Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders/Experiment 3

From BugSigDB


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

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
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.

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


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 ControlLinks
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
Faucicola 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 ControlLinks
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