Early-life gut microbiome composition and milk allergy resolution

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/27

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

27292825

DOI Digital object identifier for electronic documents.

10.1016/j.jaci.2016.03.041

URI

Authors

Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S, Clemente JC

Journal

The Journal of allergy and clinical immunology

Year

2016

Keywords:

16s rRNA sequencing, Bacteroidetes, Clostridia, Cow's milk allergy, Firmicutes, fatty acid, food allergy, metagenome, microbiome, microbiota

BACKGROUND: Gut microbiota may play a role in the natural history of cow's milk allergy. OBJECTIVE: We sought to examine the association between early-life gut microbiota and the resolution of cow's milk allergy. METHODS: We studied 226 children with milk allergy who were enrolled at infancy in the Consortium of Food Allergy observational study of food allergy. Fecal samples were collected at age 3 to 16 months, and the children were followed longitudinally with clinical evaluation, milk-specific IgE levels, and milk skin prick test performed at enrollment, 6 months, 12 months, and yearly thereafter up until age 8 years. Gut microbiome was profiled by 16s rRNA sequencing and microbiome analyses performed using Quantitative Insights into Microbial Ecology (QIIME), Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and Statistical Analysis of Metagenomic Profiles (STAMP). RESULTS: Milk allergy resolved by age 8 years in 128 (56.6%) of the 226 children. Gut microbiome composition at age 3 to 6 months was associated with milk allergy resolution by age 8 years (PERMANOVA P = .047), with enrichment of Clostridia and Firmicutes in the infant gut microbiome of subjects whose milk allergy resolved. Metagenome functional prediction supported decreased fatty acid metabolism in the gut microbiome of subjects whose milk allergy resolved (η2 = 0.43; ANOVA P = .034). CONCLUSIONS: Early infancy is a window during which gut microbiota may shape food allergy outcomes in childhood. Bacterial taxa within Clostridia and Firmicutes could be studied as probiotic candidates for milk allergy therapy.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: United States of America

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: Milk allergic reaction milk allergic reaction,milk allergy,Milk Hypersensitivity,Milk allergic reaction

Group 0 name Corresponds to the control (unexposed) group for case-control studies: milk allergy resolution

Group 1 name Corresponds to the case (exposed) group for case-control studies: children with milk allergy persistence

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: child with persistent milk allergy at age 8

Group 0 sample size Number of subjects in the control (unexposed) group: 128

Group 1 sample size Number of subjects in the case (exposed) group: 98

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

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

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 1a

Description: Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8

Abundance in Group 1: increased abundance in children with milk allergy persistence

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Bacteroidota
Enterobacter
Salmonella
Trabulsiella

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/28

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 1a

Description: Differentially abundant taxa in children with milk allergy persistence versus milk allergy resolution at age 8

Abundance in Group 1: decreased abundance in children with milk allergy persistence

NCBI	Quality Control	Links
Blautia
Clostridia
Clostridiaceae
Eubacterium
Bacillota
Peptostreptococcaceae
Prevotellaceae
Ruminococcus

Revision editor(s): Claregrieve1, WikiWorks