The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study
Related Experiment Video
Updated: Mar 8, 2026

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
Published on: February 7, 2025
Kiera Murphy1,2,3, David Curley4, Tom F O'Callaghan1,2
1Food Biosciences, Teagasc Food Research Centre, Fermoy, Co Cork, Ireland.
Insights
Human milk harbors diverse bacteria, contributing to infant gut microbiota development. Breastfeeding facilitates vertical transfer, establishing key bacterial strains in newborns.
Area of Science:
- Microbiology
- Human Milk Oligosaccharides
- Infant Gut Microbiome
Background:
- Human milk is a crucial source of nutrients and bioactive compounds for infants.
- The infant gut microbiome plays a vital role in immune system development and overall health.
- Understanding the origin and transmission of these microbes is essential for infant health.
Purpose of the Study:
- To characterize the bacterial communities in human milk and infant feces during the first three months of life.
- To investigate the presence of viable Bifidobacterium and Lactobacillus in human milk.
- To explore the hypothesis of vertical bacterial transfer from mother to infant via breastfeeding.
Main Methods:
- MiSeq sequencing was employed to analyze bacterial diversity in milk and fecal samples from 10 mother-infant pairs.
- Bacterial genera and phyla were identified and quantified.
- Viable Bifidobacterium and Lactobacillus strains were isolated and identified.
Main Results:
- Human milk exhibited a high diversity of bacteria, with over 207 genera identified.
- Proteobacteria and Firmicutes were predominant phyla, with Pseudomonas, Staphylococcus, and Streptococcus as key genera.
- A core group of 12 genera constituted a significant portion of the milk microbiota, with shared genera between milk and infant feces supporting vertical transfer.
Conclusions:
- Human milk possesses a rich and diverse bacterial community.
- Breastfeeding likely facilitates the vertical transfer of bacteria, contributing to the establishment of the infant gut microbiota.
- Specific bacterial strains, such as Bifidobacterium breve and Lactobacillus plantarum, can be transmitted from milk to infant feces.
Abstract:
Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70-88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.
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