Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children
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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
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- food allergy Food Hypersensitivity,Food intolerance,food allergy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with food allergy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with food allergy
- 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
- 22
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
- 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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, Figure 4, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls
Abundance in Group 1: increased abundance in child with food allergy
NCBI | Links |
---|---|
Oscillibacter valericigenes | |
Faecalibacterium sp. | |
s__Lachnoclostridium_bolteaes__Lachnoclostridium_bolteae |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 3, Figure 4, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls
Abundance in Group 1: decreased abundance in child with food allergy
NCBI | Links |
---|---|
Blautia sp. |
Revision editor(s): WikiWorks743
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- food allergy Food Hypersensitivity,Food intolerance,food allergy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy sibling
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with food allergy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with food allergy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings
Abundance in Group 1: increased abundance in child with food allergy
NCBI | Links |
---|---|
s__Lachnoclostridium_bolteaes__Lachnoclostridium_bolteae |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 3, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings
Abundance in Group 1: decreased abundance in child with food allergy
NCBI | Links |
---|---|
Alistipes putredinis | |
Alistipes sp. |
Revision editor(s): WikiWorks743
Experiment 3
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- food allergy Food Hypersensitivity,Food intolerance,food allergy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy sibling
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- sibling with no food allergy
- 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
- 25
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, Figure 4, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls
Abundance in Group 1: increased abundance in healthy sibling
NCBI | Links |
---|---|
Oscillibacter valericigenes | |
Faecalibacterium sp. | |
Alistipes putredinis | |
Alistipes sp. |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 3, Figure 4, Figure 5
Description: Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls
Abundance in Group 1: decreased abundance in healthy sibling
NCBI | Links |
---|---|
Blautia sp. |
Revision editor(s): WikiWorks743
Experiment 4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- age age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- <7 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 7-18 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child age 7-18
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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)?
- No
Signature 1
Source: Text
Description: Differentially abundant taxons in children <7 years compared to children 7-18 years
Abundance in Group 1: increased abundance in 7-18 years
NCBI | Links |
---|---|
Bacteroidota |
Revision editor(s): WikiWorks743
Signature 2
Source: Text
Description: Differentially abundant taxons in children <7 years compared to children 7-18 years
Abundance in Group 1: decreased abundance in 7-18 years
NCBI | Links |
---|---|
Bacillota | |
Pseudomonadota | |
Erysipelotrichaceae | |
Lachnospiraceae | |
Peptostreptococcaceae |
Revision editor(s): WikiWorks743