Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe/Experiment 2
Subjects
- 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
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Kuvale
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Himba
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Himba are also Bantu-speaking cattle herders of the Herero tradition. They reside in the same coastal lowlands as the Kuvale and share similar environmental conditions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 5, Figure 5
Description: Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: increased abundance in Himba
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillus sp. | ||
| Arachnia propionica | ||
| Arachnia |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Table 4 and 5, Figure 5
Description: Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: decreased abundance in Himba
| NCBI | Quality Control | Links |
|---|---|---|
| Cedecea | ||
| Citrobacter freundii | ||
| Citrobacter koseri | ||
| Salmonella | ||
| Salmonella sp. | ||
| Cedecea davisae |
Revision editor(s): MyleeeA
