Lack of key gut bacteria in infants linked to higher risk of allergies

Giorgia Guglielmi

08.09.2025

Specific gut bacteria are important in early life for healthy immune development.

What is already known

Conditions such as allergies and obesity have risen sharply in recent decades, often starting in the first two years of life. Changes resulting from living in industrialized populations affect infant gut bacteria, reducing Bifidobacterium strains important for health. Factors such as feeding mode and antibiotic use influence these bacteria and may impact childhood health, but the exact long-term effects aren’t yet well understood.

What this research adds

Researchers examined the gut microbiota of US infants during their first 100 days and found that about 25% lacked beneficial Bifidobacterium bacteria, especially B. infantis, which is common in less industrialized populations. Instead, other less helpful or potentially harmful bacteria took their place, especially in babies born through a C-section. These changes affected how infants metabolize important milk sugars and were linked to higher risks of allergies, eczema, and asthma by age two.

Conclusions

The findings suggest that specific gut bacteria are important in early life for healthy immune development.

Conditions such as allergies and obesity have risen sharply in recent decades, often starting in the first two years of life. Now, a study found that a lack of beneficial bacteria in infants’ guts leads to changes in metabolism and increases the risk of immune-related conditions.

The findings, published in Communications Biology, suggest that specific gut bacteria are important in early life for healthy immune development.

Changes resulting from living in industrialized populations affect infant gut bacteria, reducing Bifidobacterium strains important for health. Factors including feeding mode and antibiotic use influence these bacteria and may impact childhood health, but the exact long-term effects aren’t yet well understood.

John Jarman at the University of Rochester School of Medicine and Dentistry in New York and his colleagues set out to examine the gut microbiota of US infants during their first 100 days to understand its impact on immune health.

Altered metabolism

The researchers collected stool samples from infants aged 1 to 3 months from most US states. They found an average of 12 types of bacteria in infants, which is fewer than adults have. About 24% of babies, especially those born through a C-section, lacked bacteria such as Bifidobacterium, which are important for healthy growth. In contrast, babies born vaginally or breastfed tended to have more of these good bacteria. C-section babies who were breastfed sometimes also had more potentially harmful bacteria such as Clostridium perfringens.

Bifidobacterium, especially B. infantis, are the main bacteria that use specific sugars in breast milk, helping the baby’s immune system and gut to develop properly. Infants with higher levels of Bifidobacterium could digest these sugars better than those who lacked it.

Infants lacking Bifidobacterium showed changes in important metabolic processes such as bile acid metabolism, vitamin production, and a shift toward producing more butyrate, which has been linked to certain harmful microbes. They also had less of some beneficial immune molecules and more genes linked to antibiotic resistance.

Lifelong impact

At two years old, more than half of the infants had taken antibiotics, and about 30% had conditions such as eczema or asthma. Babies with lower levels of Bifidobacterium were about three times more likely to develop these immune-related problems compared to those with more Bifidobacterium.

The presence of B. breve was linked to a much lower risk of allergic conditions, and specific bacterial genes—including genes from viruses that infect bacteria—were associated with higher risk.

These results suggest that the makeup of the infant gut microbiota plays an important role in the development of allergies, the authors say. “Given the alarming rise in [non-communicable diseases] and their link to the infant gut microbiome, the gut microbiota offers an opportunity for early intervention with lifelong health impact.”