Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy
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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
- Germany
- Switzerland
- 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
- Food allergy Food Hypersensitivity,Food intolerance,Food allergy,food allergy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients at enrollment (t0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at enrollment (denoted by t0).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
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).
- arcsine square-root
- Statistical test
- MaAsLin2
- 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
- decreased
Signature 1
Source: Figure S2D
Description: Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: decreased abundance in Patients at enrollment (t0)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Eggerthella sp. CAG:1427 |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients at follow-up (t1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure S2D
Description: Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: increased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S2D
Description: Violin plot showing differences in genus abundances in fecal samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: decreased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella sp. CAG:1427 |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of forearm Forearm skin,Lower arm skin,Lower segment of arm skin,Skin of antebrachial region,Skin of lower arm,Skin of lower segment of arm,Skin of zeugopod of arm,Skin of forearm,skin of forearm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients at enrollment (t0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at enrollment (denoted by t0).
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 1D and Figure S5
Description: Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: increased abundance in Patients at enrollment (t0)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Arachnia | ||
| Capnocytophaga | ||
| Fusobacterium | ||
| Haemophilus | ||
| Lautropia | ||
| Neisseria | ||
| Porphyromonas | ||
| Prevotella | ||
| Pseudomonas | ||
| Veillonella sp. oral taxon 780 str. F0422 |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 1D and Figure S5
Description: Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: decreased abundance in Patients at enrollment (t0)
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients at follow-up (t1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with Immunoglobulin-E (IgE)-mediated food allergy (FA) at follow-up (denoted by t1).
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 1D and Figure S5
Description: Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: increased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Arachnia | ||
| Capnocytophaga | ||
| Veillonella sp. oral taxon 780 str. F0422 | ||
| Fusobacterium | ||
| Haemophilus | ||
| Lautropia | ||
| Neisseria | ||
| Porphyromonas | ||
| Prevotella | ||
| Pseudomonas |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 1D and Figure S5
Description: Violin plot showing differences in genus and species abundances in forearm samples among controls, patients at enrollment (t0), and patients at follow-up (t1).
Abundance in Group 1: decreased abundance in Patients at follow-up (t1)
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Location of subjects
- Switzerland
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients at enrollment (t0)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2C
Description: Violin plot showing differences in genus abundances in fecal samples at different sampling time points (at enrollment (t0), and follow-up (t1)).
Abundance in Group 1: increased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Faecalibacterium | ||
| Pseudomonas | ||
| Sellimonas |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2C
Description: Violin plot showing differences in genus abundances in fecal samples at different sampling time points (at enrollment (t0), and follow-up (t1)).
Abundance in Group 1: decreased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudoclavibacter | ||
| Veillonella |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of forearm Forearm skin,Lower arm skin,Lower segment of arm skin,Skin of antebrachial region,Skin of lower arm,Skin of lower segment of arm,Skin of zeugopod of arm,Skin of forearm,skin of forearm
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2D
Description: Violin plot showing differences in genus abundances in forearm samples at different sampling time points (at enrollment (t0), and follow-up (t1)).
Abundance in Group 1: increased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Actinomyces | ||
| Arachnia | ||
| Kingella | ||
| Knoellia | ||
| Lautropia | ||
| Neisseria |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: Violin plot showing differences in genus abundances in forearm samples at different sampling time points (at enrollment (t0), and follow-up (t1)).
Abundance in Group 1: decreased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudoxanthomonas |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of elbow Cubital region zone of skin,Elbow skin,Elbow zone of skin,Zone of skin of cubital region,Zone of skin of elbow,Skin of elbow,skin of elbow
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2E
Description: Violin plot showing differences in genus abundances in elbow samples at different sampling time points (at enrollment (t0), and follow-up (t1)).
Abundance in Group 1: increased abundance in Patients at follow-up (t1)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Lactococcus |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No nut group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nut group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Immunoglobulin-E (IgE)-mediated tree nut and/or peanut allergy at enrollment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3C
Description: Violin plot showing differences in genus abundances in fecal samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).
Abundance in Group 1: increased abundance in Nut group
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Enterocloster | ||
| Lawsonella | ||
| Phocaeicola |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3C
Description: Violin plot showing differences in genus abundances in fecal samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).
Abundance in Group 1: decreased abundance in Nut group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Neisseria | ||
| Pseudomonas | ||
| Veillonella |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of forearm Forearm skin,Lower arm skin,Lower segment of arm skin,Skin of antebrachial region,Skin of lower arm,Skin of lower segment of arm,Skin of zeugopod of arm,Skin of forearm,skin of forearm
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3D
Description: Violin plot showing differences in genus abundances in forearm samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).
Abundance in Group 1: increased abundance in Nut group
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3D
Description: Violin plot showing differences in genus abundances in forearm samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).
Abundance in Group 1: decreased abundance in Nut group
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Granulicatella | ||
| Haemophilus | ||
| Lancefieldella | ||
| Candidatus Nanogingivalis | ||
| Candidatus Nanosynbacter | ||
| Pauljensenia | ||
| Veillonella |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of elbow Cubital region zone of skin,Elbow skin,Elbow zone of skin,Zone of skin of cubital region,Zone of skin of elbow,Skin of elbow,skin of elbow
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3E
Description: Violin plot showing differences in genus abundances in elbow samples at enrollment (t0), between patients with an IgE-mediated FA other than tree nut and/or peanut, (no nut) and patients with a tree nut and/or peanut allergy (nut).
Abundance in Group 1: increased abundance in Nut group
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingomonas |
Revision editor(s): Aleru Divine
