Without these crucial microbes, babies are more likely to suffer long-term health issues

Many babies in the United States are missing helpful gut bacteria that digest breast milk and help train the immune system. In a new study, researchers analyzed the microbiome of 412 infants and found that about 25 percent had no detectable Bifidobacterium, with B. infantis present in only 8 percent.

Roughly 76 percent had low or undetectable levels of Bifidobacterium overall, and that babies with low levels were at least three times as likely to develop allergies, eczema, and asthma by age 2.

That early window matters because the immune system is learning how to respond to the world during the first months after birth.

Babies and Bifidobacterium

The study team includes Stephanie Culler of Persephone Biosciences, a San Diego based biotechnology company.

Her group partnered with academic scientists to examine infants across 48 states using metagenomics and metabolomics.

In some infants born by C-section, breastfeeding did not restore Bifidobacterium and other bacteria stepped into the milk sugar niche instead.

That shift mattered because it changed the chemical environment and allowed opportunistic species to grow.

Antibiotics during the first two years were associated with a 3.3 fold higher risk of allergic conditions compared with no antibiotics in that period.

The authors also observed more genes linked to antimicrobial resistance and virulence factors in infants with low Bifidobacterium.

“Nondetectable levels of the most fundamental family type of bacteria for the infant was really surprising to us,” said Culler.

Why Bifidobacterium matters

Early arriving infant Bifidobacteria can block potentially harmful bacteria from taking hold, as supported by a 2024 paper. Priority effects, the idea that first settlers shape the community that follows, appear to apply in the newborn gut.

These bacteria are uniquely equipped to use human milk oligosaccharides (HMOs), the complex sugars in breast milk.

When Bifidobacterium thrives, it turns those sugars into products like acetate and lactate, lowering gut pH and discouraging pathogens.

This group also helps produce vitamins and other metabolites that support immune signaling. Those chemical cues guide the developing immune system and help it react appropriately to foods and environmental exposures.

Low Bifidobacterium changes the balance of metabolites and leaves more open space for organisms that are better at resisting antibiotics.

That altered chemistry aligns with the higher load of antimicrobial resistance and virulence related genes described in the cohort.

Birth, feeding, and antibiotics

Birth mode affected which microbes showed up first. Vaginal delivery often tracked with higher Bifidobacterium when paired with breastfeeding, while some C-section infants showed low levels even if they were breastfed.

Feeding mattered because milk sugars select for particular bacteria. In infants without Bifidobacterium, organisms that can partially use those sugars sat in the same niche and limited later colonization by the usual infant strains.

Antibiotics can be life saving, yet they also disrupt early colonizers that depend on timing to establish.

When those helpful species are cleared or delayed, others can gain a foothold and steer the microbiome down a different path.

Lifestyle patterns may influence exposure too. Industrial food processing and widespread antibacterial products reduce everyday contact with Bifidobacterium and related microbes in families and communities.

Signals in the data by age 2

The researchers grouped infant microbiomes into community types and compared later health. Two community patterns without strong Bifidobacterium signals were linked to higher odds of allergic conditions by age 2.

The protective effect seemed strongest when certain species dominated early. Communities enriched in B. breve were tied to lower risk, highlighting that not all members of this genus act identically in the infant gut.

This analysis does not prove cause and effect in every case. It does show that missing cornerstone microbes in early life tracks with a higher load of risk factors and measurable changes in metabolism.

The cohort will be followed for seven years, which will help clarify which early life patterns persist. Longer follow up can also show how often microbiomes recover on their own and when they do not.

Bifidobacterium and infant health

Interest in probiotics for babies is high, yet not all contexts are the same. In 2023, the FDA issued a safety advisory warning against probiotic products given to hospitalized preterm infants after a death from probiotic associated sepsis.

That advisory focuses on preterm infants in hospital settings and on unapproved products marketed with disease claims. It does not address healthy term infants in the community, where evidence is still being built one study at a time.

The new findings point to a simple takeaway for early life research. Timing, species identity, and the milk sugar niche work together to support a microbial community that trains the immune system rather than confusing it.

This work also suggests that protecting early life microbial exposures can be part of a broader public health conversation. Nutrition, delivery practices, and careful antibiotic stewardship are all pieces of the same puzzle.

The study is published in Communications Biology.

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