Alterations in the gut microbiotas of children with food sensitization in early life
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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
Chen CC, Chen KJ, Kong MS, Chang HJ, Huang JL
Journal
Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology
Year
2016
Keywords:
454 pyrosequencing, food sensitization, linear discriminant analysis, microbiota
BACKGROUND: We hypothesized that food sensitization (FS) in children could be linked to specific gut microbiota. The aim of our study is to quantify and evaluate differences in gut microbiota composition between children with FS and healthy controls. METHODS: A case-control study of 23 children with FS and 22 healthy children was performed. Individual microbial diversity and composition were analyzed via parallel barcoded 454 pyrosequencing targeting the 16S rRNA gene hypervariable V3-V5 regions. RESULTS: The children with FS exhibited lower diversity of both the total microbiota (p = 0.01) and the bacterial phylum Bacteroidetes (p = 0.02). In these children, the number of Bacteroidetes bacteria was significantly decreased and that of Firmicutes were significantly increased compared with the healthy children. At the genus level, we observed significant increases in the numbers of Sphingomonas, Sutterella, Bifidobacterium, Collinsella, Clostridium sensu stricto, Clostridium IV, Enterococcus, Lactobacillus, Roseburia, Faecalibacterium, Ruminococcus, Subdoligranulum, and Akkermansia in the FS group. We also found significant decreases in the numbers of Bacteroides, Parabacteroides, Prevotella, Alistipes, Streptococcus, and Veillonella in this group. Furthermore, linear discriminant analysis (LDA) coupled with effect size measurements revealed the most differentially abundant taxa (increased abundances of Clostridium IV and Subdoligranulum and decreased abundances of Bacteroides and Veillonella), which could be used to identify FS. CONCLUSIONS: Our results showed that FS is associated with compositional changes in the gut microbiota. These findings could be useful for developing strategies to control the development of FS or atopy by modifying the gut microbiota.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Subjects
- Location of subjects
- China
- 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
- Food allergy Food Hypersensitivity,Food intolerance,Food allergy,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
- children with food sensitization
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with food sensitization
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- 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)
- 1 week
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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).
- raw counts
- Statistical test
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Source: Table 2, Text (Alterations at the family and genus levels)
Description: Differentially abundant taxons between food sensitization children and healthy control
Abundance in Group 1: increased abundance in children with food sensitization
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Source: Table 2, Text (Alterations at the family and genus levels)
Description: Differentially abundant taxons between food sensitization children and healthy control
Abundance in Group 1: decreased abundance in children with food sensitization
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Parabacteroides | ||
| Prevotella | ||
| Streptococcus | ||
| Veillonella |
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Source: Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)
Description: Differentially abundant taxons between food sensitization children and healthy control
Abundance in Group 1: increased abundance in children with food sensitization
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Bacillota | ||
| Clostridia | ||
| Eubacteriales | ||
| Subdoligranulum | ||
| unclassified Oscillospiraceae |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-27
Source: Figure 3, Text (Comparison of relative abundance through LDA score and cladogram analysis)
Description: Differentially abundant taxons between food sensitization children and healthy control
Abundance in Group 1: decreased abundance in children with food sensitization
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroidales | ||
| Bacteroides | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Veillonella |
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