Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Araújo V, Fehn AM, Phiri A, Wills J, Rocha J, Gayà-Vidal M
Journal
BMC microbiology
Year
2023
Keywords:
African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods
BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors). RESULTS: Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization. CONCLUSIONS: Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.

Experiment 1


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects
Angola
Zimbabwe
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).
relative abundances
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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Bulleidia
Shuttleworthella
Yokenella
Yokenella regensburgei

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter koseri

Revision editor(s): MyleeeA

Experiment 2


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Lactobacillus
Lactobacillus sp.
Arachnia propionica
Arachnia

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Cedecea
Citrobacter freundii
Citrobacter koseri
Salmonella
Salmonella sp.
Cedecea davisae

Revision editor(s): MyleeeA

Experiment 3


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Pyramidobacter
Pyramidobacter piscolens
Citrobacter youngae

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Cedecea
Cedecea davisae
Citrobacter freundii
Citrobacter portucalensis
Hafnia
Hafnia sp.

Revision editor(s): MyleeeA

Experiment 4


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter youngae
Eggerthia catenaformis

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Cedecea
Cedecea davisae
Citrobacter portucalensis
Citrobacter koseri
Citrobacter sp.

Revision editor(s): MyleeeA

Experiment 5


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Citrobacter
Citrobacter youngae
Eggerthia
Eggerthia catenaformis
Enterobacter
Enterobacter sp.
Escherichia
Escherichia coli
Filifactor alocis
Klebsiella oxytoca
Klebsiella pneumoniae
Klebsiella sp.
Lancefieldella rimae
Porphyromonas
Pseudomonas
Pseudomonas sp.
Salmonella
Salmonella sp.
Serratia
Serratia sp. (in: enterobacteria)
Yokenella
Yokenella regensburgei
Filifactor

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Fusobacterium periodonticum
Gemella sanguinis
Paraprevotella clara
Porphyromonas somerae
Porphyromonas sp.
Paraprevotella
Fusobacterium
Porphyromonas

Revision editor(s): MyleeeA

Experiment 6


Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Bacteroidia
Cardiobacterium valvarum
Catonella
Catonella morbi
Citrobacter
Citrobacter youngae
Corynebacterium matruchotii
Eggerthia
Eggerthia catenaformis
Enterobacter
Enterobacter sp.
Enterococcus
Escherichia
Escherichia coli
Filifactor
Filifactor alocis
Fusobacterium nucleatum
Hafnia
Hafnia sp.
Johnsonella
Johnsonella ignava
Kingella oralis
Klebsiella oxytoca
Klebsiella pneumoniae
Klebsiella sp.
Peptoanaerobacter
Peptostreptococcaceae
Peptostreptococcaceae bacterium
Pseudomonas sp.
Salmonella
Salmonella sp.
Yokenella
Yokenella regensburgei
[Eubacterium] saphenum
Bacteroidetes oral taxon 274
Peptoanaerobacter stomatis

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Actinomyces graevenitzii
Haemophilus sputorum
Kingella kingae
Lachnoanaerobaculum
Paraprevotella
Porphyromonas
Simonsiella
Simonsiella muelleri
Lachnoanaerobaculum sp.

Revision editor(s): MyleeeA

Experiment 7


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter youngae
Eggerthia
Eggerthia catenaformis
Peptoanaerobacter
Propionibacterium
Shuttleworthella
Bacteroidia

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Abiotrophia
Abiotrophia defectiva
Bacillus
Citrobacter freundii
Clostridioides
Clostridioides difficile
Enterococcus
Gemella sanguinis
Haemophilus paraphrohaemolyticus
Abiotrophia sp.

Revision editor(s): MyleeeA

Experiment 8


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Cedecea
Cedecea davisae
Citrobacter freundii
Klebsiella pneumoniae
Klebsiella sp.
Lachnospiraceae
Lachnospiraceae bacterium
Salmonella
Salmonella sp.
Yokenella
Yokenella regensburgei

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Lactobacillus
Lactobacillus sp.
Streptococcus sanguinis
Arachnia
Arachnia propionica

Revision editor(s): MyleeeA

Experiment 9


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter youngae

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter freundii
Hafnia sp.
Citrobacter portucalensis
Hafnia
Bulleidia
Cedecea
Yokenella

Revision editor(s): MyleeeA

Experiment 10


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter youngae
Moraxella sp.

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Actinomyces
Actinomyces sp.
Cedecea davisae
Citrobacter portucalensis
Citrobacter sp.
Lachnospiraceae
Lachnospiraceae bacterium
Streptococcus parasanguinis
Yokenella
Yokenella regensburgei
Cedecea

Revision editor(s): MyleeeA

Experiment 11


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter
Enterobacter
Pseudomonas
Escherichia
Enterobacter sp.
Citrobacter koseri
Citrobacter youngae

Revision editor(s): MyleeeA

Experiment 12


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter
Citrobacter koseri
Citrobacter youngae
Enterobacter
Enterobacter sp.
Escherichia
Escherichia coli
Fusobacterium nucleatum
Granulicatella elegans
Kingella oralis
Klebsiella oxytoca
Pseudomonas sp.
Salmonella
Salmonella sp.
Streptococcus pneumoniae
Streptococcus pseudopneumoniae
[Eubacterium] yurii

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Actinomyces
Actinomyces graevenitzii
Actinomyces sp.
Kingella kingae
Lachnospiraceae
Lachnospiraceae bacterium
Megasphaera
Schaalia odontolytica

Revision editor(s): MyleeeA

Experiment 13


Needs review

Curated date: 2024/03/24

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter youngae

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter freundii
Clostridioides difficile
Gemella sanguinis
Klebsiella pneumoniae
Parvimonas micra
Rothia sp. (in: high G+C Gram-positive bacteria)

Revision editor(s): MyleeeA

Experiment 14


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Salmonella sp.
Salmonella

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Hafnia sp.
Hafnia

Revision editor(s): MyleeeA

Experiment 15


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Salmonella
Citrobacter freundii
Salmonella sp.
Treponema lecithinolyticum
Klebsiella pneumoniae
Citrobacter youngae

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter portucalensis
Citrobacter sp.
Lactobacillus

Revision editor(s): MyleeeA

Experiment 16


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Salmonella
Cedecea
Enterobacter
Yokenella
Citrobacter
Escherichia
Hafnia
Campylobacter
Serratia
Selenomonas
Citrobacter freundii
Salmonella sp.
Enterobacter sp.
Cedecea davisae
Yokenella regensburgei
Citrobacter youngae
Klebsiella sp.
Citrobacter koseri
Klebsiella oxytoca
Klebsiella pneumoniae
Escherichia coli

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Paraprevotella clara
Paraprevotella

Revision editor(s): MyleeeA

Experiment 17


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Salmonella
Cedecea
Enterobacter
Citrobacter
Yokenella
Hafnia
Hafnia sp.
Escherichia
Escherichia sp.
Peptostreptococcaceae
Bacteroidia

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Actinomyces graevenitzii
Arachnia propionica
Lactobacillus
Lactobacillus sp.
Arachnia

Revision editor(s): MyleeeA

Experiment 18


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Salmonella
Campylobacter
Citrobacter portucalensis
Citrobacter sp.

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Abiotrophia
Abiotrophia sp.
Bacillus
Capnocytophaga gingivalis
Citrobacter freundii
Clostridioides
Clostridioides difficile
Corynebacterium sp.
Enterococcus
Escherichia coli
Gemella haemolysans
Gemella sanguinis
Haemophilus parahaemolyticus
Arachnia
[Eubacterium] brachy
Bacillus sp. (in: firmicutes)

Revision editor(s): MyleeeA

Experiment 19


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Fusobacterium nucleatum
[Eubacterium] yurii

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Simonsiella muelleri
Actinomyces graevenitzii
Simonsiella
Actinomyces

Revision editor(s): MyleeeA

Experiment 20


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Cedecea
Cedecea davisae
Citrobacter
Citrobacter freundii
Citrobacter koseri
Clostridioides
Corynebacterium sp.
Enterobacter
Enterobacter sp.
Enterococcus
Enterococcus sp.
Escherichia
Klebsiella oxytoca
Klebsiella pneumoniae
Klebsiella sp.
Pseudomonas
Rothia
Salmonella
Schaalia georgiae
Serratia
Serratia sp. (in: enterobacteria)
Yokenella
Yokenella regensburgei

Revision editor(s): MyleeeA

Experiment 21


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Simonsiella
Propionibacterium
Actinomyces graevenitzii
Kingella kingae
Simonsiella muelleri

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter freundii
Enterococcus sp.
Klebsiella oxytoca
Klebsiella sp.
Escherichia coli
Rothia aeria
Klebsiella pneumoniae
Citrobacter koseri
Clostridioides difficile
Corynebacterium sp.
Gemella sanguinis
Salmonella sp.
Yokenella regensburgei
Streptococcus salivarius
Cedecea davisae
Gemella haemolysans
Fusobacterium nucleatum
Lautropia mirabilis
Kingella oralis
Enterobacter sp.
Parvimonas micra
Serratia
Gemella
Lautropia
Enterococcus
Citrobacter
Enterobacter
Escherichia
Salmonella
Yokenella
Cedecea
Clostridioides

Revision editor(s): MyleeeA

Experiment 22


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Citrobacter freundii
Hafnia sp.
Hafnia

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Pyramidobacter
Pyramidobacter piscolens

Revision editor(s): MyleeeA

Experiment 23


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Hafnia
Cedecea
Enterobacter
Yokenella
Yokenella regensburgei
Escherichia
Citrobacter
Citrobacter freundii
Citrobacter koseri
Citrobacter portucalensis
Citrobacter sp.
Klebsiella sp.
Enterobacter sp.
Klebsiella oxytoca
Cedecea davisae
Escherichia coli
Klebsiella pneumoniae

Revision editor(s): MyleeeA

Experiment 24


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Hafnia
Enterobacter
Cedecea
Citrobacter
Yokenella
Escherichia
Salmonella
Salmonella sp.
Enterobacter sp.
Kingella oralis
Escherichia coli
Klebsiella pneumoniae
Yokenella regensburgei
Citrobacter koseri
Cedecea davisae
Citrobacter sp.
Citrobacter freundii
Klebsiella oxytoca
Klebsiella sp.
Citrobacter portucalensis
Hafnia sp.

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Actinomyces graevenitzii

Revision editor(s): MyleeeA

Experiment 25


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Hafnia
Hafnia sp.
Propionibacterium

Revision editor(s): MyleeeA

Experiment 26


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Cedecea davisae
Citrobacter portucalensis
Enterobacter sp.
Yokenella regensburgei
Citrobacter sp.
Citrobacter koseri
Klebsiella oxytoca
Cedecea
Enterobacter
Yokenella
Citrobacter

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Moraxella sp.
Capnocytophaga gingivalis

Revision editor(s): MyleeeA

Experiment 27


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Cedecea
Cedecea davisae
Enterobacter
Citrobacter
Citrobacter freundii
Citrobacter koseri
Citrobacter portucalensis
Citrobacter sp.
Yokenella regensburgei
Enterobacter sp.
Klebsiella oxytoca
Fusobacterium nucleatum
Kingella oralis
Salmonella sp.
[Eubacterium] yurii

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Capnocytophaga gingivalis
Moraxella sp.
Kingella kingae
Simonsiella muelleri
Simonsiella
Moraxella

Revision editor(s): MyleeeA

Experiment 28


Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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

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Citrobacter portucalensis
Citrobacter sp.
Propionibacterium

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/25

Curator: MyleeeA

Revision editor(s): MyleeeA

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

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Abiotrophia
Abiotrophia sp.
Bacillus
Capnocytophaga gingivalis
Citrobacter freundii
Clostridioides
Clostridioides difficile
Corynebacterium sp.
Enterococcus
Escherichia
Escherichia coli
Gemella haemolysans
Gemella sanguinis
Haemophilus parahaemolyticus
[Eubacterium] brachy
Bacillus sp. (in: firmicutes)

Revision editor(s): MyleeeA

Experiment 29


Needs review

Curated date: 2024/03/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

Needs review

Curated date: 2024/03/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

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Citrobacter youngae
Bifidobacterium breve
Eggerthia catenaformis
Enterobacter sp.
Eggerthia

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/03/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

NCBI Quality ControlLinks
Abiotrophia
<