Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study/Experiment 1
Curated date: 2022/06/10
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Aiyshaaaa, Peace Sandy
Subjects
- Location of subjects
- United Kingdom
- 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 0 name Corresponds to the control (unexposed) group for case-control studies
- Higher SES (income= > £25,000)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lower SES (income<£25,000)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lower socioeconomic status(SES) with higher deprivation by income <£25,000
- Group 0 sample size Number of subjects in the control (unexposed) group
- 457
- Group 1 sample size Number of subjects in the case (exposed) group
- 342
- 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
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- edgeR
- 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, diet
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 2A; Tabel 2
Description: Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI).
Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).
Abundance in Group 1: increased abundance in lower SES (income<£25,000)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Erysipelotrichales | ||
| Lactobacillales |
Revision editor(s): Kaluifeanyi101
Signature 2
Source: Figure 2A; Table 2
Description: Differential abundance of OTUs with socioeconomic variables and covariates. DeSeq2 calculated the differential abundance of OTUs in: (A). Between the lowest and highest levels of deprivation for education, income, and the IMD, and in models adjusted for age, Body Mass Index (BMI), health deficit (FI), and diet (HEI). Table 2. Summary of taxa assigned to OTUs found to be differentially abundant between the most-deprived and least-deprived measures of socioeconomic status in at least two models. Only taxa with multiple OTUs assigned to it, or with multiple SES factors associated with it, and with q-value <, 0.01 are discussed. OTUs relatively enriched in the least deprived compared to the highest for each SES variable are indicated with (+); those enriched in the most deprived compared to the least indicated with (−); where multiple directions of association were observed, this is indicated with (+/−).
Abundance in Group 1: decreased abundance in lower SES (income<£25,000)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Verrucomicrobiales | ||
| Rikenellaceae |
Revision editor(s): Kaluifeanyi101
