Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS, Hazelhurst S
Journal
BMC microbiology
Year
2020
Keywords:
16S, African microbiome, Epidemiological transition, Obesity, South African microbiome, Transitional microbiome
BACKGROUND: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. RESULTS: We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = - 4.7). CONCLUSIONS: Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.
Experiment 1
Subjects
- Location of subjects
- South Africa
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Female subjects situated in Bushbuckridge
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female subjects situated in Soweto
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female subjects (both obese and lean) living in Soweto whose microbiota was studied to reflect transitional changes in microbiome on account of the adoption of a more Westernized lifestyle (in terms of diet and activity levels). Soweto represented the urban site of the two; the other (Bushbuckridge) being more relatively rural.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 119
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- HIV infection, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 5a and Supplementary Table 2A
Description: Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).
Abundance in Group 1: increased abundance in Female subjects situated in Soweto
| NCBI | Quality Control | Links |
|---|---|---|
| Acetanaerobacterium | ||
| Streptococcus | ||
| Bacillota |
Signature 2
Source: Figure 5a and Supplementary Table 2A
Description: Phylum and Genus level significant differential abundance of taxa between Bushbuckbridge and Soweto cohorts (site differences).
Abundance in Group 1: decreased abundance in Female subjects situated in Soweto
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean female subjects in Bushbuckridge
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean female subjects in Soweto
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lean females in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 5b and Supplementary Table 2B
Description: Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.
Abundance in Group 1: increased abundance in Lean female subjects in Soweto
Signature 2
Source: Figure 5b and Supplementary Table 2B
Description: Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.
Abundance in Group 1: decreased abundance in Lean female subjects in Soweto
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroides | ||
| Bacteroidota | ||
| Dialister | ||
| Pseudomonadota |
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Obese female subjects in Bushbuckridge
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese female subjects in Soweto
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Obese females in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 5c and Supplementary Table 2C
Description: Phylum and Genus level significant differences between obese groups in the Soweto and Bushbuckridge cohorts.
Abundance in Group 1: decreased abundance in Obese female subjects in Soweto
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Bacillota |
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean female subjects in both cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese female subjects in both cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Obese female subjects in both the Bushbuckridge and Soweto cohorts.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 5d and Supplementary Table 2D
Description: Phylum and Genus level inter-cohort differential abundance between lean and obese groups (BMI differences).
Abundance in Group 1: increased abundance in Obese female subjects in both cohorts
| NCBI | Quality Control | Links |
|---|---|---|
| Intestinimonas | ||
| Prevotella | ||
| Bacillota | ||
| Bacteroidota |
Experiment 5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean female subjects in Bushbuckridge
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese female subjects in Bushbuckridge
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Obese females in Bushbuckridge whose microbiota is studied for transitional differences between lean and obese subjects in both Cohorts (Bushbuckridge and Soweto).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 5e and Supplementary Table 2E
Description: Phylum and Genus level differential abundance between lean and obese groups in the Bushbuckridge cohort (BMI differences).
Abundance in Group 1: increased abundance in Obese female subjects in Bushbuckridge
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean female subjects in Soweto
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese female subjects in Soweto
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Obese females in Soweto whose microbiota is studied to observe transitional changes between lean and obese groups in the Soweto cohort.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 5f and Supplementary Table 2F
Description: Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).
Abundance in Group 1: increased abundance in Obese female subjects in Soweto
Signature 2
Source: Figure 5f and Supplementary Table 2F
Description: Phylum and Genus level differential abundance between lean and obese groups in the Soweto cohort (BMI differences).
Abundance in Group 1: decreased abundance in Obese female subjects in Soweto
| NCBI | Quality Control | Links |
|---|---|---|
| Fusicatenibacter | ||
| Parabacteroides | ||
| Victivallis | ||
| Clostridium_IVClostridium_IV | ||
| Bacillota | ||
| Lentisphaerota | ||
| Bacteroidota |
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