Gut microbiota diversity across ethnicities in the United States/Experiment 1
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Reviewed Marked as Reviewed by Atrayees on 2023-6-30
Curated date: 2022/07/07
Curator: Kaluifeanyi101
Revision editor(s): WikiWorks, Claregrieve1, Kaluifeanyi101, 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
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
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
