Gut microbiome and innate immune response patterns in IgE-associated eczema
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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
- Australia
- 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
- Atopic eczema allergic,allergic dermatitis,allergic form of dermatitis,Atopic Dermatitides,Atopic Dermatitis,Atopic dermatitis,atopic dermatitis and related conditions,Atopic dermatitis and related conditions (disorder),atopic eczema,Atopic Neurodermatitides,Atopic Neurodermatitis,Atopic neurodermatitis,Besnier's prurigo,Dermatitides, Atopic,Dermatitis, Atopic,Disseminated Neurodermatitides,Disseminated Neurodermatitis,eczema,Eczema, Atopic,Eczema, Infantile,eczematous dermatitis,Infantile Eczema,Neurodermatitides, Atopic,Neurodermatitides, Disseminated,Neurodermatitis, Atopic,Neurodermatitis, Disseminated,OTHER ATOPIC DERMATITIS,Other atopic dermatitis and related conditions,Atopic eczema
- 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
- IgE associated eczema
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 1 week old Infants with typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index
- 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
- 6
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- medical procedure, delivery procedure
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2
Description: Relative abundance >1% of dominant phyla, classes, families and genera in stool samples at 1 week of age infants that remained non-allergic (controls) and in infants developing IgE-associated eczema
Abundance in Group 1: decreased abundance in IgE associated eczema
NCBI | Quality Control | Links |
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Oscillospiraceae |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mothers whose infants remained non-allergic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mothers whose infants developed IgE associated eczema
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers whose infants developed typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2
Description: Relative abundance >1% of dominant phyla, classes, families and genera in stool samples of mothers who's infants that remained non-allergic (controls) or infants developed IgE-associated eczema
Abundance in Group 1: increased abundance in Mothers whose infants developed IgE associated eczema
NCBI | Quality Control | Links |
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Bacilli | ||
Streptococcaceae | ||
Streptococcus |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery method DeliveryMethod,Delivery method,delivery method
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginally delivered infant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- caesarean delivered infant
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant born by caesarean section
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )
Description: Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week
Abundance in Group 1: increased abundance in caesarean delivered infant
NCBI | Quality Control | Links |
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Pseudomonadota |
Signature 2
Source: Figure 1a, Text (Effects of delivery mode on gut microbiome establishment )
Description: Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week
Abundance in Group 1: decreased abundance in caesarean delivered infant
NCBI | Quality Control | Links |
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Bacteroidota |