Gut microbiome and innate immune response patterns in IgE-associated eczema

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-17
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


Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi, Victoria

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

Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Oscillospiraceae

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Bacilli
Streptococcaceae
Streptococcus

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi, Victoria

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Folakunmi

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 ControlLinks
Pseudomonadota

Revision editor(s): WikiWorks, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Folakunmi

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 ControlLinks
Bacteroidota

Revision editor(s): WikiWorks, Folakunmi