Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity/Experiment 1
Curated date: 2023/03/17
Curator: Ombati
Revision editor(s): LGeistlinger, Chloe, Atrayees, Ombati, 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
- Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals with a healthy body mass index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who had a class II or class III obesity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 293
- Group 1 sample size Number of subjects in the case (exposed) group
- 294
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S4
Description: Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.
Abundance in Group 1: decreased abundance in Obese individuals
Signature 2
Source: Table S4
Description: Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.
Abundance in Group 1: increased abundance in Obese individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Megasphaera | ||
| Catenibacterium | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): Atrayees
