Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk 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
- Italy
- 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
- Milk allergic reaction milk allergic reaction,milk allergy,Milk Hypersensitivity,Milk allergic reaction
- 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
- non-IgE mediated cow's milk allergy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children aged 1-26 months with a diagnosis of non-IgE mediated cow's milk allergy based on clinical history, negative result of skin prick test, and/or negative level of IgE serum-specific anti-cow's milk proteins
- 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
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Illumina
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)?
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S1
Description: Differential microbial abundance between cow's milk allergy non IgE patients at diagnosis and healthy controls
Abundance in Group 1: increased abundance in non-IgE mediated cow's milk allergy
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Sarcina |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infant with non-IgE-mediated cow's milk allergy at diagnosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infant with non-IgE-mediated cow's milk allergy treated with EHCF
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with non-IgE mediated cow's milk allergy treated with EHCF
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S1
Description: Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF and non-IgE mediated cow's milk allergy patients at diagnosis
Abundance in Group 1: decreased abundance in infant with non-IgE-mediated cow's milk allergy treated with EHCF
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Alistipes |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S1
Description: Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis
Abundance in Group 1: decreased abundance in infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Supplementary Table S1
Description: Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients at diagnosis
Abundance in Group 1: increased abundance in infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG
| NCBI | Quality Control | Links |
|---|---|---|
| Streptomyces |
Revision editor(s): Claregrieve1
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infant with non-IgE-mediated cow's milk allergy treated with EHCF
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S1
Description: Differential microbial abundance between non-IgE-Mediated cow's milk allergy patients treated with EHCF + LGG and non-IgE mediated cow's milk allergy patients treated with EHCF
Abundance in Group 1: increased abundance in infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira | ||
| Lactobacillus | ||
| Oscillospira | ||
| Ruminococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Supplemental Table S1
Description: Differential microbial abundance between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy treated with EHCF
Abundance in Group 1: decreased abundance in infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Dialister |
Revision editor(s): Claregrieve1, WikiWorks
