“Many babies born today, even under otherwise healthy conditions, are starting life with a microbiome that is fundamentally different from what human biology evolved to expect,” she told NutraIngredients.
“This microbial gap is now linked to higher risks of allergies, immune-related conditions and other health challenges, making early microbiome restoration a central challenge—and opportunity—of modern infant care.”
Culler will be speaking during NutraIngredients’ “Matters of the Microbiome” webinar, which will look at the microbiome through different life stages on Jan. 29, 2026, at 4 p.m. CET.
Building foundations
The first 100 postnatal days are the most important period in a child’s development from a microbiome perspective, Culler explained.
“Newborns begin life with only about a dozen microbial species, and over the first three to four years, the microbiome gradually develops to resemble that of an adult,” she said. “This early window is when the gut microbiome plays a critical role in imprinting and educating the immune system, with the first 100 days being especially influential for long-term health.”
In the first three years of life, the microbiome exists in a highly dynamic state, developing from roughly a dozen microbial species at birth to the hundreds of microbes typically found in a healthy adult, Culler said.
The earliest phase is focused on initial colonization and the growth of the right microbes, which plays a central role in imprinting and educating the immune system, and as children move into toddlerhood, the focus shifts toward building immune resilience.
However, while the microbiome continues to develop, it also remains vulnerable, meaning that disruptions—such as antibiotic exposure or even dietary changes during food introduction—can alter its trajectory. During this period, both the microbiome ecosystem and the immune system are developing in parallel, and the robustness of each is closely linked.
Infant microbiome research
Existing research increasingly shows that early-life disruptions in the gut microbiome actively shape long-term health outcomes, Culler explained, referencing the recent My Baby Biome study that found that across U.S. infants, those with low or no Bifidobacterium were three to four times more likely to develop atopic conditions such as food allergies, eczema and asthma later in childhood.
The study also found that infants lacking Bifidobacterium carried higher levels of antimicrobial resistance genes, potential pathogens, toxins and virulence factors, while infants with Bifidobacterium-rich microbiomes showed significantly healthier profiles.
Furthermore, the researchers found that 76% of U.S. infants had low levels of Bifidobacterium, 25% had none at all, and 92% lacked Bifidobacterium infantis.
They linked disrupted microbiomes to early allergic disease with 30% of children showing allergies, asthma or eczema by age 2, while infant-adapted Bifidobacterium consistently reduced disease risk across the population.
“One of the most striking findings was the sheer prevalence of Bifidobacterium loss, regardless of delivery mode or feeding method, suggesting a widespread, generational decline of these foundational microbes,” Culler said.
Modern lifestyles drive loss of key gut bacteria in infants
The widespread loss of Bifidobacterium in modern infants is actively driven by the conditions of industrialized life rather than by individual birth or feeding choices alone, Culler said.
“Research shows that infants in groups such as Old Order Mennonites in the United States, hunter-gatherer communities in Africa and people living in remote parts of Europe still carry Bifidobacterium,” she said. “In contrast, its absence is largely a phenomenon of modern infancy.”
This loss reflects cumulative pressures of modernization, including reduced dietary diversity, high rates of antibiotic exposure (which has the most profound impact), increased use of C-section delivery and early formula supplementation. Together, these factors disrupt the natural microbial transfer that once reliably established Bifidobacterium as a keystone member of the infant gut microbiome, Culler added.
Proactive microbiome restoration in babies
Culler suggests that the solution to the modern infant microbiome crisis is to intentionally restore missing, infant-specific Bifidobacterium strains during the first 100 days of life, when the immune system and microbiome are being programmed together. Because modern environments no longer reliably transfer these microbes—even to vaginally delivered, breastfed babies—she says restoration must become proactive, not assumed.
Crucially, she noted that solutions must use infant-adapted, contemporary strains such as Bifidobacterium infantis to suit the evolved infant microbiome.
“This distinction is especially important because the strains introduced need to be highly efficient at consuming human milk oligosaccharides (HMOs), and what we’ve found is that strains isolated recently look genetically very different from strains isolated decades ago,” she said. “They have a distinct genetic footprint, and many of the older strains no longer appear to exist in the current population.”
Looking ahead, Culler sees microbiome support as becoming the standard of care from birth, with clinicians educated, parents informed, and the necessarily bacterial strains built into supplements, formulas or early foods so that every child can start life with the microbes human biology expects.
