Altered fecal microbiota composition associated with food allergy in infants
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L, Xiang C
Journal
Applied and environmental microbiology
Year
2014
Increasing evidence suggests that perturbations in the intestinal microbiota composition of infants are implicated in the pathogenesis of food allergy (FA), while the actual structure and composition of the intestinal microbiota in human beings with FA remain unclear. Microbial diversity and composition were analyzed with parallel barcoded 454 pyrosequencing targeting the 16S rRNA gene hypervariable V1-V3 regions in the feces of 34 infants with FA (17 IgE mediated and 17 non-IgE mediated) and 45 healthy controls. Here, we showed that several key FA-associated bacterial phylotypes, but not the overall microbiota diversity, significantly changed in infancy fecal microbiota with FA and were associated with the development of FA. The proportion of abundant Bacteroidetes, Proteobacteria, and Actinobacteria phyla were significantly reduced, while the Firmicutes phylum was highly enriched in the FA group (P < 0.05). Abundant Clostridiaceae 1 organisms were prevalent in infants with FA at the family level (P = 0.016). FA-enriched phylotypes negatively correlated with interleukin-10, for example, the genera Enterococcus and Staphylococcus. Despite profound interindividual variability, levels of 20 predominant genera were significantly different between the FA and healthy control groups (P < 0.05). Infants with IgE-mediated FA had increased levels of Clostridium sensu stricto and Anaerobacter and decreased levels of Bacteroides and Clostridium XVIII (P < 0.05). A positive correlation was observed between Clostridium sensu stricto and serum-specific IgE (R = 0.655, P < 0.001). The specific microbiota signature could distinguish infants with IgE-mediated FA from non-IgE-mediated ones. Detailed microbiota analysis of a well-characterized cohort of infants with FA showed that dysbiosis of fecal microbiota with several FA-associated key phylotypes may play a pathogenic role in FA.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 2
- 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
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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 | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Bacteria | ||
| Butyricicoccus | ||
| Clostridiaceae | ||
| Clostridium | ||
| Cytophagaceae | ||
| Nocardiaceae |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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 | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Clostridium | ||
| Eubacteriales | ||
| Clostridia |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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 | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Lachnospiraceae | ||
| Nocardiaceae |
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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 | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-28
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 | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroidales |
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