“Invisible extinction”: A third of infants lack Bifidobacterium, including breastfed babies

A study has found that one in three infants lacks Bifidobacterium despite being vaginally born and breastfed — challenging the belief that these factors ensure this bacterium’s presence. This bacterium is associated with a lower risk of allergies and improved protection against other germs. 

Out of 253 babies in Sweden, 30% had no detectable Bifidobacterium, according to researchers from Alba Health, Karolinska Institute (Sweden), Wageningen University (the Netherlands), and the University of Antwerp (Belgium).

“What’s most striking is the scale and depth of these findings,” says Willem de Vos, microbiologist and co-founder at Alba Health, a provider of at-home gut microbiome tests.

“We’ve long known that Bifidobacterium plays a defining role in shaping an infant’s immune and likely metabolic system. But seeing it absent in almost a third of a national cohort, including babies born vaginally and breastfed who we would typically expect to be best protected, is a wake-up call.”

The PREVENT study followed these infants over their first 18 months and analyzed gut bacterial composition in stool samples using deep metagenomic sequencing.

“The depth of this study is what makes it compelling. Confirming the absence of Bifidobacterium across independent methods gives real confidence in a finding that is easy to dismiss as an artifact,” comments Dr. Majdi Osman, MPH, physician-scientist at the University of Cambridge (UK) and chief medical officer at OpenBiome, a nonprofit microbiome research organization.

“It exposes a gap in how we assess infant health in the first months of life and should motivate new guidelines, interventions, and above all, clear, actionable guidance for parents.”

Pressure on global health and economy

The researchers warn that beneficial bacteria are declining — a trend referred to as an “invisible extinction” — exacerbated by antibiotics, formula feeding, and increasingly sterile living environments.

“This study gives us one of the clearest pictures yet of just how widespread the loss of key gut bacteria has become, even among infants who are breastfed and born at term. What stands out is how many of these infants would never have been identified through routine care,” says Nora Cavani, CEO and co-founder of Alba Health.

“We’ve long talked about an ‘invisible extinction’ of beneficial bacteria across modern populations — this data shows how early that story may begin and how large the scale of the problem really is. The priority now is understanding what this means for these children in the long term and making sure parents and health care providers have the tools to act on it before symptoms and conditions take hold.”

In the UK, childhood allergy rates have tripled over the past three decades, leading to 40% of children being diagnosed with an allergic condition, the team points out. 

Additionally, the World Economic Forum estimates that the loss of gut bacteria will increase chronic diseases, costing the global economy US$47 trillion by 2030.

Based on these trends, the study calls for reevaluating infant health assessments and interventions addressing gut microbiome health early in life.

“Addressing the gut microbiome in the first months of life is still not part of routine care, yet there’s growing evidence that it may carry information just as relevant to a child’s long-term health as the checks typically already carried out,” comments De Vos. 

“Studies like this are an important step forward toward understanding which infants are most at risk and why, while also providing potential solutions.”

Three types of babies

The Gut Microbes study pinpoints three gut health patterns among the infants, each linked to different outcomes.

Thriving guts were dominated by Bifidobacterium, up to 76% of gut bacteria on average, having the best health outcomes.

The second group had guts that were low in Bifidobacterium and high in Bacteroidota, which is linked to irritability.

Lastly, guts lacking Bifidobacterium had higher levels of bacteria associated with infection risk. Babies with this characteristic tended to cry significantly more often after feeding, the researchers explain, adding that they also cried excessively and had blood in their stools more often.

Babies without Bifidobacterium had other bacteria fill the gap, such as a type linked to colic symptoms in studies of European and North American infants, the researchers note. They underscore that gut health depends on the overall bacterial balance, not just the presence of one species.