Best Beginnings Episode 24: Dr. Stephanie Culler on the garden inside every baby's gut

Inside every newborn baby, something invisible is under construction.

It begins the moment they enter the world. Whether through a birth canal or an operating theatre, the first microbes to colonise a newborn's gut start shaping who they will become: how their immune system learns to work, how it distinguishes friend from foe, how it calibrates its response to the allergens, infections and inflammation it will face for the rest of a human life. Most parents never hear about this. In part because, for most of history, science could not see it. In part because what it reveals about the modern world is not comfortable.

Nine in ten babies born in the United States today are missing one or more of the key bacterial species they need for this process to go properly. That is the headline finding of the My Baby Biome study, one of the largest examinations of the infant gut microbiome ever conducted, led by Dr. Stephanie Culler, co-founder and CEO of Persephone Bioscience. Stephanie came to this work through an unexpected path. She had spent years in cancer research, studying how to fix the gut microbiomes of adult patients so they could respond better to treatment. When a colleague in paediatric science asked why she wasn't doing the same for babies, she hadn't even known there was a problem.

What she found when she looked changed the direction of her career entirely.

What the clean world took away

The causes behind the 90% finding are not a mystery. They are, in almost every case, the achievements of modern medicine and modern life. Antibiotics that prevent infections. C-section births that save lives in complicated deliveries. Infant formula that keeps babies nourished when breastfeeding is not possible. A food system that prioritises convenience and shelf life over fibre.

None of these things was chosen carelessly. All of them have had consequences. Babies born by C-section miss the exposure to the birth canal that seeds their first bacterial communities. Antibiotics administered during surgical delivery alter the microbial landscape from day one. Formula, for the most part, lacks the specific prebiotics in breast milk that the most important bacteria need to thrive. The result, repeated across millions of births, is a generation of babies whose gut ecosystems are different from those of any generation before them.

The garden and its gardeners

Stephanie describes what is happening in the infant gut through a metaphor that is both accurate and memorable. The bacteria babies most need, a group called Bifidobacterium, are what she calls keystone species: the foundation members of the ecosystem. Without them, the ecosystem does not simply struggle. It collapses. Other organisms, including potential pathogens, move in. The garden, left without its gardeners, is taken over by weeds.

Bifidobacterium do something that no other gut bacteria quite manage. They emit specific signals that tell the developing immune system how to behave: to tolerate what it should tolerate, to attack what it should attack, to reduce the inflammation that, unchecked, leads to the allergic and autoimmune conditions now affecting so many young children. In the My Baby Biome study, children with low levels of these bacteria by age two were three to four times more likely to develop what clinicians call atopic conditions: food allergies, eczema, and asthma.

What breast milk cannot do

One of the most important things Stephanie's research has found is also one of the most surprising: breastfeeding alone does not protect against this. The belief that breast milk solves everything is, she says, partially correct, and partially a myth that is keeping families in the dark.

Breast milk contains the right prebiotics, the specific compounds that Bifidobacterium need to thrive. But the bacteria themselves are not in the milk. They live in the gut. They are highly oxygen-sensitive organisms that must be present in the gut already to benefit from what breast milk offers. In a baby who is already missing them, the breast milk prebiotics end up feeding whatever else is there instead, potentially including bacteria that should not be dominant at all.

Virtually every baby today shows some level of deficiency, Stephanie says, regardless of how they were born or how they were fed. This is not a story about individual choices. It is a story about what the modern world has done to the biological inheritance every baby used to receive.

The window still open

The news, for all its weight, is not without hope. The infant microbiome is highly plastic during the first thousand days of life. It begins at birth with a handful of microbial species and expands rapidly over the following years. Interventions at any point in that window can make a real difference. Stephanie's clinical trial, the Artemis study, used a synbiotic, the missing Bifidobacterium combined with the prebiotic from breast milk, and found that it colonised the gut rapidly and held. Parents in the trial reported improvements in sleep, mood, appetite and colic symptoms in their children.

Diet matters too, and Stephanie is direct about what that means in practice: fibre, fermented foods, diversity, and getting children outside and in contact with nature as much as possible. The gut ecosystem is not only shaped by what is eaten but by the microbial richness of the surrounding environment. The hygiene hypothesis, she notes, is not just a theory. The cleaner the world a baby inhabits, the fewer the microbes available to colonise them from it.

The policy question she raises is one that runs underneath much of this: how should regulatory systems classify a product that simply restores what a baby should have had from birth? Not a drug, but not quite a supplement either. The middle ground, she argues, matters enormously, both for the speed at which these solutions can reach families, and for the children who cannot afford to wait for clinical trial timelines to catch up with what the science already shows.

Inside every baby, something invisible is still under construction, even now. What Stephanie Culler's research offers is not a reason for guilt. It is a clearer picture of what has changed, and why it matters that we look at it.