Gut microbiome and innate immune response patterns in IgE-associated eczema
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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
West CE, Rydén P, Lundin D, Engstrand L, Tulic MK, Prescott SL
Journal
Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology
Year
2015
Keywords:
16SrRNA, TLR-ligands, diversity, eczema, hygiene hypothesis, innate immunity, intestinal colonization, microbiota, molecular microbiology
BACKGROUND: Gut microbiome patterns have been associated with predisposition to eczema potentially through modulation of innate immune signalling. OBJECTIVE: We examined gut microbiome development in the first year of life in relation to innate immune responses and onset of IgE-associated eczema over the first 2.5 years in predisposed children due to maternal atopy [www.anzctr.org.au, trial ID ACTRN12606000280505]. METHODS: Microbial composition and diversity were analysed with barcoded 16S rRNA 454 pyrosequencing in stool samples in pregnancy and at ages 1 week, 1 month and 12 months in infants (n = 10) who developed IgE-associated eczema and infants who remained free of any allergic symptoms at 2.5 years of age (n = 10). Microbiome data at 1 week and 1 month were analysed in relation to previously assessed immune responses to TLR 2 and 4 ligands at 6 months of age. RESULTS: The relative abundance of Gram-positive Ruminococcaceae was lower at 1 week of age in infants developing IgE-associated eczema, compared with controls (P = 0.0047). At that age, the relative abundance of Ruminococcus was inversely associated with TLR2 induced IL-6 (-0.567, P = 0.042) and TNF-α (-0.597, P = 0.032); there was also an inverse association between the abundance of Proteobacteria (comprising Gram-negative taxa) and TLR4-induced TNF-α (rs = -0.629, P = 0.024). This relationship persisted at 1 month, with inverse associations between the relative abundance of Enterobacteriaceae (within the Proteobacteria phylum) and TLR4-induced TNF-α (rs = -0.697, P = 0.038) and Enterobacteriaceae and IL-6 (rs = -0.709, P = 0.035). Mothers whose infants developed IgE-associated eczema had lower α-diversity of Bacteroidetes (P = 0.04) although this was not seen later in their infants. At 1 year, α-diversity of Actinobacteria was lower in infants with IgE-associated eczema compared with controls (P = 0.002). CONCLUSION AND CLINICAL RELEVANCE: Our findings suggest that reduced relative abundance of potentially immunomodulatory gut bacteria is associated with exaggerated inflammatory cytokine responses to TLR-ligands and subsequent development of IgE-associated eczema.
Experiment 1
Needs review
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
- 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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
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 |
|---|---|---|
| Oscillospiraceae |
Revision editor(s): WikiWorks
Experiment 2
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
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 |
|---|---|---|
| Bacilli | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): WikiWorks
Experiment 3
Needs review
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
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 |
|---|---|---|
| Pseudomonadota |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
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 |
|---|---|---|
| Bacteroidota |
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