Ethnic variability associating gut and oral microbiome with obesity in children
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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)
NCBI | Links |
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Anaerotruncus | |
Desulfovibrio | |
Marvinbryantia | |
Oxalobacter ⚠ | |
Prevotella | |
Senegalimassilia | |
Slackia |
Revision editor(s): Kaluifeanyi101
Signature 2
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:NCBI | Links |
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Revision editor(s): Kaluifeanyi101
Experiment 2
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
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 | Links |
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Streptococcus |
Revision editor(s): Kaluifeanyi101
Signature 2
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
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
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 | Links |
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Phascolarctobacterium |
Revision editor(s): Kaluifeanyi101
Signature 2
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 | Links |
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Faecalitalea |
Revision editor(s): Kaluifeanyi101
Experiment 4
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
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 Household income (EA & AA) < $50,000.
NCBI | Links |
---|---|
Streptococcaceae | |
Streptococcus |
Revision editor(s): Kaluifeanyi101