Gut microbiota diversity across ethnicities in the United States

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Christensenellaceae
Odoribacter
Odoribacteraceae
Peptococcaceae
Rikenellaceae
Verrucomicrobiaceae
Victivallaceae
unclassified Coriobacteriaceae
unclassified Eubacteriales

Revision editor(s): Kaluifeanyi101, Claregrieve1

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Christensenellaceae
Verrucomicrobiaceae

Revision editor(s): Kaluifeanyi101

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Christensenellaceae
unclassified Eubacteriales
Verrucomicrobiaceae
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
Peptococcaceae
Christensenellaceae
unclassified Eubacteriales
Verrucomicrobiaceae
Odoribacteraceae
Odoribacter
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
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 Control	Links
unclassified Eubacteriales
Verrucomicrobiaceae
Odoribacter
Odoribacteraceae
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

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 Control	Links
Veillonella
Odoribacteraceae
Odoribacter
Rikenellaceae
unclassified Coriobacteriaceae

Revision editor(s): Kaluifeanyi101

Signature 2