Ethnic variability associating gut and oral microbiome with obesity in children
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T, Taneja V
Journal
Gut microbes
Year
2021
Keywords:
Microbiome, disparity, minorities, obesity, socioeconomic factors
Obesity is a growing worldwide problem that generally starts in the early years of life and affects minorities more often than Whites. Thus, there is an urgency to determine factors that can be used as targets as indicators of obesity. In this study, we attempt to generate a profile of gut and oral microbial clades predictive of disease status in African American (AA) and European American (EA) children. 16S rDNA sequencing of the gut and saliva microbial profiles were correlated with salivary amylase, socioeconomic factors (e.g., education and family income), and obesity in both ethnic populations. Gut and oral microbial diversity between AA and EA children showed significant differences in alpha-, beta-, and taxa-level diversity. While gut microbial diversity between obese and non-obese was not evident in EA children, the abundance of gut Klebsiella and Magasphaera was associated with obesity in AA children. In contrast, an abundance of oral Aggregatibacter and Eikenella in obese EA children was observed. These observations suggest an ethnicity-specific association with gut and oral microbial profiles. Socioeconomic factors influenced microbiota in obesity, which were ethnicity dependent, suggesting that specific approaches to confront obesity are required for both populations.
Experiment 1
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
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 , Gut microbiome measurement Ethnicity,race,Ethnic group,ethnic group,Gut microbiome measurement,gut microbiome measurement
- 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): 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)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Desulfovibrio | ||
| Marvinbryantia | ||
| Oxalobacter | ||
| Prevotella | ||
| Senegalimassilia | ||
| Slackia | ||
| Synergistales | ||
| Synergistia | ||
| Synergistota | ||
| uncultured Oscillospiraceae bacterium |
Revision editor(s): Kaluifeanyi101, Atrayees, Folakunmi
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
Curated date: 2022/06/29
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, WikiWorks, Folakunmi
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
- Ethnic group Ethnicity,race,Ethnic group,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)
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-30
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)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Kaluifeanyi101, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-30
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)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyrivibrio | ||
| Capnocytophaga | ||
| Fusobacterium | ||
| Haemophilus | ||
| Prevotella |
Revision editor(s): Kaluifeanyi101, Folakunmi
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
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.
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-30
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-30
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
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
- 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.
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-30
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.
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Kaluifeanyi101, Folakunmi
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
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
Lab analysis
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
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
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Eikenella |
Revision editor(s): Folakunmi
Experiment 6
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
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
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
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-31
Source: Figures 3C
Description: Differentially abundant taxa in obese and non-obese AA children
Abundance in Group 1: increased abundance in Obese African American children
Revision editor(s): Folakunmi
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