Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-13
Subjects
- Location of subjects
- Nepal
- 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
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lifestyle Gradient
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Increasing Lifestyle Gradient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lifestyles transitioning from more traditional to industrial.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 91
- Group 1 sample size Number of subjects in the case (exposed) group
- 91
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- currently on antibiotics
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).
- relative abundances
- Statistical test
- Jonckheere's trend test
- 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
- sex
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-13
Source: Figure 4
Description: Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.
Abundance in Group 1: increased abundance in Increasing Lifestyle Gradient
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-13
Source: Figure 4
Description: Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.
Abundance in Group 1: decreased abundance in Increasing Lifestyle Gradient
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella | ||
| Moraxella | ||
| Neisseria | ||
| Simonsiella | ||
| Streptobacillus | ||
| unclassified Bacteroidota | ||
| unclassified Porphyromonadaceae | ||
| Brachymonas |
