Soiled diapers are more than just an unpleasant part of parenting—they can provide insights into a baby’s gut microbiome and their potential health trajectory.

Researchers have recently unveiled the first two-year findings from the My Baby Biome study, a comprehensive seven-year investigation into the infant microbiomes across the United States. Published in Communications Biology in June, the results reveal a troubling scenario: over 75% of the infants studied exhibited a lack of essential gut bacteria linked to a healthy microbiome. Virtually all the babies showed some form of microbial deficiency, which significantly heightened their chances of developing allergies, asthma, or eczema in the future, the study notes.

“We found that three-quarters of infants are more susceptible to developing atopic conditions due to their microbiome composition,” stated Stephanie Culler, the study’s lead author. Culler is the CEO of Persephone Biosciences, a biotech firm based in San Diego, California, which oversees the My Baby Biome project and provided funding for this research.

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A healthy microbiome in infants is vital for immune system development, and an imbalanced microbiome increases the likelihood of autoimmune disorders like asthma and type 1 diabetes. However, the lack of extensive data on U.S. infant microbiomes has previously limited research efforts. To gather data, Culler and her team utilized social media and word-of-mouth to recruit 412 infants from 48 states, reflecting the demographic diversity of the U.S.

The research team analyzed bacterial DNA from stool samples collected from these infants, and for 150 of them, additional samples were obtained when the children turned one. They also examined other molecules in these samples to gain insights into the microbial activities within the children’s guts. Additionally, about half of the families provided health updates when their children reached the age of two.

The findings showed that only 24 percent of the infants had a microbiome considered healthy. The others lacked sufficient levels of Bifidobacterium, a key bacteria group associated with a reduced risk of various noncommunicable diseases. A quarter of the infants had no detectable levels of Bifidobacterium at all. In those lacking Bifidobacterium, higher levels of harmful microorganisms, bacteria with antimicrobial resistance genes, and pathogenic molecules were found. At two years old, these children were three times more likely to develop allergies, asthma, or eczema compared to those with a healthy microbiome.

The study did not identify any demographic or socioeconomic factors that might explain the microbiome deficiencies or the subsequent development of health conditions, suggesting that any baby could be affected, according to Culler. The researchers did note, however, that breastfeeding was linked to higher levels of Bifidobacterium in children born through vaginal delivery. Yet, even this combination of natural birth and breastfeeding did not guarantee a healthy microbiome, as many of these children still developed chronic diseases.

Similar concerns have been raised by researchers in other nations. For instance, a study in the U.K. last year found low levels of Bifidobacterium species in about one-third of 1,288 infants examined, with their gut microbiomes instead dominated by Enterococcus faecalis, a species linked to antibiotic resistance and adverse health impacts.

The recent U.S. study corroborates earlier research that highlighted the critical role of Bifidobacterium in early childhood health, noted Willem de Vos, an emeritus professor of human microbiomics at the University of Helsinki, who was not involved in the study. De Vos’s own 2024 study of 1,000 Finnish infants also indicated that Bifidobacterium species are crucial for gut flora development and are associated with positive health outcomes for at least five years. However, the new U.S. research provides a nuanced view, revealing that specific species like Bifidobacterium breve can reduce disease risk in two-year-olds, whereas Bifidobacterium longum does not appear to offer the same protective effects. “These findings are both intriguing and significant,” de Vos commented.

Erin Davis, a postdoctoral fellow in pediatric allergy and immunology at the University of Rochester, also not involved in the recent study, remarked that the species-specific impacts on health risks were particularly surprising. “It was unexpected to see how different Bifidobacterium species in infants influenced the relative risk of negative health outcomes,” she noted.

The factors contributing to changes in infants’ gut microbiomes remain unclear. However, comparisons between infant microbiomes in industrialized versus non-industrialized communities, such as the Old Order Mennonites, suggest that aspects of modern life are likely contributors. These include excessive antibiotic use, environmental oversanitization, decreased breastfeeding rates, limited physical contact with other babies, adults, and animals, among others, according to Matthew Olm, an assistant professor of integrative physiology at the University of Colorado Boulder, who was not involved in the study.

“Bifidobacteria thrive on breast milk, and it’s possible that the low breastfeeding rates of the 1970s, when only 20 percent of mothers breastfed, caused a population-level decline that we’re still experiencing,” Olm explained. “Even though over 80 percent of infants are breastfed today, the environmental levels of bifidobacteria might still be insufficient for optimal colonization of these babies.”