Exploring the influence of urbanization on gut mycobiota through dietary habits in Burkina Faso
-
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
- Burkina Faso
- 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
- Burkina Faso Rural (BF-R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Burkina Faso Semi-urban (BF-SU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in Semi-Urban area of Burkina Faso
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
Lab analysis
- Sequencing type
- ITS / ITS2
- 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
- Mann-Whitney (Wilcoxon)
- 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
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig. 4
Description: The abundance of these microbial signatures were found to increase with Semi-urbanization, evidenced by their high presence in Burkina Faso Semi-Urban Cohort.
Abundance in Group 1: increased abundance in Burkina Faso Semi-urban (BF-SU)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus flavus | ||
| Leptobacillium leptobactrum | ||
| Rhodotorula mucilaginosa |
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: The abundance of these microbial signatures seemed to decrease with urbanization, evidenced by their low presence in Burkina Faso Semi-Urban Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Semi-urban (BF-SU)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus penicillioides | ||
| Candida tropicalis | ||
| Cyberlindnera fabianii | ||
| Diutina mesorugosa | ||
| Epicoccum sorghinum | ||
| Kluyveromyces marxianus | ||
| Malassezia restricta | ||
| Saitozyma flava |
Revision editor(s): Peter03
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Burkina Faso Urban (BF-U)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in Urbanized area of Burkina Faso
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig. 4
Description: The abundance of these microbial signatures were found to increase with urbanization, evidenced by their high presence in Burkina Faso Urban Cohort.
Abundance in Group 1: increased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus flavus | ||
| Aspergillus penicillioides | ||
| Candida tropicalis | ||
| Leptobacillium leptobactrum | ||
| Rhodotorula mucilaginosa |
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: The abundance of these microbial signatures were found to decrease with urbanization, evidenced by their low presence in Burkina Faso Urban Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Cyberlindnera fabianii | ||
| Diutina mesorugosa | ||
| Epicoccum sorghinum | ||
| Kluyveromyces marxianus | ||
| Malassezia restricta | ||
| Saitozyma flava |
Revision editor(s): Peter03
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Burkina Faso Semi-Urban (BF-SU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in urbanized area of Burkina Faso
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig. 4
Description: The abundance of these microbial signatures were found to increase with urbanization, evidenced by their high presence in Burkina Faso Urban Cohort over the Semi-Urban cohort.
Abundance in Group 1: increased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus flavus | ||
| Aspergillus penicillioides | ||
| Candida tropicalis |
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: The abundance of these microbial signatures were found to decrease with urbanization, evidenced by their low presence in Burkina Faso Urban Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Cyberlindnera fabianii | ||
| Diutina mesorugosa | ||
| Epicoccum sorghinum | ||
| Kluyveromyces marxianus | ||
| Leptobacillium leptobactrum | ||
| Saitozyma flava |
Revision editor(s): Peter03
Experiment 4
Subjects
- Location of subjects
- Burkina Faso
- Italy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Italian Urban (IT-U)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Burkina Faso Rural (BF-R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in areas of Burkina Faso with no Urbanization
- Group 0 sample size Number of subjects in the control (unexposed) group
- 122
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 4
Description: These microbial signatures were found to be more dominant in the Burkina Faso Rural Cohort than in Italian Urban Cohort
Abundance in Group 1: increased abundance in Burkina Faso Rural (BF-R)
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: The abundance of these microbial signatures were found to decrease with decreasing urbanization, evidenced by their high presence in Italian Urban Cohort over Burkina Faso Rural Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Rural (BF-R)
| NCBI | Quality Control | Links |
|---|---|---|
| Leptobacillium leptobactrum | ||
| Rhodotorula mucilaginosa | ||
| [Candida] sake |
Revision editor(s): Peter03
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Burkina Faso Semi-Urban (BF-SU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in Semi-Urban areas of Burkina Faso
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 4
Description: The abundance of these microbial signatures were found to increase with decreased urbanization, evidenced by their high presence in Burkina Faso Semi-Urban Cohorts.
Abundance in Group 1: increased abundance in Burkina Faso Semi-Urban (BF-SU)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus flavus | ||
| Aspergillus penicillioides | ||
| Candida tropicalis | ||
| Cyberlindnera fabianii | ||
| Diutina mesorugosa | ||
| Epicoccum sorghinum | ||
| Kluyveromyces marxianus | ||
| Malassezia restricta |
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: The abundance of these microbial signatures were found to decrease with decrease in urbanization, evidenced by their low presence in Burkina Faso Semi-Urban Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Semi-Urban (BF-SU)
| NCBI | Quality Control | Links |
|---|---|---|
| Leptobacillium leptobactrum | ||
| Rhodotorula mucilaginosa | ||
| [Candida] sake |
Revision editor(s): Peter03
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Burkina Faso Urban (BF-U)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living in urbanized area of Burkina Faso
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 4
Description: These species increased in abundance in the Burkina Faso Urban Cohort over Italian Urban Cohort.
Abundance in Group 1: increased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillus flavus | ||
| Aspergillus penicillioides | ||
| Candida tropicalis | ||
| Diutina mesorugosa | ||
| Epicoccum sorghinum | ||
| Kluyveromyces marxianus | ||
| Malassezia restricta | ||
| Saitozyma flava |
Revision editor(s): Peter03
Signature 2
Source: Fig. 4
Description: These species were found to decrease in the Burkina Faso Urban Cohort.
Abundance in Group 1: decreased abundance in Burkina Faso Urban (BF-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Leptobacillium leptobactrum | ||
| Rhodotorula mucilaginosa | ||
| [Candida] sake |
Revision editor(s): Peter03
