyces johnsonii
Actinomyces massiliensis
Actinomyces naeslundii
Actinomyces oris
Actinomyces sp. oral taxon 180
Actinomyces sp. oral taxon 414
Alloprevotella rava
Arachnia propionica
Campylobacter curvus
Campylobacter gracilis
Capnocytophaga granulosa
Capnocytophaga leadbetteri
Capnocytophaga ochracea
Capnocytophaga sputigena
Cardiobacterium hominis
Cardiobacterium valvarum
Corynebacterium durum
Corynebacterium matruchotii
Cutibacterium acnes
Eikenella corrodens
Eikenella halliae
Enhydrobacter aerosaccus
Fusobacterium nucleatum
Gemella morbillorum
Kingella oralis
Lachnospiraceae bacterium oral taxon 096
Leptotrichia buccalis
Leptotrichia hofstadii
Leptotrichia sp. oral taxon 225
Leptotrichia sp. oral taxon 847
Leptotrichia sp. oral taxon 879
Malassezia restricta
Micrococcus luteus
Mogibacterium pumilum
Moraxella osloensis
Neisseria sicca
Pauljensenia hongkongensis
Rothia aeria
Rothia dentocariosa
Schaalia georgiae
Selenomonas noxia
Selenomonas sp. oral taxon 920
Staphylococcus epidermidis
Streptococcus anginosus
Streptococcus cristatus
Streptococcus gordonii
Streptococcus mitis
Streptococcus mutans
Streptococcus oralis
Streptococcus sanguinis
Streptococcus sobrinus
Streptococcus sp. oral taxon 056
Streptococcus vestibularis
Veillonella parvula
Corynebacterium
Kingella
Cutibacterium
Arachnia
Cardiobacterium
Eikenella
Capnocytophaga
Ottowia
Staphylococcus
Abiotrophia
Selenomonas
Tannerella
Leptotrichia
Streptococcus
Micrococcus
Enhydrobacter

Revision editor(s): KateRasheed, WikiWorks

Signature 2

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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)

NCBI	Quality Control	Links
Actinomyces graevenitzii
Actinomyces sp. HMSC035G02
Actinomyces sp. HPA0247
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Actinomyces sp. oral taxon 181
Alloprevotella
Alloprevotella sp. oral taxon 473
Atopobium
Campylobacter
Campylobacter concisus
Dialister invisus
Anaerovoracaceae
Fusobacterium
Fusobacterium periodonticum
Hoylesella shahii
Lancefieldella parvula
Lancefieldella rimae
Leptotrichia sp. oral taxon 215
Megasphaera
Megasphaera micronuciformis
Mogibacterium
Mogibacterium diversum
Neisseria flavescens
Oribacterium
Oribacterium asaccharolyticum
Oribacterium parvum
Oribacterium sinus
Porphyromonas somerae
Prevotella
Prevotella histicola
Prevotella jejuni
Prevotella melaninogenica
Prevotella pallens
Prevotella scopos
Prevotella sp. F0091
Prevotella sp. oral taxon 299
Prevotella sp. oral taxon 306
Prevotella veroralis
Rothia mucilaginosa
Schaalia odontolytica
Segatella salivae
Selenomonas flueggei
Solobacterium
Solobacterium moorei
Stomatobaculum
Stomatobaculum longum
Streptococcus australis
Streptococcus infantis
Streptococcus parasanguinis
Streptococcus sp. A12
Streptococcus sp. F0442
Streptococcus sp. HMSC034E03
Streptococcus sp. HMSC067H01
Streptococcus sp. HMSC071D03
Veillonella
Veillonella atypica
Veillonella dispar
Veillonella infantium
Veillonella rogosae
Veillonella sp. T11011-6
Veillonella tobetsuensis
[Eubacterium] infirmum
[Eubacterium] sulci
unclassified Lachnospiraceae
Neisseria subflava

Revision editor(s): KateRasheed, WikiWorks

Experiment 2

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Differences from previous experiment shown

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

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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)

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Actinomyces massiliensis
Actinomyces naeslundii
Actinomyces oris
Arachnia propionica
Campylobacter gracilis
Cardiobacterium hominis
Cardiobacterium valvarum
Eikenella corrodens
Eikenella halliae
Kingella oralis
Ottowia sp. oral taxon 894
Porphyromonas catoniae
Rothia aeria
Rothia dentocariosa
Streptococcus oralis
Streptococcus sanguinis
Streptococcus sp. oral taxon 056

Revision editor(s): KateRasheed, WikiWorks

Signature 2

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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)

NCBI	Quality Control	Links
Actinomyces graevenitzii
Actinomyces sp. HMSC035G02
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Campylobacter concisus
Chlamydia ibidis
Hoylesella shahii
Leptotrichia sp. oral taxon 215
Megasphaera micronuciformis
Mogibacterium diversum
Oribacterium asaccharolyticum
Oribacterium parvum
Oribacterium sinus
Prevotella melaninogenica
Prevotella pallens
Prevotella scopos
Prevotella sp. F0091
Segatella salivae
Solobacterium moorei
Streptococcus sp. HMSC034E03
Streptococcus sp. HMSC067H01
Streptococcus sp. HMSC071D03
Veillonella dispar
Veillonella infantium
Veillonella tobetsuensis
[Eubacterium] sulci
Fusobacterium periodonticum

Revision editor(s): KateRasheed, WikiWorks

Experiment 3

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Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, Aleru Divine, WikiWorks

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

NCBI	Quality Control	Links
Abiotrophia defectiva
Actinomyces johnsonii
Actinomyces massiliensis
Actinomyces naeslundii
Actinomyces oris
Actinomyces sp. oral taxon 180
Actinomyces sp. oral taxon 414
Alloprevotella sp. oral taxon 473
Arachnia propionica
Campylobacter curvus
Campylobacter gracilis
Capnocytophaga granulosa
Capnocytophaga leadbetteri
Capnocytophaga ochracea
Capnocytophaga sputigena
Cardiobacterium hominis
Cardiobacterium valvarum
Corynebacterium durum
Corynebacterium matruchotii
Cutibacterium acnes
Eikenella corrodens
Eikenella halliae
Enhydrobacter aerosaccus
Fusobacterium hwasookii
Fusobacterium nucleatum
Fusobacterium periodonticum
Gemella bergeri
Gemella haemolysans
Gemella morbillorum
Hoylesella saccharolytica
Kingella oralis
Leptotrichia buccalis
Leptotrichia hofstadii
Leptotrichia sp. oral taxon 215
Leptotrichia sp. oral taxon 225
Leptotrichia sp. oral taxon 847
Leptotrichia sp. oral taxon 879
Malassezia restricta
Micrococcus luteus
Moraxella osloensis
Neisseria cinerea
Neisseria sicca
Ottowia sp. oral taxon 894
Pauljensenia hongkongensis
Porphyromonas somerae
Prevotella sp. oral taxon 299
Rothia aeria
Rothia dentocariosa
Schaalia georgiae
Selenomonas artemidis
Selenomonas noxia
Selenomonas sp. FOBRC6
Selenomonas sp. oral taxon 138
Selenomonas sp. oral taxon 892
Selenomonas sp. oral taxon 920
Staphylococcus epidermidis
Streptococcus anginosus group
Streptococcus cristatus
Streptococcus gordonii
Streptococcus mitis
Streptococcus mutans
Streptococcus oralis
Streptococcus pneumoniae
Streptococcus sanguinis
Streptococcus sobrinus
Streptococcus sp. A12
Streptococcus sp. oral taxon 056
Streptococcus vestibularis
Veillonella parvula

Revision editor(s): KateRasheed, Aleru Divine, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/13

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
Campylobacter rectus
Capnocytophaga ochracea
Haemophilus parahaemolyticus
Hoylesella pleuritidis
Lactococcus lactis
Lancefieldella rimae
Lautropia mirabilis
Neisseria sp. oral taxon 014
Parvimonas micra
Porphyromonas endodontalis
Prevotella denticola
Prevotella nigrescens
Pseudoleptotrichia goodfellowii
Rothia aeria
Rothia dentocariosa
Scardovia wiggsiae
Segatella oris
Streptococcus anginosus
Streptococcus thermophilus
[Eubacterium] brachy
Oribacterium parvum
[Eubacterium] sulci
Prevotella jejuni
Prevotella pallens
Hoylesella shahii
Megasphaera micronuciformis
Actinomyces graevenitzii
Mogibacterium diversum
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Prevotella sp. oral taxon 306
Oribacterium asaccharolyticum
Segatella salivae
Prevotella histicola
Prevotella scopos
Solobacterium moorei
Neisseria subflava
Streptococcus sp. HMSC034E03
Streptococcus sp. HMSC067H01
Alloprevotella rava
Veillonella atypica
Actinomyces sp. HMSC035G02
Lancefieldella parvula
Actinomyces sp. HPA0247
Fusobacterium periodonticum
Lachnospiraceae bacterium oral taxon 096
Veillonella rogosae
Prevotella sp. oral taxon 299
Veillonella tobetsuensis
Prevotella sp. F0091
Stomatobaculum longum
Streptococcus sp. F0442
Alloprevotella sp. oral taxon 473
Oribacterium sinus
Leptotrichia sp. oral taxon 215
Prevotella melaninogenica
Selenomonas flueggei
Streptococcus australis
Streptococcus sp. HMSC071D03
Streptococcus sp. A12
Actinomyces sp. oral taxon 181
Campylobacter concisus
Prevotella veroralis
Veillonella dispar
Veillonella sp. T11011-6
Veillonella infantium
Porphyromonas somerae
[Eubacterium] infirmum
Neisseria flavescens
Dialister invisus
Schaalia odontolytica
Lachnoanaerobaculum umeaense
Streptococcus parasanguinis
Mogibacterium pumilum
Streptococcus infantis
Rothia mucilaginosa

Revision editor(s): KateRasheed, WikiWorks

Experiment 4

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Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. 3C, Supplementary Data 17

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)

NCBI	Quality Control	Links
Actinomyces graevenitzii
Actinomyces sp. HMSC035G02
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Actinomyces sp. oral taxon 181
Atopobium deltae
Campylobacter concisus
Corynebacterium argentoratense
Hoylesella shahii
Hoylesella timonensis
Lancefieldella parvula
Megasphaera micronuciformis
Mogibacterium diversum
Oribacterium asaccharolyticum
Oribacterium parvum
Oribacterium sinus
Prevotella histicola
Prevotella jejuni
Prevotella melaninogenica
Prevotella pallens
Prevotella scopos
Schaalia odontolytica
Segatella salivae
Selenomonas flueggei
Solobacterium moorei
Streptococcus sp. HMSC034E03
Streptococcus sp. HMSC067H01
Veillonella atypica
Veillonella dispar
Veillonella infantium
Veillonella rogosae
Veillonella sp. T11011-6
[Eubacterium] sulci

Revision editor(s): KateRasheed, WikiWorks

Signature 2

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Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. 3C, Supplementary Data 17

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)

NCBI	Quality Control	Links
Faecalibacterium prausnitzii
Fretibacterium fastidiosum
Rothia aeria
Thomasclavelia spiroformis
Micrococcus terreus
Parabacteroides merdae
Coprococcus catus
Lachnospira eligens
Phocaeicola massiliensis
Gemmiger formicilis
[Eubacterium] siraeum
Alistipes finegoldii
Intestinibacter bartlettii
Anaerobutyricum hallii
Firmicutes bacterium CAG:83
Parabacteroides distasonis
Bifidobacterium bifidum
Blautia obeum
Bifidobacterium pseudocatenulatum
Bacteroides caccae
Anaerostipes hadrus
Ruminococcus bromii
Bifidobacterium adolescentis
[Ruminococcus] torques
Fusicatenibacter saccharivorans
Phocaeicola vulgatus
Collinsella aerofaciens
Kocuria palustris
Agathobacter rectalis
Hoylesella oralis
Gemella morbillorum
Abiotrophia defectiva
Actinomyces oris
Capnocytophaga leadbetteri
Centipeda periodontii
Neisseria bacilliformis
Leptotrichia sp. oral taxon 225
Treponema lecithinolyticum
Acaryochloridales
Streptococcus mitis
Streptococcus sanguinis
Cardiobacterium valvarum
Campylobacter gracilis
Eikenella corrodens
Kingella oralis
Leptotrichia hofstadii
Staphylococcus epidermidis
Capnocytophaga gingivalis
Corynebacterium matruchotii
Selenomonas sp. FOBRC6
Actinomyces massiliensis
Hoylesella saccharolytica
Leptotrichia sp. oral taxon 879
Actinomyces sp. oral taxon 897
Actinomyces sp. oral taxon 414
Eikenella halliae
Streptococcus gordonii
Cutibacterium acnes
Capnocytophaga granulosa
Arachnia propionica
Actinomyces johnsonii

Revision editor(s): KateRasheed, WikiWorks

Experiment 5

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Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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: increased abundance in High Intelligence Quotients(High IQ > 85) by diet

NCBI	Quality Control	Links
Actinomyces graevenitzii
Actinomyces sp. HMSC035G02
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Actinomyces sp. oral taxon 181
Campylobacter concisus
Corynebacterium argentoratense
Hoylesella shahii
Lancefieldella parvula
Megasphaera micronuciformis
Mogibacterium diversum
Oribacterium asaccharolyticum
Oribacterium parvum
Oribacterium sinus
Prevotella histicola
Prevotella jejuni
Prevotella melaninogenica
Prevotella pallens
Prevotella scopos
Schaalia odontolytica
Segatella salivae
Selenomonas flueggei
Solobacterium moorei
Streptococcus sp. HMSC034E03
Streptococcus sp. HMSC067H01
Veillonella atypica
Veillonella dispar
Veillonella infantium
Veillonella rogosae
Veillonella sp. T11011-6
[Eubacterium] sulci

Revision editor(s): KateRasheed, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
Actinomyces johnsonii
Actinomyces massiliensis
Arachnia propionica
Corynebacterium matruchotii
Cutibacterium acnes
Eikenella halliae
Leptotrichia hofstadii
Leptotrichia sp. oral taxon 215
Streptococcus sanguinis
Micrococcus terreus
Coprococcus catus
Lachnospira eligens
Gemmiger formicilis
Phocaeicola massiliensis
Alistipes finegoldii
Intestinibacter bartlettii
Anaerobutyricum hallii
Blautia obeum
Bifidobacterium pseudocatenulatum
Firmicutes bacterium CAG:83
Bacteroides caccae
Bifidobacterium adolescentis
Anaerostipes hadrus
Ruminococcus bromii
[Ruminococcus] torques
Fusicatenibacter saccharivorans
Streptococcus mitis
Phocaeicola vulgatus
Fretibacterium fastidiosum
Collinsella aerofaciens
Kocuria palustris
Gemella morbillorum
Faecalibacterium prausnitzii
Agathobacter rectalis
Hoylesella oralis
Actinomyces oris
Actinomyces naeslundii
Leptotrichia sp. oral taxon 225
Eikenella corrodens
Cardiobacterium valvarum
Campylobacter gracilis
Centipeda periodontii
Kingella oralis
Neisseria bacilliformis
Treponema lecithinolyticum
Selenomonas sp. FOBRC6
Capnocytophaga gingivalis
Staphylococcus epidermidis
Catonella morbi
Hoylesella saccharolytica
Leptotrichia sp. oral taxon 879
Actinomyces sp. oral taxon 897
Actinomyces sp. oral taxon 414
Capnocytophaga granulosa

Revision editor(s): KateRasheed, WikiWorks

Experiment 6

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Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
Streptococcus gordonii
Porphyromonas sp. oral taxon 278
Leptotrichia buccalis
Bacteroidetes oral taxon 274
Scardovia wiggsiae
Leptotrichia sp. oral taxon 498
Capnocytophaga granulosa
Actinomyces sp. oral taxon 414
Catonella morbi
Treponema denticola
Segatella maculosa
Arachnia propionica
Corynebacterium matruchotii
Hoylesella saccharolytica
Actinomyces massiliensis
Bulleidia extructa
Campylobacter gracilis
Leptotrichia sp. oral taxon 225
Leptotrichia sp. oral taxon 879
Haemophilus haemolyticus
Leptotrichia hofstadii
Actinomyces oris
Veillonella parvula
Streptococcus mitis

Revision editor(s): KateRasheed, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
Achromobacter sp. AONIH1
Acidaminococcus intestini
Acidovorax temperans
Actinomyces graevenitzii
Actinomyces sp. ICM47
Actinomyces sp. S6-Spd3
Aerococcus christensenii
Agrobacterium pusense
Alistipes onderdonkii
Anaerotruncus colihominis
Aspergillus versicolor
Bacteroides eggerthii
Bacteroides galacturonicus
Bacteroides salyersiae
Bacteroides sp. CAG:144
Bacteroides zoogleoformans
Bifidobacterium angulatum
Bifidobacterium pseudolongum
Bifidobacterium ruminantium
Blautia hansenii
Blautia producta
Bowdeniella nasicola
Campylobacter concisus
Capnocytophaga canimorsus
Caulobacter vibrioides
Christensenella minuta
Chryseobacterium gleum
Citrobacter freundii
Citrobacter youngae
Clostridium neonatale
Clostridium perfringens
Clostridium sp. CAG:253
Comamonas thiooxydans
Corynebacterium ammoniagenes
Corynebacterium resistens
Corynebacterium striatum
Cronobacter sakazakii
Curtobacterium flaccumfaciens
Desulfovibrio fairfieldensis
Desulfovibrionaceae bacterium
Dickeya chrysanthemi
Enterobacter bugandensis
Enterobacter soli
Enterococcus hirae
Enterococcus saccharolyticus
Erwinia billingiae
Eshraghiella crossota
Eubacterium ventriosum
Flavobacterium anhuiense
Fusobacterium mortiferum
Fusobacterium varium
Hafnia alvei
Jonquetella anthropi
Klebsiella aerogenes
Lactiplantibacillus paraplantarum
Lactiplantibacillus pentosus
Lactobacillus amylovorus
Lactobacillus equicursoris
Lactococcus garvieae
Lactococcus petauri
Lancefieldella parvula
Ligilactobacillus aviarius
Ligilactobacillus ruminis
Limosilactobacillus antri
Limosilactobacillus coleohominis
Limosilactobacillus panis
Liquorilactobacillus nagelii
Lysinibacillus fusiformis
Megasphaera elsdenii
Megasphaera micronuciformis
Metamycoplasma hominis
Microbacterium oleivorans
Mobiluncus curtisii
Mobiluncus mulieris
Mogibacterium diversum
Mycoplasmopsis agalactiae
Oribacterium asaccharolyticum
Oribacterium parvum
Oribacterium sinus
Ornithinimicrobium pekingense
Paenibacillus odorifer
Parasutterella excrementihominis
Pasteurella dagmatis
Peptoniphilus grossensis
Phocaeicola coprocola
Porphyromonas cangingivalis
Porphyromonas circumdentaria
Porphyromonas crevioricanis
Prevotella melaninogenica
Prevotella pallens
Priestia flexa
Priestia megaterium
Proteus mirabilis
Roseateles puraquae
Rothia mucilaginosa
Ruminococcus champanellensis
Segatella salivae
Shouchella clausii
Sphingobacterium sp. B29
Stenotrophomonas acidaminiphila
Streptococcus gallolyticus
Streptococcus parauberis
Streptococcus pasteurianus
Streptococcus troglodytae
Streptococcus uberis
Tissierellia bacterium KA00581
Turicibacter sanguinis
Ureaplasma urealyticum
Veillonella dispar
Veillonella infantium
Veillonella montpellierensis
Xanthomonas arboricola
Xanthomonas translucens
Yersinia frederiksenii
Yersinia intermedia
[Clostridium] scindens
[Collinsella] massiliensis
[Eubacterium] sulci
Jeotgalicoccus sp.
Leifsonia sp. 71-9
Microbacterium laevaniformans
Exiguobacterium sp. RIT594
Malassezia sympodialis
Acidipropionibacterium acidipropionici
Pseudomonas sp. NS1(2017)
Ewingella americana
Pseudomonas gingeri
Pantoea allii
Suttonella indologenes
Corynebacterium singulare
Pseudomonas yamanorum
Achromobacter piechaudii
Ralstonia mannitolilytica
Sphingomonas koreensis
Bacillus sp. AFS040349
Xanthomonas hortorum
Alphaproteobacteria bacterium HGW-Alphaproteobacteria-17
Microbacterium sp. SMR1
Tetragenococcus muriaticus
Apilactobacillus kunkeei
Sphingomonadales bacterium RIFCSPHIGHO2_01_FULL_65_20
Sodalis praecaptivus
Duganella phyllosphaerae
Cytobacillus horneckiae
Burkholderia gladioli
Pseudomonas sp. HMWF006
Hyphomonas atlantica
Xanthomonas sacchari
Sphingomonas sanguinis
Methylobacterium phyllosphaerae
Gluconobacter frateurii
Fervidobacterium pennivorans
Corynebacterium pollutisoli
Jeotgalibaca sp. PTS2502
Pseudomonas granadensis
Paenibacillus nuruki
Kingella negevensis
Tepidimonas fonticaldi
Parageobacillus thermoglucosidasius
Deinococcus reticulitermitis
Chishuiella changwenlii
Agrobacterium salinitolerans
Mycoplasmopsis canis
Canicola haemoglobinophilus
Deinococcus proteolyticus
Rodentibacter caecimuris
Streptococcus hongkongensis
Aeriscardovia aeriphila
Pantoea sp. AS-PWVM4
Moraxella pluranimalium
Pseudomonas lurida
Stenotrophomonas indicatrix
Companilactobacillus futsaii
Jeotgalicoccus aerolatus
Winkia neuii
Mycobacterium avium
Hafnia paralvei
Brevibacterium iodinum
Liquorilactobacillus mali
Pseudomonas sp. OV508
Rouxiella silvae
Pseudomonas sp. 2822_17
Weissella soli
Weissella hellenica
Weissella paramesenteroides
Microbacterium hominis
Geobacillus kaustophilus
Geobacillus thermoleovorans
Geobacillus thermocatenulatus
Chryseobacterium scophthalmum
Pyramidobacter sp. C12-8
Acetobacter orientalis
Pseudomonas cerasi
Bosea vaviloviae
Sphingomonas ginsenosidimutans
Klebsiella grimontii
Lentilactobacillus parabuchneri
Macrococcoides bohemicum
Pseudomonas sp. Choline-02u-1
Pseudomonas chlororaphis
Serratia proteamaculans
Megasphaera sp. DISK 18
Herbaspirillum frisingense
Sphingobacterium nematocida
Microbacterium paraoxydans
Glutamicibacter sp.
Chryseobacterium balustinum
Pseudomonas soli
Kluyvera intermedia
Lactobacillus amylolyticus
Neisseria zoodegmatis
Arthrobacter pityocampae
Rahnella sikkimica
Ligilactobacillus saerimneri
Hyalangium minutum
Pantoea latae
Duganella sp. Leaf61
Corynebacterium freneyi
Bacillus safensis
Pediococcus sp.
Pediococcus parvulus
Secundilactobacillus collinoides
Pediococcus ethanolidurans
Lentilactobacillus parafarraginis
Lentilactobacillus rapi
Bacillus haynesii
Microbacterium sp. Leaf151
Photobacterium phosphoreum
Staphylococcus devriesei
Alteromonas macleodii
Stenotrophomonas sp. SPM
Siccibacter turicensis
Sanguibacter sp. Leaf3
Enterobacter sp. kpr-6
Neorhizobium sp. SOG26
Criibacterium bergeronii
Lysobacter enzymogenes
Actinomyces gaoshouyii
Xanthomonas euvesicatoria
Xanthomonas citri
Schleiferilactobacillus harbinensis
Shouchella rhizosphaerae
Aspergillus glaucus
Malassezia pachydermatis
Epilithonimonas hispanica
Blattabacterium punctulatus
Alcaligenes aquatilis
Helcococcus kunzii
Corynebacterium glaucum
Eremococcus coleocola
Tanticharoenia sakaeratensis
Gluconobacter albidus
Pandoraea pnomenusa
Rickettsia bellii
Pseudonocardia autotrophica
Bifidobacterium moukalabense
Lactobacillus hominis
Serratia sp. Leaf51
Tetzosporium hominis
Companilactobacillus alimentarius
Tersicoccus sp. Bi-70
Dickeya dadantii
Pseudorhodobacter sp. MZDSW-24AT
Flavobacterium aquidurense
Companilactobacillus crustorum
Fructilactobacillus fructivorans
Arcanobacterium haemolyticum
Bordetella bronchiseptica
Schaalia radingae
Serratia grimesii
Janthinobacterium lividum
Corynebacterium vitaeruminis
Cupriavidus sp.
Gulbenkiania indica
Chryseobacterium gambrini
Pseudomonas syringae group
Staphylococcus condimenti
Aster yellows witches'-broom phytoplasma
Onion yellows phytoplasma
Serratia ficaria
Dietzia timorensis
Sphingopyxis terrae
Dialister sp. CAG:357
Acetobacter senegalensis
Achromobacter ruhlandii
Alicyclobacillus acidocaldarius
Limosilactobacillus frumenti
Peribacillus simplex
Clostridium tyrobutyricum
Yersinia ruckeri
Brachybacterium sp. UMB0905
Blastomonas sp.
Novosphingobium sp. AAP93
Rahnella sp. AA
Rickettsia asembonensis
Rickettsia hoogstraalii
Rickettsia canadensis
Acinetobacter genomosp. 15BJ
Acinetobacter_sp_CIP_110321Acinetobacter_sp_CIP_110321
Acinetobacter proteolyticus
Clavibacter cf. michiganensis LMG 26808
Acetobacter syzygii
Cobetia marina
Deinococcus sp. RL
Bavariicoccus seileri
Veillonella seminalis
Paucilactobacillus wasatchensis
Secundilactobacillus malefermentans
Solilutibacter tolerans
Peptoniphilus sp. oral taxon 386
Carnobacterium inhibens
Exiguobacterium indicum
Fulvimonas soli
Nocardia nova
Truepera radiovictrix
Thermus arciformis
[Eubacterium] minutum
Candidatus Erwinia dacicola
Ciceribacter selenitireducens
Campylobacter upsaliensis
Microbacterium sp. AR7-10
Pseudomonas sp. URMO17WK12:I2
Aliarcobacter butzleri
Acidovorax sp. MR-S7
Pseudomonas grimontii
Pseudomonas sp. 57B-090624
Brevibacillus parabrevis
Brucella lupini
Brucella haematophila
Pseudomonas kuykendallii
Actinobaculum massiliense
Metapseudomonas otitidis
Burkholderiales bacterium RIFCSPHIGHO2_01_FULL_63_240
Pseudoalteromonas nigrifaciens
Rouxiella badensis
Actinotignum urinale
Psychrobacter immobilis
Shewanella baltica
Erwinia persicina
Aureimonas altamirensis
Agrobacterium deltaense
Paenibacillus pasadenensis
Enterobacter sp. FS01
Actinotignum timonense
Kosakonia oryzae
Roseateles terrae
Atlantibacter hermannii
Paenirhodobacter enshiensis
Limnospira maxima
Leuconostoc suionicum
Lactococcus chungangensis
Mycobacterium lepraemurium
Porphyromonas gingivicanis
Achromobacter denitrificans
Escherichia sp. ESNIH1
Helicobacter canis
Mycolicibacterium llatzerense
Deinococcus geothermalis
Acinetobacter brisouii
Paraburkholderia tropica
Latilactobacillus fuchuensis
Lentilactobacillus farraginis
Acinetobacter bereziniae

Revision editor(s): KateRasheed, WikiWorks

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/15

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/15

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
[Eubacterium] sulci
Prevotella pallens
Oribacterium parvum
Prevotella jejuni
Megasphaera micronuciformis
Mogibacterium diversum
Oribacterium asaccharolyticum
Prevotella scopos
Actinomyces graevenitzii
Actinomyces sp. ICM47
Veillonella atypica
Actinomyces sp. S6-Spd3
Segatella salivae
Solobacterium moorei
Streptococcus australis
Streptococcus sp. HMSC067H01
Fusobacterium periodonticum
Streptococcus sp. HMSC034E03
Leptotrichia sp. oral taxon 215
Oribacterium sinus
Prevotella melaninogenica
Veillonella sp. T11011-6
Lancefieldella parvula
Actinomyces sp. HMSC035G02
Campylobacter concisus
Veillonella dispar
Veillonella infantium
Schaalia odontolytica

Revision editor(s): KateRasheed, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2024/11/15

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

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

NCBI	Quality Control	Links
Streptococcus mitis
Streptococcus oralis
Corynebacterium durum
Veillonella parvula
Streptococcus sanguinis
Actinomyces oris
Kingella oralis
Streptococcus cristatus
Leptotrichia sp. oral taxon 225
Actinomyces naeslundii
Eikenella halliae
Staphylococcus epidermidis
Capnocytophaga granulosa
Scardovia wiggsiae
Leptotrichia hofstadii
Streptococcus mutans
Arachnia rubra
Corynebacterium matruchotii
Streptococcus gordonii
Cutibacterium acnes
Leptotrichia sp. oral taxon 879

Revision editor(s): KateRasheed, WikiWorks

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2025/01/01

Curator: KateRasheed

Revision editor(s): WikiWorks, KateRasheed

Differences from previous experiment shown

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-2

Curated date: 2025/01/01

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: 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)

NCBI	Quality Control	Links
Actinomyces graevenitzii
Actinomyces sp. S6-Spd3
Hoylesella shahii
Megasphaera micronuciformis
Mogibacterium diversum
Oribacterium asaccharolyticum
Oribacterium parvum
Prevotella jejuni
Prevotella pallens
Solobacterium moorei
[Eubacterium] sulci
Actinomyces sp. ICM47
Segatella salivae
Veillonella rogosae
Prevotella scopos
Prevotella histicola
Streptococcus sp. HMSC067H01
Veillonella tobetsuensis
Fusobacterium periodonticum
Lancefieldella parvula
Actinomyces sp. HMSC035G02
Prevotella melaninogenica
Veillonella atypica
Oribacterium sinus
Streptococcus australis
Streptococcus sp. HMSC034E03
Leptotrichia sp. oral taxon 215
Actinomyces sp. oral taxon 181
Prevotella sp. oral taxon 299
Campylobacter concisus
Prevotella sp. oral taxon 306
Veillonella infantium
Veillonella dispar
Porphyromonas somerae
Selenomonas flueggei
Haemophilus sputorum
Streptococcus sp. A12
Veillonella sp. T11011-6
Lachnospiraceae bacterium oral taxon 096
Stomatobaculum longum
Lancefieldella rimae
Alloprevotella rava
Schaalia odontolytica
Streptococcus sp. F0442
Alloprevotella sp. oral taxon 473
Neisseria flavescens
[Eubacterium] infirmum
Streptococcus sp. HMSC071D03
Lachnoanaerobaculum umeaense
Streptococcus infantis
Rothia mucilaginosa
Dialister invisus
Slackia exigua
Gemella sanguinis

Revision editor(s): KateRasheed, WikiWorks

Signature 2