Ethnic variability associating gut and oral microbiome with obesity in children

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Babu JR, Geetha T, Taneja V
Journal
Gut microbes
Year
2021
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


Needs review

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)

NCBI Links
Anaerotruncus
Desulfovibrio
Marvinbryantia
Oxalobacter
Prevotella
Senegalimassilia
Slackia

Revision editor(s): Kaluifeanyi101

Signature 2

Needs review

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:
NCBI Links

Revision editor(s): Kaluifeanyi101

Experiment 2


Needs review

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)

NCBI 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 Links
Butyrivibrio
Capnocytophaga
Fusobacterium
Haemophilus
Prevotella

Revision editor(s): Kaluifeanyi101

Experiment 3


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
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.

NCBI 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 Links
Faecalitalea

Revision editor(s): Kaluifeanyi101

Experiment 4


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

Needs review

Curated date: 2022/06/30

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

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