Gut microbiota diversity across ethnicities in the United States

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Brooks AW, Priya S, Blekhman R, Bordenstein SR
Journal
PLoS biology
Year
2018
Composed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities. However, the influence of ethnicity on the gut microbiota remains largely unexplored and lacks reproducible generalizations across studies. By distilling associations between ethnicity and differences in two US-based 16S gut microbiota data sets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. Interestingly, a majority of these microbial taxa, including the most heritable bacterial family, Christensenellaceae, overlap with genetically associated taxa and form co-occurring clusters linked by similar fermentative and methanogenic metabolic processes. These results demonstrate recurrent associations between specific taxa in the gut microbiota and ethnicity, providing hypotheses for examining specific members of the gut microbiota as mediators of health disparities.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1, WikiWorks, Peace Sandy

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 Ethnicity,race,Ethnic group,ethnic group
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Caucasians
Group 1 name Corresponds to the case (exposed) group for case-control studies
Asian Pacific
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Asian Pacific sampled from the American Gut Project (AGP) data set
Group 0 sample size Number of subjects in the control (unexposed) group
1237
Group 1 sample size Number of subjects in the case (exposed) group
88
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
NA

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
Mann-Whitney (Wilcoxon)
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, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Figure 4

Description: Differential microbial abundance between Caucasian and Asian Pacific subjects

Abundance in Group 1: increased abundance in Asian Pacific

NCBI Quality ControlLinks
Veillonella

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Figure 4

Description: Differential microbial abundance between Caucasian and Asian Pacific subjects

Abundance in Group 1: decreased abundance in Asian Pacific

NCBI Quality ControlLinks
Christensenellaceae
Odoribacter
Odoribacteraceae
Peptococcaceae
Rikenellaceae
Verrucomicrobiaceae
Victivallaceae
unclassified Coriobacteriaceae
unclassified Eubacteriales

Revision editor(s): Kaluifeanyi101, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Hispanic
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Hispanics sampled from the American Gut Project (AGP) data set
Group 1 sample size Number of subjects in the case (exposed) group
37

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: increased abundance in Hispanic

NCBI Quality ControlLinks
Odoribacter
Odoribacteraceae
Peptococcaceae
Rikenellaceae
Veillonella
Victivallaceae
unclassified Eubacteriales
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f

Abundance in Group 1: decreased abundance in Hispanic

NCBI Quality ControlLinks
Christensenellaceae
Verrucomicrobiaceae

Revision editor(s): Kaluifeanyi101

Experiment 3


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
African Americans
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
African Americans sampled from the American Gut Project (AGP) data set
Group 1 sample size Number of subjects in the case (exposed) group
13

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities; f

Abundance in Group 1: increased abundance in African Americans

NCBI Quality ControlLinks
Peptococcaceae
Veillonella
Victivallaceae
Odoribacteraceae
Odoribacter

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: decreased abundance in African Americans

NCBI Quality ControlLinks
Christensenellaceae
unclassified Eubacteriales
Verrucomicrobiaceae
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 4


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Asian Pacific
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Asian Pacific sampled from Human Microbiome Project (HMP) data set
Group 0 sample size Number of subjects in the control (unexposed) group
211
Group 1 sample size Number of subjects in the case (exposed) group
34

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: increased abundance in Asian Pacific

NCBI Quality ControlLinks
Veillonella
Victivallaceae

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: decreased abundance in Asian Pacific

NCBI Quality ControlLinks
Peptococcaceae
Christensenellaceae
unclassified Eubacteriales
Verrucomicrobiaceae
Odoribacteraceae
Odoribacter
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 5


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/07

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Hispanics
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Hispanics sampled from Human Microbiome Project (HMP) data set
Group 1 sample size Number of subjects in the case (exposed) group
43

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/08

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: increased abundance in Hispanics

NCBI Quality ControlLinks
Peptococcaceae
Christensenellaceae
Veillonella
Victivallaceae

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/08

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: decreased abundance in Hispanics

NCBI Quality ControlLinks
unclassified Eubacteriales
Verrucomicrobiaceae
Odoribacter
Odoribacteraceae
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 6


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/08

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
African Americans
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
African Americans sampled from Human Microbiome Project (HMP) data set
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/08

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: increased abundance in African Americans

NCBI Quality ControlLinks
Veillonella
Odoribacteraceae
Odoribacter
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-23

Curated date: 2022/07/08

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Ethnicity-associated taxa match between the HMP and AGP. Bar plots depict the log10 transformed relative abundance for individuals possessing the respective taxon within each ethnicity, ubiquity appears above (AGP) or below (HMP) bars, and the 25th and 75th percentiles are shown with extending whiskers. Mann–Whitney U tests evaluate differences in abundance and ubiquity for all individuals between pairs of ethnicities.

Abundance in Group 1: decreased abundance in African Americans

NCBI Quality ControlLinks
Peptococcaceae
Christensenellaceae
unclassified Eubacteriales
Verrucomicrobiaceae
Victivallaceae

Revision editor(s): Kaluifeanyi101