Early-life gut microbiome composition and milk allergy resolution.
Gut microbiota may play a role in the natural history of cow's milk allergy.



We sought to examine the association between early-life gut microbiota and the resolution of cow's milk allergy.



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).



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).



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.
Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY. Electronic address: supinda@post.harvard.edu.
Supinda
S
Bunyavanich
Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.
Nan
N
Shen
Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
Alexander
A
Grishin
Department of Pediatrics, Johns Hopkins University, Baltimore, Md.
Robert
R
Wood
Department of Pediatrics, University of North Carolina, Chapel Hill, NC.
Wesley
W
Burks
Emmes Corporation, Rockville, Md.
Peter
P
Dawson
Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark.
Stacie M
SM
Jones
Department of Pediatrics, National Jewish Health, Denver, Colo.
Donald Y M
DYM
Leung
Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
Hugh
H
Sampson
Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
Scott
S
Sicherer
Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Division of Clinical Immunology and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY.
Jose C
JC
Clemente
D001419:Bacteria / Q000145:classification / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D003876:Dermatitis, Atopic / Q000503:physiopathology; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000235:genetics / Q000502:physiology*; D006801:Humans; D007073:Immunoglobulin E / Q000097:blood; D007223:Infant; D008297:Male; D016269:Milk Hypersensitivity / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D012336:RNA, Ribosomal, 16S; D007073:Immunoglobulin E
16s rRNA sequencing; Bacteroidetes; Clostridia; Cow's milk allergy; Firmicutes; fatty acid; food allergy; metagenome; microbiome; microbiota