The infant gut microbiota is crucial for immune and metabolic development, and maternal factors, including a mother’s microbiota and breast milk, can influence early gut colonization. Now, researchers have found that the early infant gut microbiota is shaped by the interplay with maternal gut microbes and breast milk composition.

The findings, published in Cell Host & Microbe, suggest that supporting maternal gut health and optimizing breast milk composition could help shape healthy infant gut development.

Breast milk is known to provide not only nutrients but also human milk oligosaccharides (HMOs)—complex sugars in breast milk that feed beneficial gut bacteria such as Bifidobacterium, which initially dominate the infant microbiota. However, it remains unclear how maternal gut microbes, breast milk composition, and infant gut microbes interact over time.

To address this question, researchers led by Lishi Deng at Ghent University in Belgium followed 152 mothers and their babies in rural Burkina Faso.

Microbiota profiles

The team collected maternal stool samples during pregnancy, breast milk samples from 2 weeks to 4 months, and infant stool samples at 1-2 and 5-6 months. Almost all infants were exclusively breastfed for about six months. 

The infant gut was initially dominated by helpful bacteria such as Bifidobacterium and Escherichia, while mothers’ guts and milk contained much more diverse microbial communities. 

Early on, infants fell into three distinct gut microbiota profiles—Bifidobacterium-dominant, Escherichia-dominant, and pathogen-rich. By six months, however, these differences disappeared and the infant gut communities became more diverse. Breast milk composition also changed: early milk was richer in certain sugars, proteins, vitamins, and minerals that declined over time, the researchers found.

Two-way interaction 

Differences in mothers’ gut microbes during the third trimester of pregnancy were associated with distinct gut microbiota patterns in infants at 1-2 months of age. For example, mothers whose babies had a Bifidobacterium-rich gut profile at 1-2 months tended to produce higher levels of HMOs. Later, at 5–6 months, other breast milk nutrients—such as iron, vitamins, and minerals—became more important than HMOs.

The researchers also found evidence that an infant’s early gut microbes were linked to changes in milk composition months later, suggesting that babies may influence the milk they receive.

The findings, the authors say, “offer insights into early-life microbial development and inform future mechanistic studies and microbiome-targeted interventions, particularly in low-resource settings.”