Ethnic variability associating gut and oral microbiome with obesity in children

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Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): 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

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

Statistical test: PERMANOVA

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

Shannon Estimator of species richness and species evenness: more weight on species richness: increased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: increased
Richness Number of species: increased

Signature 1

Needs review

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 1B; Figure 1C

Description: Principal coordinate analysis (PCoA) plot based on the bray-Curtis distance matrix constructed using ASVs. The percentage of variability explained by the corresponding coordinate is indicated on the axes. Each point represents a sample – red symbols indicate the AA population and blue symbols indicate the EA population. The lines indicate vectors representing the relationships between ASVs and each sample category. The ellipses serve as a visual guide to group differences. A comparison of beta diversity between AA and EA populations showed significant differences in community structure (p ≤ .05).

Figure 1C. Differential abundance of taxa in AA and EA populations at 10% false discovery rate. Each dot represents a participant. The relative abundances were plotted on the square-root scale to better visualize the low abundance taxa.

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

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Signature 2

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Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 1C

Description: Differential abundance of taxa in AA and EA populations at a 10% false discovery rate. Each dot represents a participant. The relative abundances were plotted on the square-root scale to better visualizes the low abundance taxa.

No statistically significant decrease in the abundance of an OTU was seen in group 1 relative to group 0.

Abundance in Group 1:

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Experiment 2

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Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

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

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

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)
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: PERMANOVA

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

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

Needs review

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 2B; Figure 2C

Description: The bray-Curtis distance matrix for beta diversity between AA and EA populations was analyzed using PERMANOVA. Comparison between AA and EA groups showed a significant difference in beta diversity (p ≤ .05). C, Genus-level differentially abundant taxa in AA and EA groups at a 10% false discovery rate were presented. The relative abundances were plotted on the square-root scale to better visualize the low abundance taxa. Streptococcus was present with an increased abundance in AA children compared to EA children, and 5 genera, butyrivibrio, capnocytophaga, fusobacterium, haemophilus, and prevotella, were abundant in EA but not in AA groups

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

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Streptococcus

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Signature 2

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Curated date: 2022/06/29

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Source: Figure 2B; Figure 2C

Description: : The bray-Curtis distance matrix for beta diversity between AA and EA populations was analyzed using PERMANOVA. Comparison between AA and EA groups showed a significant difference in beta diversity (p ≤ .05). C, Genus-level differentially abundant taxa in AA and EA groups at a 10% false discovery rate were presented. The relative abundances were plotted on the square-root scale to better visualize the low abundance taxa. Streptococcus was present with an increased abundance in AA children compared to EA children.

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

NCBI	Links
Butyrivibrio
Capnocytophaga
Fusobacterium
Haemophilus
Prevotella

Revision editor(s): Kaluifeanyi101

Experiment 3

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Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Socioeconomic statusSocioeconomic status

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.
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: PERMANOVA

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

Needs review

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

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

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Signature 2

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Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

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

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Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Socioeconomic statusSocioeconomic status

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: Oral microbiota of children from low-income households (EA & AA) < $50,000.
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: PERMANOVA

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