A new study out of Brazil adds to growing evidence that early nutrition choices can have long-lasting effects on children’s health. Researchers found that infants who consumed ultra-processed foods (UPFs) in their first year of life had significant changes in their gut microbiota—particularly if they were no longer being breastfed.

Published in Clinical Nutrition, the study followed 728 children from birth through their first year as part of the ongoing MINA Study (Maternal-Infant in Acre), a birth cohort based Brazil.

Researchers looked specifically at gut microbiota diversity—a key indicator of immune and digestive system development. Children who were breastfed had higher levels of Bifidobacterium, a beneficial bacteria often associated with better gut and immune health. But for those no longer breastfed and consuming high levels of UPFs—including packaged snacks, soft drinks, chocolate drinks, artificial juices, and instant noodles—the microbial profile shifted.

These children had more Selimonas and Finegoldia, bacteria rarely found in breastfed infants but commonly seen in individuals with obesity and gastrointestinal disorders later in life.

“We also found that breastfeeding attenuated the harmful effects of consuming ultra-processed foods on the composition of the gut microbiota,” said lead author Lucas Faggiani.“The group of children who received breast milk and did not consume ultra-processed products had a more stable microbiota and better health markers, mainly due to the greater abundance of Bifidobacterium.”

Although prior studies have explored the effects of breastfeeding or processed food on gut health, this research is unique due to its scale, regional context, and focus on the first year of life—when the immune system is still developing.

“To date, there hasn’t been a study with so many participants that has analyzed the composition of the intestinal microbiota during the first year of life in relation to the consumption of ultra-processed products,” said co-author, Marly Cardoso. “Although the region is difficult to access, these products can be easily obtained and end up replacing traditional foods and even breastfeeding.”

Data was collected between 2016 and 2017 through stool samples, infant growth assessments, and detailed dietary and breastfeeding surveys. Microbial DNA from the samples was sequenced using advanced genome sequencing technology and analyzed using bioinformatics tools.

In addition to Selimonas and Finegoldia, researchers also found higher levels of Firmicutes in weaned children—even those who did not consume UPFs. This genus is typically more common in adults, suggesting premature microbiota development. Another genus that showed up more frequently in the UPF-fed group was Blautia. Though its role is still debated, its presence adds another layer to the conversation about how diet shapes health from infancy onward.

The team also reported that over 80% of the children studied had consumed ultra-processed foods within their first year of life—despite the World Health Organization’s recommendation to avoid these products before age two.

“We’d noticed that consumption of ultra-processed products occurred in more than 80% of the children taking part in the study in the first year of life,” said Cardoso. “Given these results, we’re continuing to follow these children to monitor possible adverse health outcomes in the long term.”

While more research is needed to determine how gut changes affect later life outcomes, this study reinforces the importance of early nutrition decisions. For parents and caregivers, the takeaway is practical: do not feed your children ultra-processed food (nor should parents should really be feeding themselves that) and supporting breastfeeding could help lay the foundation for better gut—and overall—health in child development to help insure a healthier future

LD Faggiani et al, Effect of ultra-processed food consumption on the gut microbiota in the first year of life: Findings from the MINA–Brazil birth cohort study, Clinical Nutrition (2025). DOI: 10.1016/j.clnu.2025.01.030.