Breast milk is often associated with nutrition, comfort, and immune protection. Less attention is paid to the living microbes it contains. New research shows that these bacteria help shape a baby’s gut during early life.
Gut bacteria influence digestion, vitamin production, immune training, and energy use. A large study explains how bacteria from milk help build a baby’s gut microbiome and how certain microbes remain stable over time.
Researchers from the University of Chicago followed mothers and babies during early months after birth.
The results show that breast milk is more than just food. Milk works as a biological system that helps guide early gut development.
Why breast milk bacteria matter
Early life marks a critical window for gut development. During early months, microbes colonize a newborn gut and begin forming long term patterns.
Breast milk supplies nutrients but also delivers bacteria that help start and support gut communities.
Milk contains helpful microbes such as Bifidobacterium species. Such bacteria digest human milk sugars called human milk oligosaccharides.
Digestion products then support gut cells and immune activity. Lack of such microbes links to higher risk of immune and metabolic problems later in life.
Studying milk bacteria remains difficult. Milk holds high fat levels and very small bacterial amounts. Despite these challenges, advanced genetic tools now allow deeper analysis.
Studying mother-infant pairs
Study first author Dr. Pamela Ferretti is a postdoctoral researcher in the Blekhman Lab.
“Breast milk is the recommended sole source of nutrition for an infant’s first months of life, but important questions about the milk microbiome remained unanswered because the analytical challenges are intimidating,” said Dr. Ferretti.
“We decided to tackle this endeavor because our collaboration presented a unique opportunity to combine key resources.”
The researchers analyzed 507 samples from 195 mother-infant pairs. Milk samples came from one and three months after birth.
Infant stool samples came from one and six months after birth. Most infants received only breast milk during early months.
Bacteria found inside breast milk
Milk samples showed lower bacterial diversity than infant stool, but they still displayed a distinct bacterial pattern.
Bifidobacterium longum appeared more often than expected, occurring in over half of milk samples and in nearly all infant gut samples.
Earlier studies using limited methods focused on skin bacteria such as Staphylococcus. Whole genome analysis revealed bifidobacteria as major milk residents.
“Even though B. longum is well-documented as being highly prevalent in the infant gut, it was surprising to find such a strong signature of that species in the breast milk samples because previous milk studies mostly reported other bacterial taxa like Staphylococcus and Streptococcus,” said Dr. Ferretti.
“We think these results will prompt some reevaluation in the field.”
Milk also contained Bifidobacterium breve and Bifidobacterium bifidum. Oral bacteria such as Streptococcus salivarius appeared as well.
The presence of oral microbes supports an idea called retrograde flow. During feeding, bacteria from a baby’s mouth may move back into milk ducts.
Tracking bacteria from milk to gut
The researchers used metagenomic sequencing instead of older methods. Full genome analysis allows tracking bacteria at strain level. Strain level matching offers strong evidence of direct transfer.
“Metagenomic analysis is trickier and more complicated, but it really paid off because it allowed us to obtain information at the level of different bacterial strains – which is key, because that’s the only level where we could actually claim to know about transmission,” noted Dr. Ferretti.
Twelve clear cases showed identical bacterial strains in both milk and infant gut. Shared strains included beneficial bifidobacteria and also microbes such as Escherichia coli and Klebsiella pneumoniae.
All mothers and infants remained healthy. The presence of such microbes does not signal disease but shows natural microbial variety.
Stability and growth of gut microbes
Infant gut communities changed over time. B. longum became more common by six months.
Infants with gut communities dominated by B. longum showed greater stability across months. This stability supports consistent digestion and immune signaling.
Exclusive breastfeeding supported higher levels of bifidobacteria. The introduction of formula or mixed feeding was linked to reduced dominance of these microbes.
Delivery mode also mattered. Vaginal birth linked to higher persistence of early microbes compared to cesarean birth.
Microbes inside milk and infant gut carried genes for building essential amino acids. Early gut bacteria exhibited a strong ability to make amino acids such as valine and lysine. Such activity helps support growth during early months.
Milk also carried microbes with resistance genes against certain antibiotics. Infant gut samples showed similar resistance patterns.
Shared resistance genes appeared more often among mother infant pairs showing shared bacterial strains.
Future research directions
“This study nearly doubled the number of metagenomic breast milk samples that are publicly available, and pairs them with extensive information on mothers’ health and lifestyle,” said Dr. Ferretti.
“We’re hopeful that our findings and future analyses that use this dataset will really push the field forward.”
Future work may explore milk sugars, environmental chemicals, and long term health outcomes.
“Ultimately, we’re interested in looking at longer health trajectories to see if factors in breast milk and early life are predictive of health outcomes later in life,” Dr. Ferretti concluded.
The study is published in the journal Nature Communications.
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