Gut microbiota diversity across ethnicities in the United States/Experiment 6
Curated date: 2022/07/08
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, WikiWorks, ChiomaBlessing
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
- 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 0 sample size Number of subjects in the control (unexposed) group
- 211
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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)
- .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
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
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 |
|---|---|---|
| Peptococcaceae | ||
| Christensenellaceae | ||
| unclassified Eubacteriales | ||
| Verrucomicrobiaceae | ||
| Victivallaceae |
Revision editor(s): Kaluifeanyi101
