Breast milk not only nourishes the baby, but can also decisively influence the configuration of their gut microbiota during the first months of life. An international team led by the Spanish National Research Council (CSIC) has discovered that exclusive breastfeeding is associated with a lower presence of antibiotic resistance genes in the gut of infants, a finding that opens new perspectives in the fight against one of the greatest health challenges of the 21st century.
The study, published in the journal Cell Reports Medicine , analyzed the so-called gut resistome, the set of genes that allow bacteria to resist antimicrobials. Researchers identified that human milk oligosaccharides (HMOs), complex molecules that infants do not directly digest, play a fundamental role in this process. These sugars, which constitute the third most abundant component of breast milk , act as a selective food source for beneficial bacteria of the genus Bifidobacterium , helping to create an intestinal ecosystem in which microorganisms carrying resistance genes have more difficulty proliferating.
What is the resistome and why does it matter in childhood?
Antibiotic resistance has become a global threat that, according to the World Health Organization, could cause millions of deaths in the coming decades if no action is taken. Although traditionally associated with the overuse of these drugs, resistance genes can become established in gut bacteria from the earliest stages of life, even when the baby has not been directly exposed to medication. Therefore, the first few months represent a critical window for the formation of the gut microbiota and, consequently, the resistome.
The study was conducted using fecal samples from 57 one-month-old infants belonging to the MAMI cohort, a project in the Valencian Community that follows mothers and children from birth to six years of age. The results were subsequently validated with an independent cohort from the Netherlands, LLNEXT, which included data from 199 infants. This double verification strengthens the robustness of the conclusions, as similar patterns have been observed in different populations.
Exclusive breastfeeding as a natural shield
Researchers observed that exclusively breastfed infants exhibited a lower abundance and diversity of antimicrobial resistance genes compared to those fed other types of nutrition. This relationship persisted even after adjusting for other factors such as delivery method, suggesting that breastfeeding has an independent protective effect . According to M. Carmen Collado, a researcher at the Spanish National Research Council (CSIC) at the Institute of Agrochemistry and Food Technology (IATA), “promoting breastfeeding appears to be an effective strategy for reducing antimicrobial resistance genes present in intestinal bacterial communities during a critical period.”
Another important finding is that the type of delivery also influences the resistome. Babies born via cesarean section showed differences in the diversity of resistance genes compared to those born vaginally. However, breastfeeding appeared to mitigate some of this impact, further underscoring the importance of promoting breastfeeding in all cases, especially when a cesarean section is unavoidable.
The role of oligosaccharides and maternal genetics
One of the most novel contributions of the study is the identification of a direct link between HMOs and resistome composition. These molecules, which vary in quantity and type among mothers, are partly determined by the so-called secretory state, associated with the FUT2 gene. Mothers with this genetic profile produce milk with higher concentrations of specific oligosaccharides such as 2′-fucosylactose (2′FL) and 6′-sialylacose (6′SL), which were associated with a lower presence of resistance genes in the infant's gut.
Infants breastfed by secretory mothers showed a greater presence of beneficial bacteria of the genus Bifidobacterium , capable of using these sugars as an energy source. As Anna Samarra, a researcher trained at the IATA-CSIC and currently at the University of California, San Diego, explains, “the first months of life represent a critical window in which the gut microbiota is forming and in which different environmental factors, such as the type of delivery or feeding, can leave a lasting mark.” This finding highlights that maternal genetics influences the quality of the milk and, consequently, the future health of the infant.
A step forward in the fight against antimicrobial resistance
The finding does not mean that breast milk completely eliminates antibiotic resistance, but it does provide valuable scientific evidence. Understanding how the bioactive components of human milk modulate the gut ecosystem could help in the future to develop preventative strategies against antimicrobial resistance, which causes the death of thousands of people worldwide each year. The authors of the study, which also involved researchers from the University of Valencia, the University Clinical Hospital of Valencia, the University of Trento, the University of Chile, the University of Groningen, and the University of California, San Diego, caution that larger longitudinal studies are still needed to fully understand the mechanisms involved.
Lars Bode, principal investigator at the Human Milk Institute at the University of California, San Diego, emphasizes that “maternal genetics, through secretory status, determines the milk glycan profile, which influences the early formation of the infant’s gut resistome.” These results reinforce the idea that breast milk is not just food, but an active biological agent capable of beneficially shaping the newborn’s microbiome.
The scientific community considers this type of research essential for understanding the complexity of human milk and its long-term health impact. Antibiotic resistance is a problem that knows no borders and requires innovative solutions. This discovery, coordinated from Spain with international collaboration, positions breastfeeding as a natural and accessible tool to help prevent this phenomenon from the first days of life.
