Probiotics Can Restore a Healthy Gut Microbiome in Breastfed Infants, New Study Shows
Scientists have been paying closer attention to the infant gut microbiome over the past decade, and what they are finding is both fascinating and concerning. In many high-resource regions such as the United States and Europe, a once-dominant and highly beneficial gut bacterium called Bifidobacterium infantis has been steadily disappearing from the guts of babies. A new study published in the journal mSphere provides encouraging evidence that this loss may not be permanent. According to the research, supplementing exclusively breastfed infants with a specific probiotic strain, B. infantis EVC001, can successfully restore beneficial gut bacteria even months after birth.
The study, known as the REMEDI study, focused on infants between 2 and 4 months of age, a period when the gut microbiome is already becoming more established and potentially less flexible. Despite this, researchers found that B. infantis was able to colonize the gut effectively, challenging the long-held idea that microbiome restoration must happen immediately after birth.
At the center of this research is the growing realization that early-life gut bacteria play a critical role in shaping digestive health, immune development, and long-term wellbeing. The decline of B. infantis in modern infants has raised concerns among microbiologists and pediatric researchers, making the findings of this study especially significant.
Why Bifidobacterium infantis Is So Important
Bifidobacterium infantis is not just another probiotic. It is uniquely adapted to the infant gut, particularly in babies who are fed human milk. Breast milk contains complex carbohydrates known as human milk oligosaccharides, or HMOs. These sugars are indigestible by infants themselves, but they serve as a rich food source for certain gut bacteria.
What makes B. infantis special is its ability to efficiently break down and metabolize HMOs. This gives it a strong advantage over other microbes in the infant gut, allowing it to thrive, persist, and shape the overall microbial environment. When B. infantis is present in high numbers, it helps create an acidic gut environment that discourages the growth of potentially harmful bacteria.
In contrast, many commonly marketed probiotics do not have this ability. They may pass through the digestive system temporarily without truly colonizing or providing long-lasting benefits. This distinction is central to why researchers are so interested in restoring B. infantis rather than simply adding any probiotic strain.
The Disappearance of a Once-Dominant Infant Microbe
Historically, B. infantis was a dominant member of the gut microbiome in breastfed infants worldwide. However, studies over recent years have shown that it is now rare or entirely absent in many infants living in high-income countries. Researchers believe several modern factors may be contributing to this shift.
These include increased antibiotic use, higher rates of cesarean deliveries, reduced exposure to maternal microbes during birth, and changes in infant feeding practices. While these advances have saved countless lives, they may also be unintentionally altering how infant gut ecosystems develop.
The loss of B. infantis has been linked to imbalanced gut microbiomes, higher levels of intestinal inflammation, and changes in how the immune system is trained during early life. This makes restoring the bacterium an important goal for infant health research.
Inside the REMEDI Study Design
The REMEDI study was designed to test whether supplementing older, exclusively breastfed infants with B. infantis could recreate the benefits previously observed in newborns. Earlier studies had shown strong effects when supplementation began immediately after birth, but it was unclear whether similar results could be achieved later.
Researchers enrolled exclusively breastfed infants between 2 and 4 months old and divided them into several groups. These groups received high, medium, or low doses of the B. infantis EVC001 probiotic, while a separate group received a placebo. Importantly, the lower doses tested in the study reflect amounts that are already commercially available, making the findings more relevant to real-world use.
To track changes in the gut microbiome, researchers collected stool samples before supplementation, during the intervention, and after supplementation had ended. These samples were carefully analyzed to determine how the microbial communities responded over time.
Key Findings and What They Mean
The results were striking. Infants who received B. infantis showed a significant increase in beneficial gut bacteria, regardless of whether they were given high, medium, or low doses. Even more notably, B. infantis remained present in the gut after supplementation stopped, indicating true colonization rather than temporary passage.
This finding sets B. infantis apart from many other probiotics, which often disappear once supplementation ends. The persistence observed in this study is likely due to the bacterium’s ability to feed on HMOs in breast milk, giving it a natural and sustainable food source.
Another important takeaway is that restoration was possible beyond the newborn stage. The infant gut microbiome, while more established at 2 to 4 months, was still receptive to meaningful and lasting change. This opens the door for interventions in infants who may have missed early supplementation opportunities.
Dose Flexibility and Real-World Relevance
One of the most practical findings from the REMEDI study is that all tested doses were effective. This suggests that families and healthcare providers may have flexibility when it comes to timing, access, and dosage. It also makes large-scale implementation more feasible, especially in settings where high-dose formulations may not be available.
The ability to achieve lasting benefits with short-term supplementation is particularly encouraging. It suggests that even brief interventions, when paired with breastfeeding, could have long-term impacts on gut health.
How the Infant Gut Microbiome Shapes Health
Early-life gut bacteria do much more than help digest food. They play a critical role in training the immune system, helping it distinguish between harmless substances and potential threats. A well-balanced microbiome in infancy has been associated with lower risks of allergies, infections, and inflammatory conditions later in life.
Bifidobacterium-rich gut communities are also linked to reduced intestinal inflammation and improved gut barrier function. By restoring B. infantis, researchers hope to support healthier developmental trajectories during a period when the body is especially sensitive to environmental cues.
How This Study Fits Into the Bigger Picture
The REMEDI study builds on earlier research showing that B. infantis supplementation in newborns can lead to long-lasting colonization and measurable health benefits throughout infancy. What makes this study different is its focus on older infants, demonstrating that the window for microbiome restoration is wider than previously thought.
Together, these findings suggest that the modern loss of B. infantis is not an irreversible consequence of contemporary living. With the right approach, it may be possible to reintroduce and sustain beneficial microbes that humans coevolved with for thousands of years.
As research into the infant microbiome continues, studies like this provide valuable insights into how science can work alongside natural processes like breastfeeding to support infant health in a changing world.
Research paper: https://journals.asm.org/doi/10.1128/msphere.00518-25
