Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Ethiopia
- Madagascar
- 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
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Madagascar
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adadle
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 431
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure S6 B
Description: LEfSe analysis using primer set 1 data, showing bacterial families associated with Adadle or Madagascar.
Abundance in Group 1: increased abundance in Adadle
Revision editor(s): YokoC
Signature 2
Source: Figure S6 B
Description: LEfSe analysis using primer set 1 data, showing bacterial families associated with Adadle or Madagascar.
Abundance in Group 1: decreased abundance in Adadle
Revision editor(s): YokoC
Experiment 2
Subjects
- Location of subjects
- Central African Republic
- Ethiopia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Central African Republic
- Group 0 sample size Number of subjects in the control (unexposed) group
- 274
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure S6 B
Description: LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.
Abundance in Group 1: increased abundance in Adadle
Revision editor(s): YokoC
Signature 2
Source: Figure S6 B
Description: LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.
Abundance in Group 1: decreased abundance in Adadle
Revision editor(s): YokoC
Experiment 3
Subjects
- Location of subjects
- Ethiopia
- Sweden
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Industrial Lifestyle
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adadle Agropastoral Lifestyle
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 484
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with agropastoral and industrial lifestyles.
Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle
Revision editor(s): YokoC
Signature 2
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with agropastoral and industrial lifestyles.
Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle
Revision editor(s): YokoC
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Traditional Lifestyle
- Group 0 sample size Number of subjects in the control (unexposed) group
- 107
Lab analysis
Statistical Analysis
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.
Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Coprobacillaceae | ||
| Coriobacteriaceae | ||
| Eggerthellaceae | ||
| Enterobacteriaceae | ||
| Erysipelotrichaceae | ||
| Streptococcaceae |
Revision editor(s): YokoC
Signature 2
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.
Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle
Revision editor(s): YokoC
Experiment 5
Subjects
- Location of subjects
- Bangladesh
- El Salvador
- Ethiopia
- Peru
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Transitional Lifestyle
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.
Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Carnobacteriaceae | ||
| Coprobacillaceae | ||
| Coriobacteriaceae | ||
| Erysipelotrichaceae | ||
| Leptotrichiaceae | ||
| Puniceicoccaceae | ||
| Streptococcaceae |
Revision editor(s): YokoC
Signature 2
Source: Figure S6 D
Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.
Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Clostridiaceae | ||
| Lactobacillaceae | ||
| Oscillospiraceae | ||
| Peptostreptococcaceae | ||
| Veillonellaceae | ||
| Oscillospirales UCG-010Oscillospirales UCG-010 |
Revision editor(s): YokoC
Experiment 6
Subjects
- Location of subjects
- Ethiopia
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- COPRO-seq COPRO-seq,cOPRO-seq
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mOTUs2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MetaPhlAn3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Taxonomic profiling of shotgun metagenomic sequencing using MetaPhlAn3.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure S7 A
Description: Species with a significantly different abundance between the two profiling tools, mOTUs2 and MetaPhlAn3
Abundance in Group 1: increased abundance in MetaPhlAn3
Revision editor(s): YokoC
Signature 2
Source: Figure S7 A
Description: Species with a significantly different abundance between the two profiling tools, mOTUs2 and MetaPhlAn3.
Abundance in Group 1: decreased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces dentalis | ||
| Actinomyces sp. | ||
| Actinomyces sp. ICM39 | ||
| Actinomyces viscosus | ||
| Arachnia propionica | ||
| Bacteroides sp. | ||
| Bifidobacterium sp. | ||
| Blautia sp. KLE 1732 | ||
| Candidatus Nanosynbacter lyticus | ||
| Senegalimassilia anaerobia | ||
| Streptococcus intermedius | ||
| Streptococcus sp. | ||
| Streptococcus sp. HSISM1 | ||
| bacterium LF-3 | ||
| unclassified Bacilli | ||
| unclassified Bacillota | ||
| unclassified Eggerthellaceae | ||
| unclassified Lachnospiraceae | ||
| unclassified Oscillospiraceae | ||
| unclassified Peptostreptococcaceae | ||
| uncultured Candidatus Saccharibacteria bacterium | ||
| uncultured Clostridium sp. | ||
| uncultured Collinsella sp. | ||
| uncultured Eubacterium sp. | ||
| uncultured Faecalibacterium sp. | ||
| uncultured Prevotella sp. | ||
| uncultured Streptococcus sp. | ||
| uncultured Sutterella sp. | ||
| Eggerthella lenta [C Clostridioides difficile]Eggerthella lenta [C Clostridioides difficile] | <i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review"> | |
| unknown Lactobacillalesunknown Lactobacillales | ||
| uncultured Mogibacterium sp. | ||
| uncultured Butyricicoccus sp. |
Revision editor(s): YokoC
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Primer set 1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S8 B
Description: Significantly different families between primer set 1 and MetaPhlAn3.
Abundance in Group 1: increased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiales Family XIII bacterium | ||
| Eubacteriaceae | ||
| unclassified Bacillales |
Revision editor(s): YokoC
Signature 2
Source: Figure S8 B
Description: Significantly different families between primer set 1 and MetaPhlAn3.
Abundance in Group 1: decreased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Butyricicoccaceae | ||
| Coprobacillaceae | ||
| Gemellaceae | ||
| [Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group |
Revision editor(s): YokoC
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Primer set 2
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S8 B
Description: Significantly different families between primer set 2 and MetaPhlAn3.
Abundance in Group 1: increased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiales Family XIII bacterium | ||
| Corynebacteriaceae | ||
| Eubacteriaceae | ||
| Micrococcaceae | ||
| unclassified Bacillales |
Revision editor(s): YokoC
Signature 2
Source: Figure S8 B
Description: Significantly different families between primer set 2 and MetaPhlAn3.
Abundance in Group 1: decreased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Coprobacillaceae |
Revision editor(s): YokoC
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Primer set 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Taxonomic profiling of shotgun metagenomic sequencing using mOTUs2.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Figure S8 B
Description: Significantly different families between primer set 1 and mOTUs2.
Abundance in Group 1: increased abundance in MetaPhlAn3
Revision editor(s): YokoC
Signature 2
Source: Figure S8 B
Description: Significantly different families between primer set 1 and mOTUs2.
Abundance in Group 1: decreased abundance in MetaPhlAn3
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Butyricicoccaceae | ||
| Coprobacillaceae | ||
| Gemellaceae | ||
| [Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group |
Revision editor(s): YokoC
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Primer set 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mOTUs2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Taxonomic profiling of the samples obtained through shotgun metagenomic sequencing using mOTUs2.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S8 B
Description: Significantly different families between primer set 2 and mOTUS2.
Abundance in Group 1: increased abundance in mOTUs2
Revision editor(s): YokoC
Signature 2
Source: Figure S8
Description: Significantly different families between primer set 2 and mOTUs2.
Abundance in Group 1: decreased abundance in mOTUs2
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Coprobacillaceae |
Revision editor(s): YokoC
Experiment 11
Subjects
- Location of subjects
- Central African Republic
- Ethiopia
- Madagascar
- 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
- Cluster P+
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster P-
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sequenced samples from Children 2-5 years old, clustered through Euclidean distance and Ward's linkeage method into P- cluster, which is one of two clusters.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 526
- Group 1 sample size Number of subjects in the case (exposed) group
- 233
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.5
Signature 1
Source: Figure 3 C
Description: Heatmap of the most abundant genera with significantly different relative abundance between two clusters (P+ and P-) in the Primer 1 set.
Abundance in Group 1: increased abundance in Cluster P-
Revision editor(s): YokoC
Signature 2
Source: Figure 3C
Description:
Abundance in Group 1: decreased abundance in Cluster P-
Revision editor(s): YokoC
Experiment 12
Subjects
- Location of subjects
- Bangladesh
- Cameroon
- China
- El Salvador
- Ethiopia
- Malawi
- Peru
- Sweden
- United Republic of Tanzania
- United States of America
- Venezuela
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
Signature 1
Source: Figure 3C
Description: Heatmap of the most abundant genera with significantly different relative abundance between two clusters (P9+ and P9−).
Abundance in Group 1: increased abundance in Cluster P-
Revision editor(s): YokoC
Experiment 13
Subjects
- Location of subjects
- Ethiopia
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Industrial
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adadle Agropastoral
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BloSSUM bacteria found in 2-5 year old children from Adadle woreda district with an agropastoral lifestyle from the Metagenomic data data, profiled taxonomically with mOTUs2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Signature 1
Source: Figure S9 B
Description: Relative abundance comparison between Adadle agropastoral and Industrial lifestyles.
Abundance in Group 1: decreased abundance in Adadle Agropastoral
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae |
Revision editor(s): YokoC
