Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders/Experiment 4

From BugSigDB


Needs review

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): 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
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

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)
0.2
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


Signature 1

Needs review

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed

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)

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

Revision editor(s): KateRasheed

Signature 2

Needs review

Curated date: 2024/11/14

Curator: KateRasheed

Revision editor(s): KateRasheed

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)

NCBI Quality ControlLinks
Actinomyces johnsonii
Actinomyces massiliensis
Arachnia propionica
Corynebacterium matruchotii
Cutibacterium acnes
Eikenella halliae
Leptotrichia hofstadii
Leptotrichia sp. oral taxon 215
Streptococcus gordonii
Streptococcus sanguinis
Streptococcus mutans
Pauljensenia hongkongensis
Leptotrichia sp. oral taxon 879
Schaalia georgiae
Capnocytophaga granulosa
Kingella oralis
Streptococcus sp. oral taxon 056
Actinomyces naeslundii
Campylobacter gracilis
Actinomyces sp. oral taxon 414
Actinomyces oris
Selenomonas artemidis
Selenomonas sp. oral taxon 920
Streptococcus vestibularis
Leptotrichia sp. oral taxon 225
Selenomonas sp. FOBRC6
Staphylococcus epidermidis
Corynebacterium durum
Leptotrichia buccalis
Leptotrichia sp. oral taxon 498
Rothia dentocariosa
Cardiobacterium valvarum
Streptococcus oralis
Selenomonas noxia
Actinomyces sp. oral taxon 180
Selenomonas sp. oral taxon 138
Eikenella corrodens
Streptococcus anginosus group
Cardiobacterium hominis
Micrococcus luteus
Centipeda periodontii
Streptococcus cristatus
Capnocytophaga leadbetteri
Capnocytophaga ochracea
Actinomyces sp. oral taxon 897
Veillonella parvula
Streptococcus mitis
Selenomonas infelix
Ottowia sp. oral taxon 894
Treponema lecithinolyticum
Moraxella osloensis
Malassezia restricta
Rothia aeria
Capnocytophaga sputigena
Kocuria palustris
Actinomyces sp. oral taxon 448
Cutibacterium granulosum
Enhydrobacter aerosaccus
Leptotrichia sp. oral taxon 847
Capnocytophaga gingivalis
Kocuria rhizophila
Campylobacter curvus
Staphylococcus capitis
Candida albicans
Corynebacterium kroppenstedtii
Gemella morbillorum
Fretibacterium fastidiosum
Dolosigranulum pigrum
Selenomonas sp. F0473
Cutibacterium namnetense
Paracoccus yeei
Faecalibacterium prausnitzii
Corynebacterium pseudogenitalium
Agathobacter rectalis
Corynebacterium pseudodiphtheriticum
Janibacter indicus
Segatella copri
Corynebacterium accolens
Acinetobacter ursingii
Staphylococcus simulans
Paracoccus salipaludis
Kocuria indica
Actinomyces radicidentis

Revision editor(s): KateRasheed