Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis/Experiment 1
Curated date: 2022/06/23
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Peace Sandy, Fiddyhamma
Subjects
- Location of subjects
- China
- 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
- Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- underdeveloped cities vs developed cities
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 7009 Individuals' fecal samples from underdeveloped cities with GDP/capita of 22.1K to 25.3K CNY, and those from developed cities with GDP/capita of 149.5K to 136.1K CNY. (continuous variables)
- Group 1 sample size Number of subjects in the case (exposed) group
- 7009
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Unspecified.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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, sex, Confounders controlled for: "bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.bristol stool scale, geographic area
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4a
Description: Associations between OTUs and host economic status. a Stacked plot showing the number of OTUs that are positively associated with income or spending (continuous variables).
Colors correspond to taxonomies in the legend.
Abundance in Group 1: increased abundance in underdeveloped cities vs developed cities
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Betaproteobacteria | ||
| Lachnospiraceae | ||
| Parabacteroides | ||
| Rikenellaceae | ||
| Ruminococcus | ||
| Veillonellaceae |
Revision editor(s): Kaluifeanyi101
Signature 2
Source: Figure 4a
Description: Associations between OTUs and host economic status. A Stacked plot showing the number of OTUs that are negatively associated with income or spending (continuous variables). Colors correspond to taxonomies in the legend.
Abundance in Group 1: decreased abundance in underdeveloped cities vs developed cities
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Gammaproteobacteria | ||
| Peptostreptococcaceae | ||
| Prevotella | ||
| Ruminococcus |
Revision editor(s): Kaluifeanyi101
