Ethnic variability associating gut and oral microbiome with obesity in children

Your review change was submittedDuplicate this Experiment Add a new Signature

Flag for review

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

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks, Atrayees

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances
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

Flag for review

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

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Atrayees

Source: Figure 1C

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

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

NCBI	Quality Control	Links
Anaerotruncus
Desulfovibrio
Marvinbryantia
Oxalobacter
Prevotella
Senegalimassilia
Slackia
Synergistota
Synergistia
Synergistales
Oscillospiraceae

Revision editor(s): Kaluifeanyi101, Atrayees

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2022/06/29

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks

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

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)

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

Not specified

Statistical test

PERMANOVA

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)

NCBI	Quality Control	Links
Streptococcus

Revision editor(s): Kaluifeanyi101

Signature 2

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.

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

NCBI	Quality Control	Links
Butyrivibrio
Capnocytophaga
Fusobacterium
Haemophilus
Prevotella

Revision editor(s): Kaluifeanyi101

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): 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

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.

Lab analysis

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

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.

NCBI	Quality Control	Links
Phascolarctobacterium

Revision editor(s): Kaluifeanyi101

Signature 2

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

NCBI	Quality Control	Links
Faecalitalea

Revision editor(s): Kaluifeanyi101

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

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

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.

Lab analysis

Statistical Analysis

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