Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Angola
- 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
- Kwepe
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Kwepe are small stock herders possibly linked to early pastoral migrations from eastern to southern Africa. They dwell in the coastal lowlands of the Angola Namib Desert, which is characterized by an arid and warm climate.
- 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 Kwepe
| NCBI | Quality Control | Links |
|---|---|---|
| Bulleidia | ||
| Shuttleworthella | ||
| Yokenella | ||
| Yokenella regensburgei |
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 Kwepe
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter koseri |
Experiment 2
Subjects
- 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.
Lab analysis
Statistical Analysis
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 |
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 |
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tjimba
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
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 Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Pyramidobacter | ||
| Pyramidobacter piscolens | ||
| Citrobacter youngae |
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 Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Cedecea | ||
| Cedecea davisae | ||
| Citrobacter freundii | ||
| Citrobacter portucalensis | ||
| Hafnia | ||
| Hafnia sp. |
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kwisi
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
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 Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae | ||
| Eggerthia catenaformis |
Signature 2
Source: Supplementary Table 4 and 5, Figure 5
Description: Differential abundance (FDR adjusted p_value <0.05) between Population 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 Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Cedecea | ||
| Cedecea davisae | ||
| Citrobacter portucalensis | ||
| Citrobacter koseri | ||
| Citrobacter sp. |
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
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 Twa
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 Twa
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium periodonticum | ||
| Gemella sanguinis | ||
| Paraprevotella clara | ||
| Porphyromonas somerae | ||
| Porphyromonas sp. | ||
| Paraprevotella | ||
| Fusobacterium | ||
| Porphyromonas |
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
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 Tshwa
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 Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii | ||
| Haemophilus sputorum | ||
| Kingella kingae | ||
| Lachnoanaerobaculum | ||
| Paraprevotella | ||
| Porphyromonas | ||
| Simonsiella | ||
| Simonsiella muelleri | ||
| Lachnoanaerobaculum sp. |
Experiment 7
Subjects
- Location of subjects
- Angola
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
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 !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae | ||
| Eggerthia | ||
| Eggerthia catenaformis | ||
| Peptoanaerobacter | ||
| Propionibacterium | ||
| Shuttleworthella | ||
| Bacteroidia |
Signature 2
Source: Supplementary Table 4 and 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 !Xun
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Kwepe
- 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.
Lab analysis
Statistical Analysis
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: decreased abundance in Himba
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: increased abundance in Himba
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillus sp. | ||
| Streptococcus sanguinis | ||
| Arachnia | ||
| Arachnia propionica |
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tjimba
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba. They may represent a subgroup or offshoot of the Himba community.
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
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 population.
Abundance in Group 1: increased abundance in Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae |
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 population.
Abundance in Group 1: decreased abundance in Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter freundii | ||
| Hafnia sp. | ||
| Citrobacter portucalensis | ||
| Hafnia | ||
| Bulleidia | ||
| Cedecea | ||
| Yokenella |
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kwisi
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae | ||
| Moraxella sp. |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Kwisi
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Twa
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter | ||
| Enterobacter | ||
| Pseudomonas | ||
| Escherichia | ||
| Enterobacter sp. | ||
| Citrobacter koseri | ||
| Citrobacter youngae |
Experiment 12
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tshwa
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Actinomyces graevenitzii | ||
| Actinomyces sp. | ||
| Kingella kingae | ||
| Lachnospiraceae | ||
| Lachnospiraceae bacterium | ||
| Megasphaera | ||
| Schaalia odontolytica | ||
| Lachnoanaerobaculum |
Experiment 13
Subjects
- Location of subjects
- Angola
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter freundii | ||
| Clostridioides difficile | ||
| Gemella sanguinis | ||
| Klebsiella pneumoniae | ||
| Parvimonas micra | ||
| Rothia sp. (in: high G+C Gram-positive bacteria) |
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Himba
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tjimba
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Tjimba inhabit the same coastal lowlands as the Kuvale and Himba.
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Salmonella sp. | ||
| Salmonella |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Tjimba
| NCBI | Quality Control | Links |
|---|---|---|
| Hafnia sp. | ||
| Hafnia |
Experiment 15
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kwisi
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Salmonella | ||
| Citrobacter freundii | ||
| Salmonella sp. | ||
| Treponema lecithinolyticum | ||
| Klebsiella pneumoniae | ||
| Citrobacter youngae |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter portucalensis | ||
| Citrobacter sp. | ||
| Lactobacillus |
Experiment 16
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Twa
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Twa
| NCBI | Quality Control | Links |
|---|---|---|
| Arachnia | ||
| Paraprevotella | ||
| Paraprevotella clara |
Revision editor(s): MyleeeA, KateRasheed, WikiWorks
Experiment 17
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tshwa
Revision editor(s): MyleeeA, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii | ||
| Arachnia | ||
| Arachnia propionica | ||
| Lactobacillus | ||
| Lactobacillus sp. |
Experiment 18
Subjects
- Location of subjects
- Angola
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Salmonella | ||
| Salmonella sp. | ||
| Citrobacter youngae |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in !Xun
Revision editor(s): MyleeeA, KateRasheed, WikiWorks
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Twa
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium nucleatum | ||
| [Eubacterium] yurii |
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 population.
Abundance in Group 1: decreased abundance in Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Simonsiella muelleri | ||
| Actinomyces graevenitzii | ||
| Simonsiella | ||
| Actinomyces |
Experiment 20
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in !Xun
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Tshwa
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
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 population.
Abundance in Group 1: increased abundance in !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Simonsiella | ||
| Propionibacterium | ||
| Actinomyces graevenitzii | ||
| Kingella kingae | ||
| Simonsiella muelleri |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: decreased abundance in !Xun
Experiment 22
Subjects
- Location of subjects
- Angola
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Tjimba
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kwisi
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter freundii | ||
| Hafnia sp. | ||
| Hafnia |
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Kwisi
| NCBI | Quality Control | Links |
|---|---|---|
| Pyramidobacter | ||
| Pyramidobacter piscolens |
Experiment 23
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Twa
Experiment 24
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tshwa
Signature 2
Source: Supplementary Table 4 and 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 population.
Abundance in Group 1: increased abundance in Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii |
Experiment 25
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Hafnia | ||
| Hafnia sp. | ||
| Propionibacterium |
Experiment 26
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Kwisi
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 Twa
Signature 2
Source: Supplementary Table 4 and 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 Twa
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella sp. | ||
| Capnocytophaga gingivalis |
Experiment 27
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tshwa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table 4 and 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 Tshwa
Signature 2
Source: Supplementary Table 4 and 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 Tshwa
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga gingivalis | ||
| Moraxella sp. | ||
| Kingella kingae | ||
| Simonsiella muelleri | ||
| Simonsiella | ||
| Moraxella |
Experiment 28
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- !Xun
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4 and 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 !Xun
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter portucalensis | ||
| Citrobacter sp. | ||
| Propionibacterium |
Signature 2
Source: Supplementary Table 4 and 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 !Xun
Experiment 29
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pastoralists
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Foragers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- They are the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: increased abundance in Foragers
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter youngae | ||
| Bifidobacterium breve | ||
| Eggerthia catenaformis | ||
| Enterobacter sp. | ||
| Eggerthia |
Signature 2
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: decreased abundance in Foragers
Experiment 30
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peripatetics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Includes the Twa, Tjimba, Kwisi, and Kwepe in southwestern Angola, these groups have a mobile lifestyle without a fixed settlement. They inhabit coastal lowlands and may have mixed livelihoods, combining aspects of both pastoralism and foraging.
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: increased abundance in Peripatetics
Signature 2
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: decreased abundance in Peripatetics
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium | ||
| Lachnoanaerobaculum | ||
| Lactobacillus | ||
| Paraprevotella |
Experiment 31
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Peripatetics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Foragers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- They are represented by the !Xun group from Kunene Province, Angola, they traditionally rely on hunting and gathering for subsistence in an area characterized by open savanna woodland.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence patterns according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: increased abundance in Foragers
| NCBI | Quality Control | Links |
|---|---|---|
| Propionibacterium | ||
| Bifidobacterium breve |
Signature 2
Source: Supplementary Table 6 and 7
Description: Differential abundance (FDR adjusted p_value <0.05) between subsistence methods according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first subsistence method of the comparison, and negative values represent taxa enriched in the second one.
Abundance in Group 1: decreased abundance in Foragers
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
- 30 Experiment 30
- 31 Experiment 31
