The study, published in the journal Gut Microbes and led by digital health company Alba Health, followed 253 Swedish infants over their first 18 months, collecting 744 stool samples, and used deep metagenomic sequencing to analyse gut bacterial composition in detail.
“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,” Nora Cavani, CEO and co-founder of Alba Health, and lead author of the study said of the results.
“What stands out is how many of these infants would never have been identified through routine care. 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.”
Invisible extinction
‘Invisible extinction’, the gradual loss of beneficial microbes, particularly Bifidobacterium, in modern infants, is attributed to several factors of modern lifestyles.
Dr. Willem M de Vos, study co-author and co-founder and CSO of Alba Health, which won NutraIngredients’ Probiota Pioneer competition in 2025, told NI not enough is yet understood about direct causes of the phenomenon. However, he said research suggests factors including antibiotic use, cesarean delivery, shorter periods of breastfeeding, smaller households and more sterile living environments could all contribute to the reduced transfer of microbes from mothers and environment to infants.
Bifidobacterium helps babies digest breast milk and trains the immune system to fight off illness. A 2025 study in the journal Nature linked it to a better response to childhood vaccines, and a 2026 study found that specific strains lowered the risk of developing allergies. Invisible extinction has also been linked to a higher risk of asthma.
The researchers of the new study noted the results are particularly apt as food allergy diagnosis in England has more than doubled between 2008 and 2018, with the steepest rise in children under five. Eczema prevalence among children in high-income countries has also risen over nearly three decades.
Speaking about the new research, de Vos noted: “Studies like this are an important step forward towards understanding which infants are most at risk, and why, while also providing potential solutions.”
Study details
The research team, which also included scientists from Karolinska Institute, Wageningen University and the University of Antwerp, followed the infants during early life and collected stool samples alongside health and lifestyle information. Families submitted samples by post at approximately three-month intervals.
The researchers used deep metagenomic sequencing to analyze the bacterial composition of the samples and identify the genes associated with different microbial communities. They also used independent methods to validate the absence of Bifidobacterium and compared bacterial profiles with factors such as birth mode, hospital stay and reported infant symptoms.
This finding challenged the assumption that breastfeeding and vaginal birth reliably promote the presence of these beneficial bacteria, the researchers noted.
They found no detectable Bifidobacterium in 30% of stool samples. Among the affected infants, 58% were born vaginally, and most infants were breastfed. Cesarean birth was more common among infants whose samples lacked Bifidobacterium than among those with healthy levels (42% compared with 19%).
Longer hospital stays were also more common in the affected group, but neither factor fully explained the absence of the bacteria. In around half of the affected infants, researchers still detected no Bifidobacterium six months later.
De Vos explained that some breastfed infants may not develop detectable levels of Bifidobacterium because their mothers did not transmit HMO-utilizing strains of the bacteria, or because repeated antibiotic use compromised the growth of transmitted strains.
The researchers identified three distinct gut microbiome profiles. The first consisted of infants whose gut bacteria were dominated by Bifidobacterium, which accounted for an average of 76% of their gut microbiome; these infants had the most favorable reported health outcomes.
The second profile featured lower levels of Bifidobacterium and higher levels of bacteria belonging to the group Bacteroidota, and researchers associated this pattern with greater irritability.
The third profile comprised infants with no detectable Bifidobacterium. Other bacteria occupied a greater proportion of their gut microbiomes, including some previously associated with colic or infection risk. These infants cried after feeding significantly more often and showed trends towards excessive crying and blood in the stool.
The researchers also identified differences in the functional potential of the bacterial communities. Samples from infants without detectable Bifidobacterium contained more genes potentially associated with inflammation, whereas samples from infants with healthy levels contained more genes involved in producing anti-inflammatory compounds.
“What’s most striking is the scale and depth of these findings,” de Vos said. “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.”
Why breastfeeding alone may not guarantee beneficial gut bacteria
The study refines the understanding of the relationship between breastfeeding and the development of Bifidobacterium in the infant gut, but it does not overturn the established view that breastfeeding remains the gold standard, de Vos said.
That said, most infants in the study received breast milk, researchers found no differences in breastfeeding practices between infants with and without Bifidobacterium, as roughly half of the infants were exclusively breastfed and the other half received mixed feeding.
“We’re seeing that breast milk provides the fuel, but does not guarantee the presence of the right microbes to use it,” de Vos said.
He noted that while the study did not examine maternal microbiomes or breast milk composition, so they cannot determine whether these have changed over generations, evidence from the UK and US suggests that infants are losing beneficial bacterial strains, potentially reflecting disruptions in mother-to-infant transmission.
Considering the future of infant formula development, de Vos noted that HMOs, prebiotics, probiotics and synbiotics are likely to play an increasingly important role, but that more research is needed.
“What our data suggests is that the response is likely to depend on the baby’s starting point,” de Vos said. “An infant with no detectable Bifidobacterium is in a different position from one with a thriving population, and adding a prebiotic will be less effective if there is nothing to feed.”
He added that the infant nutrition industry should stop assuming that all infants respond uniformly to nutritional interventions.
“Infant products are developed and tested for the average baby, yet nearly a third of the infants in our study lacked the very bacterium many of those products aim to support,” de Vos said. “Trials should record, and ideally stratify by, whether infants have Bifidobacterium at the start.”
He noted that industry may be moving towards a future where infant nutrition products are designed around specific bacterial strains rather than broader probiotic categories
“The evidence increasingly points to differences between species and strains,” de Vos said. “So ‘contains Bifidobacterium’ is now often too blunt a description. Strain-level evidence in infants is still limited, though, and this is an emerging area rather than a settled one.”
He explained that future research should investigate how the absence of Bifidobacterium species influences the colonization of the infant gut by alternative microbial taxa, including pathobionts, and how these changes affect immune development, gut health and long-term health outcomes.
“This requires repeated longitudinal studies with careful analysis of health metadata - these are planned in our follow-up work by exploiting the Swedish registry data,” he told NI.
Source: Gut Microbes; doi: https://doi.org/10.1038/s41564-025-02244-9 “Nationwide cohort study reveals low bifidobacteria and distinct microbiota composition and function in Swedish newborns.” Authors: Cavani, E. et al.
