The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence/Experiment 1
Curated date: 2022/07/21
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Aiyshaaaa, Peace Sandy
Subjects
- Location of subjects
- Israel
- 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
- Low SES
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High SES
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children from the higher SES village (A) SES scores below the median score of 6.4 based on (a) residential SES rank; (b) the number of paternal schooling years; and (c) household crowding index.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 70
- 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
- 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).
- raw counts
- Statistical test
- Linear Regression
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 2D;
Description: Figure 2D. A heatmap of the multivariable model describing the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).
Abundance in Group 1: increased abundance in High SES
| NCBI | Quality Control | Links |
|---|---|---|
| Delftia | ||
| Rikenellaceae | ||
| Barnesiellaceae | ||
| Clostridium | ||
| Erysipelotrichaceae | ||
| Parabacteroides | ||
| Odoribacter | ||
| Ruminococcus |
Revision editor(s): Kaluifeanyi101, Peace Sandy
Signature 2
Source: Figure 2D
Description: Figure 2D. A heatmap of the multivariable model describing the top 50 associations between the independent variables and bacterial features. Positive associations are colored in red, while inverse associations are colored in blue. The color gradient represents the strength of the association (the effect size), with darker colors representing the stronger associations. The effect size was calculated by the following formula: (−log(qval)*SIGN (coeff)).
Abundance in Group 1: decreased abundance in High SES
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacterium | ||
| Coriobacteriaceae | ||
| Bulleidia | ||
| Mogibacterium | ||
| Prevotella | ||
| Eubacterium | ||
| Dorea | ||
| Adlercreutzia |
Revision editor(s): Kaluifeanyi101, Peace Sandy
