The human microbiota is associated with cardiometabolic risk across the epidemiologic transition/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- Ghana
- South Africa
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Risk factor Factor, Risk,Factors, Risk,Risk Factors,Risk factor,risk factor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-CMD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CMD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the CMD group had Cardiometabolic Risk (CM) risk defined as at least 3 CM risk factors from five: waist circumference, elevated blood pressure, elevated blood fasting glucose, elevated triglyceride and low HDL concentration in USA, RSA, and Ghana
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).
- centered log-ratio
- Statistical test
- ANCOM
- 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, sex, Confounders controlled for: "country" 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.country
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 3C
Description: Specific oral bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: increased abundance in CMD
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Rothia | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 3C
Description: Specific oral bacterial taxa are differentially abundant (in relative terms) between study sites with and without elevated CM risk (only significantly differential exact sequence variants (ESVs) with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: decreased abundance in CMD
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Fusobacterium | ||
| Neisseria sp. | ||
| Haemophilus | ||
| Rothia |
Revision editor(s): Aleru Divine
