Relationship between breast milk and infant gut microbiota and allergic diseases in early life.
- 1Department of Pediatrics, Peking University Third Hospital, Beijing, China.
Abstract
Infant gut microbiota (IGM) development is shaped by multiple maternal, environmental, and feeding-related factors. Human milk contains microbial communities and bioactive components that may contribute to early microbial colonization and immune development. The aim of this study was to characterize paired human milk and IGM across early developmental time points and to examine their associations with allergic and allergy-related outcomes ascertained at the approximately 3-year follow-up. This retrospective cohort analysis included 60 mother-infant pairs, comprising 39 breastfed and 21 non-breastfed infants. At the approximately 3-year follow-up, children were classified into the allergy group (n=42) or non-allergy group (n=18) using the allergic/allergy-related history reported by parents at follow-up, including events with first onset after age 3 years. Infant fecal microbiota were evaluated in the eligible cohort, whereas human milk analyses were restricted to dyads with available milk samples. Microbiota at 1, 4, and 6 months were characterized by 16S ribosomal RNA (rRNA) gene sequencing, followed by diversity, differential-abundance, and correlation analyses. Exploratory analyses identified nominal between-group differences in the relative abundance of several taxa at individual time points; however, none of the taxon-level comparisons remained significant after false discovery rate (FDR) correction. Beta-diversity analysis of the IGM showed a nominal between-group difference at 1 month (Jaccard-based PERMANOVA, P=0.04), but not at 4 or 6 months. Linear discriminant analysis effect size (LEfSe) and correlation analyses suggested time-dependent microbial patterns that differed between the allergy and non-allergy groups, with the most prominent exploratory signals occurring early in infancy. These taxon-level findings should be regarded as hypothesis-generating. Exploratory differences in human milk and infant gut microbial communities were associated with allergic and allergy-related outcomes ascertained at the approximately 3-year follow-up. Because no taxon-level comparison remained significant after FDR correction, individual microbial signals should be interpreted as hypothesis-generating rather than confirmatory. Paired milk-gut patterns were consistent with potential maternal-infant microbial sharing, but strain-level transmission and causal relationships cannot be established by the present study design or 16S rRNA gene sequencing. Larger prospective studies with rigorous low-biomass controls, repeated-measures/compositional models, and strain-resolved functional analyses are needed.
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BibTeX
@article{liu2026relationship,
title = {{Relationship between breast milk and infant gut microbiota and allergic diseases in early life.}},
author = {Mengyuan Liu and Qiong Jia and Kunhong Lin and Yangxin Xiao and Xuyan Zhao and Zhifan Gai and Yan Xing},
journal = {Translational pediatrics},
year = {2026},
month = sep,
doi = {10.21037/tp-2026-0732},
url = {https://europepmc.org/article/MED/42996733},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Relationship between breast milk and infant gut microbiota and allergic diseases in early life.
AU - Mengyuan Liu
AU - Qiong Jia
AU - Kunhong Lin
AU - Yangxin Xiao
AU - Xuyan Zhao
AU - Zhifan Gai
AU - Yan Xing
PY - 2026
DA - 2026/09/30
JO - Translational pediatrics
DO - 10.21037/tp-2026-0732
UR - https://europepmc.org/article/MED/42996733
AB - Infant gut microbiota (IGM) development is shaped by multiple maternal, environmental, and feeding-related factors. Human milk contains microbial communities and bioactive components that may contribute to early microbial colonization and immune development. The aim of this study was to characterize paired human milk and IGM across early developmental time points and to examine their associations with allergic and allergy-related outcomes ascertained at the approximately 3-year follow-up. This retrospective cohort analysis included 60 mother-infant pairs, comprising 39 breastfed and 21 non-breastfed infants. At the approximately 3-year follow-up, children were classified into the allergy group (n=42) or non-allergy group (n=18) using the allergic/allergy-related history reported by parents at follow-up, including events with first onset after age 3 years. Infant fecal microbiota were evaluated in the eligible cohort, whereas human milk analyses were restricted to dyads with available milk samples. Microbiota at 1, 4, and 6 months were characterized by 16S ribosomal RNA (rRNA) gene sequencing, followed by diversity, differential-abundance, and correlation analyses. Exploratory analyses identified nominal between-group differences in the relative abundance of several taxa at individual time points; however, none of the taxon-level comparisons remained significant after false discovery rate (FDR) correction. Beta-diversity analysis of the IGM showed a nominal between-group difference at 1 month (Jaccard-based PERMANOVA, P=0.04), but not at 4 or 6 months. Linear discriminant analysis effect size (LEfSe) and correlation analyses suggested time-dependent microbial patterns that differed between the allergy and non-allergy groups, with the most prominent exploratory signals occurring early in infancy. These taxon-level findings should be regarded as hypothesis-generating. Exploratory differences in human milk and infant gut microbial communities were associated with allergic and allergy-related outcomes ascertained at the approximately 3-year follow-up. Because no taxon-level comparison remained significant after FDR correction, individual microbial signals should be interpreted as hypothesis-generating rather than confirmatory. Paired milk-gut patterns were consistent with potential maternal-infant microbial sharing, but strain-level transmission and causal relationships cannot be established by the present study design or 16S rRNA gene sequencing. Larger prospective studies with rigorous low-biomass controls, repeated-measures/compositional models, and strain-resolved functional analyses are needed.
SN - 2224-4336
SN - 2224-4344
ER -