Ethnic variability associating gut and oral microbiome with obesity in children

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Reviewed Marked as Reviewed by Atrayees on 2023-7-3

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Kaluifeanyi101, Atrayees, Peace Sandy, Folakunmi, Tosin

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: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Ethnic group Ethnicity,race,Ethnic group,ethnic group

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Gut microbiome of European American children (EA)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Gut microbiome of African American children (AA)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut microbiome of 30 African American children (18 female, 12 male; age 6 - 10 years)

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 30

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

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

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: PERMANOVA

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, household income, education level, sex

Alpha Diversity

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-3

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Kaluifeanyi101, Atrayees, Folakunmi

Source: Figure 1C

Description: Differential abundance of taxa in the gut microbiota variability of AA and EA populations at 10% false discovery rate.

Abundance in Group 1: increased abundance in Gut microbiome of African American children (AA)

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Anaerotruncus
Desulfovibrio
Marvinbryantia
Oxalobacter
Prevotella
Senegalimassilia
Slackia
Synergistales
Synergistia
Synergistota
uncultured Oscillospiraceae bacterium

Revision editor(s): WikiWorks, Kaluifeanyi101, Atrayees, Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-31

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Folakunmi, Kaluifeanyi101

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oral opening Mouth,Oral fissure,Oral orifice,Oral part of face,Oral opening,oral opening

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral microbiota of European American children (EA)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Oral microbiota of African American children (AA)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Oral microbiota of 30 African American children (18 female, 12 male; age 6 - 10 years)

Alpha Diversity

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Source: Figure 2C

Description: Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate

Abundance in Group 1: increased abundance in Oral microbiota of African American children (AA)

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Streptococcus

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Source: Figure 2C

Description: Genus-level differentially abundant taxa in the oral microbiota comparison between AA and EA groups at a 10% false discovery rate

Abundance in Group 1: decreased abundance in Oral microbiota of African American children (AA)

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Butyrivibrio
Capnocytophaga
Fusobacterium
Haemophilus
Prevotella

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-31

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Folakunmi, Kaluifeanyi101

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Household income (EA & AA) =>$50,000.

Group 1 name Corresponds to the case (exposed) group for case-control studies: Household income (EA & AA) < $50,000.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut microbiota of children from low-income households (EA & AA) < $50,000.

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, ethnic group, education level, sex

Alpha Diversity

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks

Source: Figure 6B

Description: Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families with low income (P ≤ .05).

Abundance in Group 1: increased abundance in Household income (EA & AA) < $50,000.

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Phascolarctobacterium

Revision editor(s): Kaluifeanyi101, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks

Source: Figure 6B

Description: Both groups had an increased abundance of gut Phascolarcobacteria, with a decrease in Faecalitalea (both belonging to the phylum Firmicutes) in families with low income (P ≤ .05).

Abundance in Group 1: decreased abundance in Household income (EA & AA) < $50,000.

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Faecalitalea

Revision editor(s): Kaluifeanyi101, WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-1-31

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Kaluifeanyi101, Folakunmi, Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oral opening Mouth,Oral fissure,Oral orifice,Oral part of face,Oral opening,oral opening

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Household income Household income,household income

Group 0 name Corresponds to the control (unexposed) group for case-control studies: High income in European American households =>$50,000.

Group 1 name Corresponds to the case (exposed) group for case-control studies: Low income in European American households < $50,000.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Oral microbiota of children from low-income EA households < $50,000.

Alpha Diversity

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Source: FIGURE 6D

Description: Differentially abundant taxa analysis of oral microbiota showed an increased abundance of Streptococcus in EA children from low-income families. No differentially abundant taxa were associated with income in AA children (not shown).

Abundance in Group 1: increased abundance in Low income in European American households < $50,000.

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Streptococcaceae
Streptococcus

Revision editor(s): Kaluifeanyi101, Folakunmi, WikiWorks

Experiment 5

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-31

Curated date: 2024/01/30

Curator: Folakunmi

Revision editor(s): WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity

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

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

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

Group 0 sample size Number of subjects in the control (unexposed) group: 22

Group 1 sample size Number of subjects in the case (exposed) group: 8

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

Alpha Diversity

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-1-30

Curated date: 2024/01/30

Curator: Folakunmi

Revision editor(s): Folakunmi, WikiWorks

Source: Figures 3E

Description: Oral microbial diversity was associated with obesity in EA children. Genera Aggregatibacter and Eikenella abundance was increased in obese compared to non-obese EA children.

Abundance in Group 1: increased abundance in Obese EA children

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Aggregatibacter
Eikenella

Revision editor(s): Folakunmi, WikiWorks

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-1-31

Curated date: 2024/01/30

Curator: Folakunmi

Revision editor(s): Folakunmi, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-obese African American children

Group 1 name Corresponds to the case (exposed) group for case-control studies: Obese African American children

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Not specified

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 9

Alpha Diversity

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: increased

Signature 1