Profiling the Salivary microbiome of the Qatari population

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Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/30

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Subjects

Location of subjects: Qatar

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: Sex design sex_design,Sex design,sex design

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Males

Group 1 name Corresponds to the case (exposed) group for case-control studies: Females

Group 0 sample size Number of subjects in the control (unexposed) group: 555

Group 1 sample size Number of subjects in the case (exposed) group: 442

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 2

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex, smoking status

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Source: Figure 1c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)

Abundance in Group 1: decreased abundance in Females

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Bergeyella
Tannerella
Bacteroidota

Revision editor(s): Suwaiba, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Source: Figure 1c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in males (green) and females (red)

Abundance in Group 1: increased abundance in Females

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Treponema
Mycoplasma
Corynebacterium
Spirochaetota

Revision editor(s): Suwaiba, Atrayees

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Aging ageing,AGING BIOL,Aging, Biological,BIOL AGING,Biological Aging,Senescence,Aging,aging

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Adults

Group 1 name Corresponds to the case (exposed) group for case-control studies: Elderly

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: People older than 65years of age

Group 0 sample size Number of subjects in the control (unexposed) group: 979

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.007

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: decreased

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, ChiomaBlessing

Source: Figure 2c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).

Abundance in Group 1: increased abundance in Elderly

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Bacteroidota
Prevotella
Spirochaeta
Treponema
Candidatus Saccharibacteria

Revision editor(s): Suwaiba, Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, Peace Sandy

Source: Figure 2c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in Elderly (green) and Adults (red).

Abundance in Group 1: decreased abundance in Elderly

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Abiotrophia
Actinomyces
Actinomycetota
Aggregatibacter
Anaeroglobus
Bacillota
Campylobacter
Candidatus Saccharibacteria
Catonella
Dialister
Eikenella
Fusobacteriota
Gemella
Granulicatella
Haemophilus
Kingella
Lachnoanaerobaculum
Lautropia
Leptotrichia
Megasphaera
Mogibacterium
Peptostreptococcaceae
Pseudomonadota
Rothia
Selenomonas
Stomatobaculum
Streptococcus
Veillonella
Candidatus Nanosynbacter sp. TM7-053

Revision editor(s): Suwaiba, Atrayees, Peace Sandy

Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Atrayees, Suwaiba

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Gingival bleeding Bleeding gums,Gingival haemorrhage,Gingival hemorrhage,Gingivorrhagia,Gingival bleeding,gingival bleeding

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Participants without gingivitis bleeding

Group 1 name Corresponds to the case (exposed) group for case-control studies: Participants with gingival bleeding

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants reported suffering from a bleeding gum

Group 0 sample size Number of subjects in the control (unexposed) group: 913

Group 1 sample size Number of subjects in the case (exposed) group: 84

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 2

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 3c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red)

Abundance in Group 1: increased abundance in Participants with gingival bleeding

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Bacteroidota
Capnocytophaga
Prevotella

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, Peace Sandy

Source: Figure 3c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report bleeding (green) and the participants that reported bleeding gums (red)

Abundance in Group 1: decreased abundance in Participants with gingival bleeding

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Actinomycetota
Alloprevotella
Bacillota
Candidatus Saccharibacteria
Fusobacteriota
Gemella
Granulicatella
Haemophilus
Lautropia
Leptotrichia
Megasphaera
Neisseria
Pseudomonadota
Streptococcus
Veillonella
Candidatus Nanosynbacter featherlites

Revision editor(s): Suwaiba, Atrayees, Peace Sandy

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Atrayees, Suwaiba

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Oral ulcer Mouth sore,Mouth ulcer,Oral mucosal ulceration,Oral ulcer,oral ulcer

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Participants without oral ulcers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Participants with oral ulcers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants who reported suffering from oral ulcers

Group 0 sample size Number of subjects in the control (unexposed) group: 960

Group 1 sample size Number of subjects in the case (exposed) group: 37

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 4c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red)

Abundance in Group 1: increased abundance in Participants with oral ulcers

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Bacteroidota
Capnocytophaga
Prevotella

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 4c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not report any mouth ulcer (green) and the participants that reported having mouth ulcers (red)

Abundance in Group 1: decreased abundance in Participants with oral ulcers

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Bacillota
Fusobacteriota
Gemella
Granulicatella
Haemophilus
Leptotrichia
Megasphaera
Neisseria
Pseudomonadota
Streptococcus
Veillonella
Actinomycetota

Revision editor(s): Suwaiba

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Dentures false teeth,Dentures,dentures

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Participants without dentures

Group 1 name Corresponds to the case (exposed) group for case-control studies: Participants with dentures

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants who reported using dentures

Group 0 sample size Number of subjects in the control (unexposed) group: 861

Group 1 sample size Number of subjects in the case (exposed) group: 136

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Source: Figure 5c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red)

Abundance in Group 1: increased abundance in Participants with dentures

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Actinomycetota
Pseudomonadota
Neisseria
Streptococcus
Pseudoramibacter

Revision editor(s): Suwaiba, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-19

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Source: Figure 5c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that did not use dentures (green) and the participants that reported using dentures (red)

Abundance in Group 1: decreased abundance in Participants with dentures

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Campylobacter
Oscillospiraceae

Revision editor(s): Suwaiba, Atrayees

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Smoking behavior smoking,Smoking behavior,smoking behavior

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-smokers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Smokers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants classified as smokers

Group 0 sample size Number of subjects in the control (unexposed) group: 733

Group 1 sample size Number of subjects in the case (exposed) group: 264

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-20

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 6c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red)

Abundance in Group 1: increased abundance in Smokers

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Bacteroidota
Prevotella

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-20

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 6c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in smokers (green) and non- smokers (red)

Abundance in Group 1: decreased abundance in Smokers

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Pseudomonadota
Synergistota
Lactococcus
Corynebacterium
Gemella
Capnocytophaga
Streptococcus

Revision editor(s): Suwaiba

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Coffee consumption caffeine consumption,Coffee consumption,coffee consumption

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-coffee drinkers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Coffee drinkers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants considered coffee drinkers

Group 0 sample size Number of subjects in the control (unexposed) group: 887

Group 1 sample size Number of subjects in the case (exposed) group: 110

Lab analysis

Statistical Analysis

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: increased

Chao1 Abundance-based estimator of species richness: increased

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-20

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

Source: Figure 7c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)

Abundance in Group 1: increased abundance in Coffee drinkers

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Candidatus Saccharibacteria
Actinomycetota
Pseudomonadota
Bacillota
Lautropia
Granulicatella
Haemophilus
Veillonella
Streptococcus

Revision editor(s): Suwaiba, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-20

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba

Source: Figure 7c

Description: Graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial phyla and genera; among the two groups. LDA scores indicate overrepresented bacteria in individuals that do not drink coffee (green) and the participants that are considered coffee drinkers (red)

Abundance in Group 1: decreased abundance in Coffee drinkers

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Bacteroidota
Fusobacteriota
Prevotella

Revision editor(s): Suwaiba

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/31

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, LGeistlinger

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Tea consumption measurement Tea consumption measurement,tea consumption measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non tea drinkers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Tea drinkers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants considered tea drinkers

Group 0 sample size Number of subjects in the control (unexposed) group: 229

Group 1 sample size Number of subjects in the case (exposed) group: 768

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

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

Richness Number of species: increased

Signature 1