Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer
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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
Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R, O'Keefe SJD
Journal
Nature communications
Year
2024
Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.
Experiment 1
Needs review
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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rural Xhosa Cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Urban Xhosa Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People from Urban Xhosa of South Africa transitioning from traditional high-fiber to Western diets
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Oral or I.V antibiotic therapy within the last 6 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Fig. 1D
Description: Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts
Abundance in Group 1: increased abundance in Urban Xhosa Cohort
Revision editor(s): Scholastica
Signature 2
Needs review
Source: Fig. 1D
Description: Significantly differential bacterial genera identified by linear discriminant analysis (LDA) effect size (LEfSe) in fecal samples of Rural Xhosa versus Urban Xhosa cohorts
Abundance in Group 1: decreased abundance in Urban Xhosa Cohort
Revision editor(s): Scholastica
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Fig. 3C
Description: Differentially abundant viral contigs (VCs) in rural (n=19) compared to urban (n=9) Xhosa fecal samples
Abundance in Group 1: increased abundance in Urban Xhosa Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Muribaculaceae | ||
| Prevotella | ||
| Bacteroides | ||
| Agathobaculum |
Revision editor(s): Scholastica
Signature 2
Needs review
Source: Fig. 3C
Description: Differentially abundant viral contigs (VCs) in rural (n=19) compared to urban (n=9) Xhosa fecal samples
Abundance in Group 1: decreased abundance in Urban Xhosa Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Parabacteroides | ||
| Bacteroides | ||
| Lactococcus | ||
| Leuconostoc | ||
| Prevotella |
Revision editor(s): Scholastica
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ingested food Ingested food,ingested food
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Food from rural Xhosa households
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Food from urban Xhosa households
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Food samples collected from representative households of urban Xhosa of South Africa
- 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
- 6
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Figure 4D
Description: Significantly different abundance at the genus level. Statistical analysis using a two-sided Wilcoxon test corrected for multiple testing by the Benjamini–Hochberg method using normalized samples
Abundance in Group 1: decreased abundance in Food from urban Xhosa households
| NCBI | Quality Control | Links |
|---|---|---|
| Rosenbergiella | ||
| Weissella |
Revision editor(s): Idiaru angela
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Manual digit skin Digit of hand skin,Digit of terminal segment of free upper limb skin,Digitus manus skin,Finger skin,Fore limb digit skin,Hand digit skin,Skin of digit of hand,Skin of digit of terminal segment of free upper limb,Skin of digitus manus,Skin of finger,Skin of hand digit,Skin of terminal segment of free upper limb digit,Terminal segment of free upper limb digit skin,Manual digit skin,manual digit skin
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rural Xhosa Cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Urban Xhosa Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hand skin swabs from urban Xhosa cohort of South Africa
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Supplementary Table 3
Description: Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts
Abundance in Group 1: increased abundance in Urban Xhosa Cohort
Revision editor(s): Scholastica
Signature 2
Needs review
Source: Supplementary Table 3
Description: Significantly different abundant bacterial genera or families on hand skin swabs from rural versus urban Xhosa cohorts
Abundance in Group 1: decreased abundance in Urban Xhosa Cohort
Revision editor(s): Scholastica
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