Altered fecal microbiota composition associated with food allergy in infants
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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
- China
- 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 controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants with food allergies
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with food allergy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Metastats
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 1a, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: increased abundance in infants with food allergies
NCBI | Links |
---|---|
Clostridiaceae | |
Cytophagaceae | |
Nocardiaceae |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 1a, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: decreased abundance in infants with food allergies
NCBI | Links |
---|---|
Alcaligenaceae | |
Eubacteriales Family XIII. Incertae Sedis | |
Phyllobacteriaceae | |
Xanthomonadaceae | |
Flavobacteriaceae | |
Moraxellaceae |
Revision editor(s): WikiWorks743
Signature 3
Source: Supplemental Table 3, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: increased abundance in infants with food allergies
NCBI | Links |
---|---|
Bacillota | |
Fusobacteriota |
Revision editor(s): WikiWorks743
Signature 4
Source: Supplemental Table 3, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: decreased abundance in infants with food allergies
NCBI | Links |
---|---|
Bacteroidota | |
Pseudomonadota | |
Actinomycetota | |
Verrucomicrobiota |
Revision editor(s): WikiWorks743
Signature 5
Source: Supplemental Table 4, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: increased abundance in infants with food allergies
NCBI | Links |
---|---|
Anaerostipes | |
Clostridium | |
Enterococcus | |
Faecalibacterium | |
Flavonifractor | |
Lactobacillus | |
Prevotella | |
Staphylococcus |
Revision editor(s): WikiWorks743, Merit
Signature 6
Source: Supplemental Table 4, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: decreased abundance in infants with food allergies
NCBI | Links |
---|---|
Bacteroides | |
Blautia | |
Lachnospiraceae | |
Megamonas | |
Megasphaera | |
Peptostreptococcaceae | |
Streptococcus | |
Veillonella |
Revision editor(s): WikiWorks743, Fatima, Merit
Experiment 2
Subjects
- Location of subjects
- China
- 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 controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants with food allergies
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with food allergy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 1d, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: increased abundance in infants with food allergies
NCBI | Links |
---|---|
Actinomycetales | |
Bacteria | |
Butyricicoccus | |
Clostridiaceae | |
Clostridium | |
Cytophagaceae | |
Nocardiaceae |
Revision editor(s): WikiWorks743, Merit
Signature 2
Source: Figure 1d, Text
Description: Differentially abundant taxons between infants with food allergy and health controls
Abundance in Group 1: decreased abundance in infants with food allergies
Revision editor(s): WikiWorks743
Experiment 3
Subjects
- Location of subjects
- China
- 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
- infants non-IgE mediated
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants IgE mediated
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant IgE mediated
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure 2a, Text
Description: Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants
Abundance in Group 1: increased abundance in infants IgE mediated
NCBI | Links |
---|---|
Clostridiaceae | |
Clostridium | |
Eubacteriales | |
Clostridia |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 2a, Text
Description: Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants
Abundance in Group 1: decreased abundance in infants IgE mediated
NCBI | Links |
---|---|
Bacteroidaceae | |
Bacteroides | |
Erysipelotrichaceae | |
Erysipelotrichales | |
Erysipelotrichia | |
Lachnospiraceae | |
Nocardiaceae |
Revision editor(s): WikiWorks743, Merit
Experiment 4
Subjects
- Location of subjects
- China
- 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
- infants non-IgE mediated
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants IgE mediated
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant IgE mediated
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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: Figure 2c, Text
Description: Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants
Abundance in Group 1: increased abundance in infants IgE mediated
NCBI | Links |
---|---|
Clostridium |
Revision editor(s): WikiWorks743
Signature 2
Source: Figure 2c, Text
Description: Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants
Abundance in Group 1: decreased abundance in infants IgE mediated
NCBI | Links |
---|---|
Bacteroides | |
Bacteroidales |
Revision editor(s): WikiWorks743, Merit