Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Subjects

Location of subjects: Canada

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: Supragingival dental plaque , Saliva Supragingival plaque,Supragingival dental plaque,supragingival dental plaque,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Microbiome measurement Microbiome measurement,microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral swab from severe early childhood caries (S-ECC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Supragingival plaque from severe early childhood caries (S-ECC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC)

Group 0 sample size Number of subjects in the control (unexposed) group: 40

Group 1 sample size Number of subjects in the case (exposed) group: 40

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Use of antibiotics

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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).: raw counts

Statistical test: DESeq2

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)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Source: FIG. 3B

Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group

Abundance in Group 1: increased abundance in Supragingival plaque from severe early childhood caries (S-ECC)

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Abiotrophia defectiva
Capnocytophaga sputigena
Corynebacterium durum
Corynebacterium matruchotii
Kingella kingae
Kingella oralis
Lautropia mirabilis
Rothia aeria
Rothia dentocariosa
Segatella maculosa
Segatella oris
Selenomonas artemidis
Selenomonas sputigena
Streptococcus anginosus
Streptococcus mutans
Streptococcus salivarius
Prevotella sp. HMT 472Prevotella sp. HMT 472
Actinomyces sp. HMT 180Actinomyces sp. HMT 180
Leptotrichia sp. HMT 498Leptotrichia sp. HMT 498
Ottowia sp. HMT 894Ottowia sp. HMT 894
Kingella sp. HMT 012Kingella sp. HMT 012
Capnocytophaga sp. HMT 326Capnocytophaga sp. HMT 326
Mitsuokella sp. HMT 131Mitsuokella sp. HMT 131

Revision editor(s): Rahila, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Source: FIG. 3B

Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group

Abundance in Group 1: decreased abundance in Supragingival plaque from severe early childhood caries (S-ECC)

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Gemella morbillorum
Granulicatella elegans
Haemophilus influenzae
Haemophilus parainfluenzae
Hoylesella nanceiensis
Simonsiella muelleri
Sneathia vaginalis
Porphyromonas sp. HMT 930Porphyromonas sp. HMT 930
Bergeyella sp. HMT 931Bergeyella sp. HMT 931
Alloprevotella sp. HMT 473Alloprevotella sp. HMT 473
Veillonella sp. HMT 780Veillonella sp. HMT 780

Revision editor(s): Rahila, Scholastica

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Saliva , Supragingival dental plaque Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Supragingival plaque,Supragingival dental plaque,supragingival dental plaque

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral swab from caries-free

Group 1 name Corresponds to the case (exposed) group for case-control studies: Supragingival plaque from caries-free

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Source: FIG. 3C

Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group

Abundance in Group 1: increased abundance in Supragingival plaque from caries-free

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Abiotrophia defectiva
Actinomyces gerencseriae
Aggregatibacter aphrophilus
Campylobacter gracilis
Campylobacter rectus
Capnocytophaga gingivalis
Capnocytophaga granulosa
Capnocytophaga leadbetteri
Capnocytophaga sputigena
Cardiobacterium hominis
Corynebacterium durum
Corynebacterium matruchotii
Eikenella corrodens
Kingella oralis
Lautropia mirabilis
Leptotrichia hongkongensis
Rothia aeria
Rothia dentocariosa
Selenomonas artemidis
Selenomonas sputigena
Streptococcus intermedius
Bergeyella sp. HMT 322Bergeyella sp. HMT 322
Fusobacterium sp. HMT 203Fusobacterium sp. HMT 203
P.[XI][G-7] yurii subspp. yurii & margaretiaeP.[XI][G-7] yurii subspp. yurii & margaretiae
Prevotella sp. HMT 472Prevotella sp. HMT 472
Prevotella sp. HMT 317Prevotella sp. HMT 317
Lachnospiraceae [G-3] bacterium HMT 100Lachnospiraceae [G-3] bacterium HMT 100
Capnocytophaga sp. HMT 326Capnocytophaga sp. HMT 326
Leptotrichia sp. HMT 392Leptotrichia sp. HMT 392
Leptotrichia sp. HMT 212Leptotrichia sp. HMT 212
Absconditabacteria (SR1) [G-1] bacterium HMT 345Absconditabacteria (SR1) [G-1] bacterium HMT 345
Kingella sp. HMT 012Kingella sp. HMT 012

Revision editor(s): Rahila, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/04/21

Curator: Rahila

Revision editor(s): Rahila, Scholastica

Source: FIG. 3C

Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group

Abundance in Group 1: decreased abundance in Supragingival plaque from caries-free

NCBI	Quality Control	Links
Gemella morbillorum
Granulicatella elegans
Haemophilus parainfluenzae
Porphyromonas pasteri
Prevotella melaninogenica
Rothia mucilaginosa
Sneathia vaginalis
Porphyromonas sp. HMT 930Porphyromonas sp. HMT 930
Veillonella sp. HMT 780Veillonella sp. HMT 780
Alloprevotella sp. HMT 473Alloprevotella sp. HMT 473

Revision editor(s): Rahila, Scholastica

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Supragingival dental plaque , Saliva Supragingival plaque,Supragingival dental plaque,supragingival dental plaque,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral swab from severe early childhood caries (S-ECC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Supragingival plaque from severe early childhood caries (S-ECC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Supragingival plaque samples of children < 72 months of age with severe early childhood caries (S-ECC)

Lab analysis

Sequencing type: ITS / ITS2

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group

Abundance in Group 1: increased abundance in Supragingival plaque from severe early childhood caries (S-ECC)

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Candida dubliniensis
Candida albicans
Thelephoraceae
Ramicandelaber taiwanensis
Fusarium sp.
Stereum rugosum
Wallemia tropicalis

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group

Abundance in Group 1: decreased abundance in Supragingival plaque from severe early childhood caries (S-ECC)

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Agaricomycetes
Malassezia restricta
Trichosporon asahii
Malassezia globosa

Revision editor(s): Scholastica

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Saliva , Supragingival dental plaque Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Supragingival plaque,Supragingival dental plaque,supragingival dental plaque

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral swab from caries-free

Group 1 name Corresponds to the case (exposed) group for case-control studies: Supragingival plaque from caries-free

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Supragingival plaque samples of children < 72 months of age who are caries-free, confirmed by a dental examination

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group

Abundance in Group 1: increased abundance in Supragingival plaque from caries-free

NCBI	Quality Control	Links
Blumeria sp.
Malassezia restricta
Trichosporon asahii
Ramicandelaber taiwanensis
Fusarium sp.
Meyerozyma guilliermondii
Malasseziales
Cryptomycota
Chytridiomycota
Wallemia tropicalis

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the caries-free group

Abundance in Group 1: decreased abundance in Supragingival plaque from caries-free

NCBI	Quality Control	Links
Agaricomycetes
Ascomycota

Revision editor(s): Scholastica

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Oral swab from severe early childhood caries (S-ECC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Oral swap samples of children < 72 months of age who are caries-free, confirmed by a dental examination

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-5

Curated date: 2024/06/05

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differential abundance analysis of fungal taxa in oral swab samples within the caries-free group versus oral swab samples within the S-ECC (severe early childhood caries) group

Abundance in Group 1: increased abundance in Oral swab from severe early childhood caries (S-ECC)

NCBI	Quality Control	Links
Candida dubliniensis
Malassezia restricta
Candida tropicalis

Revision editor(s): Scholastica

Signature 2