Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Atrayees on 2023-6-13

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

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/03/17

Curator: Ombati

Revision editor(s): Ombati, Chloe, Atrayees

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

NCBI Quality ControlLinks
Cloacibacillus
Ruminococcus
unclassified Oscillospiraceae
unclassified Eubacteriales
unclassified Coriobacteriaceae
Anaerotruncus
Oscillospira
Eggerthella
unclassified Rikenellaceae
unclassified Clostridiaceae
Blautia
Akkermansia

Revision editor(s): Ombati, Chloe, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/06/08

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Acidaminococcus
Megasphaera
Catenibacterium
Prevotella
Streptococcus

Revision editor(s): Atrayees