Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized/Experiment 1

From BugSigDB


Needs review

Curated date: 2024/11/24

Curator: Tosin

Revision editor(s): Tosin

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
Combination of Foragers, recently settled, agriculturalists, expats.
Group 1 name Corresponds to the case (exposed) group for case-control studies
American Industrial
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Expatriates that immigrated to the USA within the last 20 years.
Group 0 sample size Number of subjects in the control (unexposed) group
85
Group 1 sample size Number of subjects in the case (exposed) group
6
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Current antibiotic use

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
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
sex


Signature 1

Needs review

Curated date: 2024/11/24

Curator: Tosin

Revision editor(s): Tosin

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 American Industrial

NCBI Quality ControlLinks
Atopobium

Revision editor(s): Tosin

Signature 2

Needs review

Curated date: 2024/11/24

Curator: Tosin

Revision editor(s): Tosin

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 American Industrial

NCBI Quality ControlLinks
Granulicatella
Moraxella
Neisseria
Simonsiella
Streptobacillus
unclassified Bacteroidota
unclassified Porphyromonadaceae

Revision editor(s): Tosin