Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants

Lisa F Stinson; Isabella Norrish; Faith Mhembere; Ali Sadiq Cheema; Christopher A Mullally; Matthew S Payne; Donna T Geddes

doi:10.1080/19490976.2025.2557981

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Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants

Journal article

Open access

Peer reviewed

Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants

Lisa F Stinson, Isabella Norrish, Faith Mhembere, Ali Sadiq Cheema, Christopher A Mullally, Matthew S Payne and Donna T Geddes

Gut microbes, Vol.17(1), 2557981

2025

DOI: https://doi.org/10.1080/19490976.2025.2557981

PMID: 40948418

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Abstract

Bacteria - classification

Bacteria - genetics

Bacteria - isolation & purification

Bifidobacterium - genetics

Bifidobacterium - isolation & purification

Breast Feeding

Cesarean Section

Child, Preschool

Feces - microbiology

Female

Gastrointestinal Microbiome

Humans

Infant

Infant, Newborn

Longitudinal Studies

Male

Milk, Human - microbiology

RNA, Ribosomal, 16S - genetics

Gut microbiome establishment in early life is influenced by maternal, infant, and environmental factors, with disruptions linked to later disease risk. Although infant diet is a major determinant of microbial composition, longitudinal data in breastfed infants, particularly in the context of birth interventions, remain limited. We profiled 698 stool samples from 84 predominantly or exclusively breastfed infants in the BLOSOM cohort, spanning 10 time points from 1 week to 2 years of age using full-length 16S rRNA gene sequencing and targeted qPCR. After an initial volatile period, microbiome composition and diversity stabilized between months 2 and 5. Introduction of solid foods then triggered a marked ecological shift, with significant increases in diversity (p < 1 × 10−11) and broad compositional restructuring. In contrast, weaning had minimal impact on overall microbiota structure but was associated with lower abundances of several Bifidobacterium species, highlighting the sustained bifidogenic effect of human milk. Cesarean delivery was associated with transient reductions in Bacteroides abundance and prevalence, but did not affect Bifidobacterium, likely due to the bifidogenic effects of human milk. Reductions in Bacteroides, however, were not reflected in quantitative analyses, emphasizing the importance of absolute abundance measures. Our results offer novel insight into gut microbiome development under optimal feeding conditions, suggesting that breastfeeding may buffer early-life microbiome perturbations, while diet transitions exert major and lasting effects.

Details

Title: Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants
Authors/Creators: Lisa F Stinson - Community Arts Network
Isabella Norrish - The University of Western Australia
Faith Mhembere - The University of Western Australia
Ali Sadiq Cheema - The Kids Research Institute Australia
Christopher A Mullally - Murdoch University, School of Medical, Molecular and Forensic Sciences
Matthew S Payne - The University of Western Australia
Donna T Geddes - The University of Western Australia
Publication Details: Gut microbes, Vol.17(1), 2557981
Publisher: Taylor & Francis Group, LLC.
Identifiers: 991005814049507891
Murdoch Affiliation: School of Medical, Molecular and Forensic Sciences
Language: English
Resource Type: Journal article

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