Gut microbiota diversity across ethnicities in the United States/Experiment 4

From BugSigDB


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

Curated date: 2022/07/07

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
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
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

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