Summary: A Brazilian study of 728 infants found that ultra-processed foods can harm gut microbiota diversity, with stronger effects in children who were not breastfed. Breastfed infants had higher levels of beneficial Bifidobacterium, while non-breastfed children consuming processed products showed elevated levels of bacteria linked to obesity and gastrointestinal issues.
The study also found that breastfeeding can help buffer the harmful effects of ultra-processed foods on gut health. These findings raise concerns as over 80% of infants in the study consumed ultra-processed products before age two, despite WHO guidelines.
Key Facts:
- Harmful Bacteria Increase: Non-breastfed infants consuming ultra-processed foods had higher levels of bacteria linked to obesity and gut issues.
- Breastfeeding Offers Protection: Breast milk was associated with higher levels of beneficial Bifidobacterium and reduced harmful effects.
- Widespread Early Exposure: Over 80% of infants consumed ultra-processed foods before age two, despite global health recommendations.
Source: FAPESP
A Brazilian study of 728 children up to one year of age shows that the consumption of ultra-processed foods can negatively affect the diversity and abundance of the intestinal microbiota, with a more pronounced effect in children who are not breastfed.
The results were published in the journal Clinical Nutrition, as part of the “MINA Study – Maternal-Infant in Acre: birth cohort of the Brazilian Western Amazon”, which is following a group of children born between 2015 and 2016 in Cruzeiro do Sul, in the state of Acre, Brazil, with funding from FAPESP.

Children who were still receiving breast milk had higher levels of Bifidobacterium, a genus of bacteria known to be associated with good gut health.
On the other hand, those who were not breastfed and consumed ultra-processed products, such as packaged snacks, filled cookies, chocolate drinks, soft drinks, artificial juices, ice cream, instant noodles, among others, had a higher abundance of genera such as Selimonas and Finegoldia, which are not very abundant in the group of breastfed children and are typically present in individuals with obesity or gastrointestinal diseases in adolescence and adulthood.
“We also found that breastfeeding attenuated the harmful effects of consuming ultra-processed foods on the composition of the gut microbiota.
“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,” says the first author of the study, Lucas Faggiani, who is doing his doctoral studies at the School of Public Health of the University of São Paulo (FSP-USP) and received FAPESP grants during his undergraduate studies.
“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, just when the immune system is forming.
“Although the region is difficult to access, these products can be easily obtained and end up replacing traditional foods and even breastfeeding,” explains Marly Cardoso, professor at FSP-USP and coordinator of the project.
In addition to the sample size, Faggiani adds, the study stands out for being a population-based cohort in an Amazon region with a high level of social vulnerability, which contributes to the study of variables that are little explored in the literature on this subject.
Long term
The researchers collected samples between 2016 and 2017, when the children taking part in the cohort turned one year old. The samples were collected and stored according to a protocol developed at the Institute of Tropical Medicine (IMT) of the USP School of Medicine, coordinated by Ester Sabino, a professor at the institution.
The anal swabs with the stool samples were stored at low temperatures and sent to São Paulo.
While collecting these samples and data such as the children’s weight and height, the mothers answered a questionnaire that included whether or not they were breastfeeding and the eating habits of the family and the child.
The microbiota samples were sent to a specialized company in South Korea for automated genome sequencing, which is much faster than traditional sequencing. In Brazil, with the data in hand, the researchers performed the analysis using bioinformatics tools.
In addition to the levels associated with Bifidobacterium (abundant in breastfed children and low in weaned children), Selimonas and Finegoldia (high in non-breastfed children and those consuming ultra-processed foods), the researchers also detected a higher occurrence of the Firmicutes genus in the group of children who were no longer breastfed, even in those who did not consume ultra-processed foods.
The genus is a potential marker of an adult microbiota, suggesting early maturity.
Another genus found in abundance in the weaned and ultra-processed consumer group was Blautia. Although some studies have found the same association, there is still no consensus on whether it is beneficial or harmful.
“There’s a lack of robust studies to establish a cause-and-effect relationship between this genus and health outcomes,” comments Faggiani.
“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, when the World Health Organization’s (WHO) recommendation is not to offer these products before the age of two.
“Given these results, we’re continuing to follow these children to monitor possible adverse health outcomes in the long term,” concludes Cardoso.
The work was also supported by FAPESP through a postdoctoral fellowship awarded to Paula de França, co-author of the article.
About this microbiome and diet research news
Author: Heloisa Reinert
Source: FAPESP
Contact: Heloisa Reinert – FAPESP
Image: The image is credited to Neuroscience News
Original Research: Open access.
“Effect of ultra-processed food consumption on the gut microbiota in the first year of life: Findings from the MINA–Brazil birth cohort study” by Lucas Faggiani et al. Clinical Nutrition
Abstract
Effect of ultra-processed food consumption on the gut microbiota in the first year of life: Findings from the MINA–Brazil birth cohort study
Background and aims
The first years of life are fundamental for the establishment of the gut microbiota, with diet being one of the main early exposures.
During this period, the beneficial effect of breastfeeding on modulating the gut microbiota is well known; however, there are important gaps in the literature on the effects of ultra-processed food (UPF) consumption, particularly in longitudinal and large sample designs.
Through a prospective birth cohort study, we investigated the effects of UPF consumption on the gut microbiota of children during the first year of life.
Methods
This study included children from the MINA–Brazil birth cohort with gut microbiota data (16S rRNA) available at the 1-year follow-up (n = 728). Data on breastfeeding practices were collected after childbirth and during follow-up visits. Complementary feeding was measured using a semi-structured questionnaire, referring to the day before the interview at the 1-year follow-up.
A combined variable was generated according to breastfeeding practices and UPF consumption and was used as an independent variable in the adjusted median regression models, with alpha diversity parameters as the dependent variable.
Beta diversity was analyzed using PERMANOVA according to Bray–Curtis dissimilarity and Distance-based Redundancy Analysis (db-RDA) adjusted for covariates. Relative abundance was analyzed using ANCOM-BC (corrected by FDR) and MaAsLin2 adjusted for covariates.
Results
Weaned children who consumed UPF showed a significant increase in alpha diversity for all parameters in the median regression models (Observed ASVs: p = 0.005; Shannon index: p = 0.036; Chao index: p = 0.026; Simpson index: p = 0.012) and in beta diversity (PERMANOVA: p = 0.006; db-RDA: p < 0.001) compared to breastfed children who did not consume UPF.
Breastfed children who did not consume UPF had a higher relative abundance of Bifidobacterium than weaned children who consumed UPF (both p < 0.001 for ANCOM-BC and MaAsLin2) and a lower relative abundance of Firmicutes (p < 0.001 for MaAsLin2), Blautia (both p < 0.001 for ANCOM-BC and MaAsLin2), Sellimonas (p = 0.008 for ANCOM-BC) and Finegoldia (p = 0.045 for MaAsLin2) than weaned children who consumed UPF.
Conclusion
These findings suggest that UPF consumption may negatively impact the diversity and abundance of the gut microbiota, with a more pronounced effect in children who have already been weaned.