Sociodemographic variation in the oral microbiome

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Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/04/12

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Claregrieve1, Atrayees

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

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: College graduate or more

Group 1 name Corresponds to the case (exposed) group for case-control studies: Less than High school diploma

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Less than High school diploma

Group 0 sample size Number of subjects in the control (unexposed) group: 87

Group 1 sample size Number of subjects in the case (exposed) group: 65

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).: relative abundances

Statistical test: edgeR

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.01

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: education level

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/04/13

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species based on education level.

Abundance in Group 1: decreased abundance in Less than High school diploma

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Alloprevotella

Revision editor(s): Kelvin Joseph, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species based on education level.

Abundance in Group 1: increased abundance in Less than High school diploma

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Porphyromonas
Campylobacter
Prevotella
Veillonella
Filifactor
Scardovia
Streptococcus

Revision editor(s): Atrayees

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/04/24

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Some college or associate's degree

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Some college or associate's degree

Group 1 sample size Number of subjects in the case (exposed) group: 67

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/01

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species based on education level.

Abundance in Group 1: decreased abundance in Some college or associate's degree

NCBI	Quality Control	Links
Corynebacterium

Revision editor(s): Kelvin Joseph, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species based on education level.

Abundance in Group 1: increased abundance in Some college or associate's degree

NCBI	Quality Control	Links
Scardovia
Lactobacillus
Alloprevotella
Veillonella

Revision editor(s): Kelvin Joseph, Atrayees

Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Differences from previous experiment shown

Subjects

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

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

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

Group 0 sample size Number of subjects in the control (unexposed) group: 86

Group 1 sample size Number of subjects in the case (exposed) group: 72

Lab analysis

Statistical Analysis

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

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and alternate smokers

Abundance in Group 1: decreased abundance in Alternative smokers

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Anaeroglobus
Pseudomonas
Streptococcus
Alloscardovia
Actinomyces
Stomatobaculum

Revision editor(s): Kelvin Joseph, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and alternate smokers

Abundance in Group 1: increased abundance in Alternative smokers

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Fusobacterium
Neisseria
Streptobacillus
Porphyromonas
Bergeyella
Lautropia
Cardiobacterium
Gemella
Alloprevotella

Revision editor(s): Kelvin Joseph, Atrayees

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Differences from previous experiment shown

Subjects

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

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

Group 1 sample size Number of subjects in the case (exposed) group: 43

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and former smokers

Abundance in Group 1: decreased abundance in Former smokers

NCBI	Quality Control	Links
Veillonella
Lactobacillus
Alloprevotella
Campylobacter
Prevotella
Pseudomonas

Revision editor(s): Kelvin Joseph, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and former smokers

Abundance in Group 1: increased abundance in Former smokers

NCBI	Quality Control	Links
Neisseria
Bergeyella
Lautropia
Haemophilus
Peptococcus
Capnocytophaga

Revision editor(s): Atrayees

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Never smokers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Never smokers

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and never smokers

Abundance in Group 1: decreased abundance in Never smokers

NCBI	Quality Control	Links
Megasphaera
Stomatobaculum
Prevotella
Campylobacter
Leptotrichia
Veillonella

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and never smokers

Abundance in Group 1: increased abundance in Never smokers

NCBI	Quality Control	Links
Neisseria
Bergeyella
Streptococcus
Porphyromonas
Gemella
Lactococcus
Haemophilus
Lautropia
Bifidobacterium
Actinobacillus

Revision editor(s): Atrayees

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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

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

Group 1 sample size Number of subjects in the case (exposed) group: 38

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and secondhand smokers

Abundance in Group 1: decreased abundance in Secondhand smokers

NCBI	Quality Control	Links
Veillonella
Leptotrichia
Lactobacillus
Rothia
Streptococcus
Anaeroglobus
Actinomyces

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in cigarette smokers and secondhand smokers

Abundance in Group 1: increased abundance in Secondhand smokers

NCBI	Quality Control	Links
Bergeyella
Peptostreptococcus
Gemella
Alloprevotella
Neisseria
Prevotella

Revision editor(s): Atrayees

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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

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

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

Group 0 sample size Number of subjects in the control (unexposed) group: 97

Group 1 sample size Number of subjects in the case (exposed) group: 22

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: race

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in Non-Hispanic whites and Asians.

Abundance in Group 1: increased abundance in Asian

NCBI	Quality Control	Links
Alloprevotella

Revision editor(s): Atrayees

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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

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

Group 1 sample size Number of subjects in the case (exposed) group: 71

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in Non-Hispanic whites and Hispanics

Abundance in Group 1: increased abundance in Hispanic

NCBI	Quality Control	Links
Prevotella
Porphyromonas
Campylobacter
Filifactor
Treponema
Fusobacterium
Alloprevotella
Veillonella

Revision editor(s): Atrayees

Experiment 9

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Non-Hispanic black

Group 1 sample size Number of subjects in the case (exposed) group: 75

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks

Abundance in Group 1: decreased abundance in Non-Hispanic black

NCBI	Quality Control	Links
Veillonella
Cardiobacterium
Streptobacillus

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in Non-Hispanic whites and Non-Hispanic blacks

Abundance in Group 1: increased abundance in Non-Hispanic black

NCBI	Quality Control	Links
Prevotella
Campylobacter
Atopobium
Lactobacillus
Anaeroglobus
Bifidobacterium
Filifactor
Alloprevotella
Acholeplasma
Porphyromonas

Revision editor(s): Atrayees

Experiment 10

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Females

Group 0 sample size Number of subjects in the control (unexposed) group: 132

Group 1 sample size Number of subjects in the case (exposed) group: 150

Lab analysis

Statistical Analysis

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

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in males and females

Abundance in Group 1: decreased abundance in Females

NCBI	Quality Control	Links
Actinobacillus
Treponema
Porphyromonas

Revision editor(s): Atrayees

Experiment 11

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: age group 20-29

Group 1 name Corresponds to the case (exposed) group for case-control studies: age group 35-64

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: age group 35-64

Group 0 sample size Number of subjects in the control (unexposed) group: 70

Group 1 sample size Number of subjects in the case (exposed) group: Not specified

Lab analysis

Statistical Analysis

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

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in age group 20-29 and age group 35-64

Abundance in Group 1: decreased abundance in age group 35-64

NCBI	Quality Control	Links
Porphyromonas
Pseudomonas
Alloprevotella
Atopobium
Leptotrichia
Fusobacterium
Actinobacillus

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-15

Curated date: 2023/06/15

Curator: Atrayees

Revision editor(s): Atrayees

Source: Spreadsheet

Description: The relative abundance of selected species in age group 20-29 and age group 35-64

Abundance in Group 1: increased abundance in age group 35-64

NCBI	Quality Control	Links
Streptococcus
Lactobacillus
Leptotrichia

Revision editor(s): Atrayees

Experiment 12