Low diversity of the gut microbiota in infants with atopic eczema

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-26

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

22153774

DOI Digital object identifier for electronic documents.

10.1016/j.jaci.2011.10.025

URI

Authors

Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, Jenmalm MC

Journal

The Journal of allergy and clinical immunology

Year

2012

BACKGROUND: It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts. OBJECTIVE: We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development. METHODS: Microbial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830). RESULTS: Infants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P = .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P = .02 and P = .01) and the phylum Proteobacteria at 12 months of age (P = .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R [edgeR] test: P = .008, q = 0.02). CONCLUSION: Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema.

Experiment 1

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Subjects

Location of subjects: Sweden

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 infant

Group 1 name Corresponds to the case (exposed) group for case-control studies: infant with atopic eczema

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: infant with atopic eczema- at 12 months

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 20

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

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: edgeR

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

Signature 1

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Source: Table 3

Description: Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life

Abundance in Group 1: increased abundance in infant with atopic eczema

NCBI	Quality Control	Links
Enterococcus
Peptostreptococcaceae

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Signature 2

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Source: Table 3

Description: Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life

Abundance in Group 1: decreased abundance in infant with atopic eczema

NCBI	Quality Control	Links
Pseudomonadota

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2

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Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: infant with atopic eczema- at 1 month

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Curated date: 2024/02/26

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Source: Table 2

Description: Relative abundance of dominant taxa in stool samples obtained at 1 month from infants with atopic eczema compared to infants without atopic eczema during the first 2 years of life

Abundance in Group 1: decreased abundance in infant with atopic eczema

NCBI	Quality Control	Links
Bacteroidota
Bacteroides

Revision editor(s): ChiomaBlessing