Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

37700874

DOI Digital object identifier for electronic documents.

10.2147/JAA.S422537

URI

Authors

Wan J, Song J, Lv Q, Zhang H, Xiang Q, Dai H, Zheng H, Lin X, Zhang W

Journal

Journal of asthma and allergy

Year

2023

Keywords:

allergic asthma, allergic rhinitis, childhood, gut microbiome, metagenomic sequencing

PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing. METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing. RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group. CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.

Experiment 1

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Curated date: 2024/04/08

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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: Atopic asthma allergic asthma,Atopic asthma,atopic asthma

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: Allergic asthma

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children with allergic asthma

Group 0 sample size Number of subjects in the control (unexposed) group: 19

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): Within 2 months

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

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: 3.0

Matched on Factors on which subjects have been matched on in a case-control study: age, body mass index, sex

Alpha Diversity

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

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Signature 1

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Curated date: 2024/04/08

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Source: FIG 4 (B)

Description: Taxonomic changes in the intestinal microbial.(B) Histogram of the linear discriminant analysis (LDA) scores for crucial bacteria classification with different abundances between allergic asthma and healthy groups. The Significance was calculated from LDA effect size (LEfSe) at P<0.05 (Kruskal–Wallis test) and LDA score>3.

Abundance in Group 1: increased abundance in Allergic asthma

NCBI	Quality Control	Links
Dorea longicatena
Streptococcus salivarius
Collinsella aerofaciens
Bifidobacterium pseudocatenulatum
Ruminococcus sp. 5_1_39BFAA
Bifidobacterium longum

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Experiment 2

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Allergic rhinitis allergic form of rhinitis,allergic rhinitis,Alrh,atopic rhinitis,non-seasonal allergic rhinitis,Perenial allergic rhinitis,perennial allergic rhinitis,pollenosis,seasonal allergic rhinitis,Allergic rhinitis

Group 1 name Corresponds to the case (exposed) group for case-control studies: Allergic rhinitis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children with allergic rhinitis

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Statistical Analysis

Alpha Diversity

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

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Signature 1

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Curated date: 2024/04/08

Curator: Rahila

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Source: FIG 4 (c)

Description: Taxonomic changes in the intestinal microbial. (C) Histogram of the linear discriminant analysis (LDA) scores for crucial bacteria taxonomic with different abundance between allergic rhinitis and healthy groups. Significance was obtained by LDA effect size (LEfSe) at P<0.05 (Kruskal–Wallis test) and LDA score>3.

Abundance in Group 1: increased abundance in Allergic rhinitis

NCBI	Quality Control	Links
Burkholderiales bacterium 1_1_47
Gemella haemolysans
Dorea longicatena
Streptococcus salivarius
Bifidobacterium pseudocatenulatum
Escherichia unclassifiedEscherichia unclassified
Gemella unclassifiedGemella unclassified
Bifidobacterium bifidum
Escherichia coli