How the Human Milk Microbiome Shapes the Infant Gut - New Study Explained

The human milk microbiome — the community of bacteria present in breast milk — is emerging as a key contributor to infant gut development.

Content outline

• Human Milk: More Than Just Nutrition

• Understanding The Human Milk Microbiome: Study Design Explained

• What Were The Main Findings Of The Study?

• How Bifidobacterium longum Links the Human Milk and Infant Gut Microbiomes

• How Bifidobacterium longum Dominance Supports a Stable Infant Gut

• Shared Bacterial Strains Include Commensals, Pathobionts, And Those Usually Found In The Gut And Mouth

• Antimicrobial Resistance Genes in Breast Milk and the Infant Gut

• Summary: What does this research mean for future human milk studies?

Human Milk: More Than Just Nutrition

Human milk, for at least the first 6 months of an infant’s life, is the ideal source of nutrition [1]. It’s brimming with nutrients, antibodies, and oligosaccharides that help to build and nourish the developing microbes in the gut. Breastfeeding is also a great way to strengthen the bond between mother and child [2].

However, what is far less understood, is the microbial community that resides in human breast milk itself and the health benefits this ecosystem can bring. In this article, we delve into the results of a recently published study by Ferretti and colleagues, which helps to shed some light on how some bacterial strains found in breast milk could be contributing to the developing infant gut. 

Understanding The Human Milk Microbiome: Study Design Explained

Studying human milk is more difficult than it sounds because of its fatty composition and its relatively low microbial content. Previous research has used amplicon sequencing to analyze the bacterial DNA in breast milk. Although this can successfully identify the different species within a sample, most of the bacterial genome is still unknown.

In this current study, the researchers used metagenomic or shotgun analysis. This technique allows scientists to study all of the genetic material in a sample [3]. Analysing 507 samples collected from 195 mother and infant pairs at 1, 3, and 6 months after birth, the researchers were able to detect the different bacterial strains in the mother’s milk and the infant's gut. Infant stool samples were collected and analysed at 1 and 6 months.    

What Were The Main Findings Of The Study?

How Bifidobacterium longum Links the Human Milk and Infant Gut Microbiomes

Breast milk contained fewer different types of bacteria than babies’ stool samples, meaning the infant's gut was more diverse than the milk. Over the first few months, bacterial diversity increased slightly in both milk and baby stool. In milk, the most common bacteria were types of Bifidobacterium, especially Bifidobacterium longum, along with smaller amounts of bacteria usually found on the skin and in the mouth (Figure 1). Whether a mother was a “secretor” (a genetic trait that affects certain milk sugars, such as 2’-FL) did not appear to significantly change the overall mix of bacteria in her milk.

Figure 1. The most prominent bacteria in human breast milk. The milk microbiome was dominated by Bifidobacteria longum. 

At one month old, babies’ gut bacteria were largely made up of Bifidobacterium species — particularly B. longum, B. breve, and B. bifidum — alongside some other common early-life bacteria such as Escherichia coli and Bacteroides fragilis. B. longum was especially widespread, appearing in over half of milk samples and nearly all infant stool samples (Figure 2). As babies grew, Bifidobacterium became even more dominant overall. When researchers grouped stool samples by the most abundant species present, around half were led by non-Bifidobacterium species, while the rest were mainly dominated by one of three Bifidobacterium species, most commonly B. longum (29.3%).

Figure 2. Most prevalent bacteria in infant gut microbiomes. 

Although breast milk and infant stool microbiomes had clearly different overall bacterial profiles, they shared one key player: Bifidobacterium longum. This species appears to be the main link between the milk microbiome and the baby’s gut microbiome. Two subtypes — B. longum subsp. longum and B. longum subsp. infantis — were often found together in both milk and stool samples:

• 81.4% of milk and stool samples

• 52.1% of milk samples at 1 month

• 83.4% of stool samples at 1 month

• 95.6% of stool samples at 6 months

How Bifidobacterium longum Dominance Supports a Stable Infant Gut

To understand how stable these bacterial communities were over time, researchers looked at which species were most dominant in milk and infant stool samples. 

Bifidobacterium longum was the clear frontrunner in both. About half of the breast milk samples were dominated by B. longum, and this pattern was relatively stable — nearly two-thirds of mothers whose milk was dominated by B. longum at one month still showed the same dominance at three months. In contrast, milk samples dominated by other species, such as B. breve, were much less stable. In babies, B. longum became more common over time: stool samples dominated by this species rose from around 16% at one month to nearly 47% at six months, while samples dominated by non-Bifidobacterium species fell substantially.

Looking more closely at the infant gut, B. longum was present in almost all babies at one month, and other Bifidobacterium species were also common. Overall, these beneficial bacteria increased both in presence and in abundance between one and six months of age. One subtype, B. longum subsp. infantis, showed a particularly striking rise over time. While there was variation between individual babies, the overall trend was clear: as infants grew — especially those who were still exclusively breastfed at six months — Bifidobacterium species became more dominant in the gut (Figure 3).

Figure 3. Relative abundance of Bifidobacteria species at 1 and 6 months of age in the infant gut microbiome. 

When researchers tracked changes over time, they found that B. longum (particularly the infantis subtype) increased, while bacteria such as E. coli and Veillonella dispar declined. Babies who were exclusively breastfed for six months showed the strongest increases in B. longum and B. breve, along with a reduction in potentially harmful bacteria like Clostridium perfringens. Introducing solid foods at six months did not appear to cause major differences in overall gut bacteria at that stage. Importantly, babies whose gut microbiome was dominated by B. longum at both one and six months had the most stable bacterial communities over time, suggesting this species may play a key role in shaping early gut development.

Shared Bacterial Strains Include Commensals, Pathobionts, And Those Usually Found In The Gut And Mouth

Researchers wanted to understand whether bacteria are passed from a mother’s breast milk to her baby’s gut. They found that some bacteria are shared, but the overlap is relatively small and decreases over time:

• At 1 month, around 10% of bacteria in a baby’s stool were also found in their mother’s milk.

• By 6 months, this dropped to just over 7%.

• The most commonly shared species was Bifidobacterium longum.

• Other shared bacteria included Staphylococcus epidermidis and Bifidobacterium breve.

However, while certain mother–baby pairs showed similar levels of beneficial bacteria, this pattern was not strong enough to apply across the whole group.

When scientists examined specific bacterial strains (more precise genetic matches), they found limited but clear evidence of direct mother-to-baby transfer — mainly at one month. Key findings included:

• Only a small number of exact strain matches were identified

• About 1 in 5 strains present at 1 month were still found at 6 months

• Babies born vaginally were more likely to retain early strains than those born by C-section

• Breastfeeding at six months, antibiotic use, and maternal genetics did not significantly affect long-term strain persistence

Antimicrobial Resistance Genes in Breast Milk and the Infant Gut

Researchers examined antimicrobial resistance genes (ARGs) — sometimes called the “resistome” — in both breast milk and the infant gut. They found that milk and stool contained different types and amounts of resistance genes. Breast milk had fewer overall resistance gene types than infant stool, and the most common resistance class in milk was against macrolide-lincosamide-streptogramin (MLS) antibiotics. Over time, resistance gene diversity increased in both milk and stool, although this rise was only statistically significant in milk. In infants, the gut resistome was mainly dominated by resistance to tetracycline, MLS, aminoglycosides, and beta-lactam antibiotics.

Importantly, babies whose gut microbiome was rich in bifidobacteria carried significantly fewer resistance genes. Factors such as birth method, antibiotic exposure, solid food introduction, or mixed feeding did not significantly change overall resistance patterns — and many infants carried resistance genes even without known antibiotic exposure. While overall resistance patterns in milk and infant stool were not strongly correlated across the whole group, individual mother–baby pairs shared more resistance genes than expected by chance. The infant resistome at one month was also moderately predictive of patterns seen at six months, suggesting early microbial influences may persist.

Summary: What does this research mean for future human milk studies?

This study highlighted the microbiome composition of human milk and how it can support the development of the infant gut microbiome during the first 6 months of life. One of the major findings was that mothers and their infants share bacterial strains and antimicrobial resistance genes, suggesting that breast milk plays a key role in establishing and developing both the infant gut microbiome and resistome. It is also vital for a more stable gut microbiome.

Future research will focus on analyzing specific metabolites in human milk, like human milk oligosaccharides (HMOs) and environmental factors, like PFAS (forever chemicals), that can be passed on and their impact on the infant gut. Eventually, this research will enable scientists to determine whether factors in breast milk and early life can play a role in health outcomes later in life.

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Author details

Written by: Leanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome. She has written extensively on inflammatory bowel disease, prebiotics, and microbiome research.

Her work focuses on translating complex medical science into evidence-based, practical health guidance.