Exclusive breastfeeding during the first month of life reduces the presence of drug-resistant microorganisms, according to a study published in Nature Communications. The work led by the Institute of Agrochemistry and Food Technology (IATA), located in the UV Science Park, analyzed samples of babies and mothers from the Valencian Community, revealing the importance of breastfeeding for short- and long-term health
An international study led by the Institute of Agrochemistry and Food Technology (IATA), located in the scientific-academic area of the UV Science Park (PCUV), shows that exclusive breastfeeding during the first month of life has a protective effect against the emergence of bacteria carrying antibiotic resistance genes, one of the main public health problems. This is due to the impact that breastfeeding has on the composition of the infant intestinal microbiota, the set of microorganisms inhabiting the intestine, and the presence of bifidobacteria, associated with a lower load of this type of genes and other pathogenic microorganisms. The results are published in Nature Communications.
The research is led by the MAINBIOTICS laboratory of the IATA-CSIC group of lactic and probiotic bacteria, in collaboration with the Institute of Functional Biology and Genomics (IBFG, CSIC-University of Salamanca), the Valencia Biomedicine Institute (IBV-CSIC) and other entities in Spain and Italy. The data come from faecal samples collected during the first year of life of 66 babies and their mothers from the 'MAMI cohort', a population group in the Valencian Community who follow up from birth to six years of age to study how the childhood microbiota is formed and evolves, led by CSIC and the Pediatrics Service of the University Clinical Hospital of Valencia.
"A high presence of bifidobacteria in the child’s intestine is associated with a set of microbiome genes that confer antimicrobial resistance, which we call resistome, less diverse and with lower load of resistance genes. On the other hand, a lower abundance of these bacteria is associated with a more diverse microbiome, and with the presence of potentially pathogenic microorganisms that have a greater load of resistance genes", Ma Carmen Collado, IATA researcher leading the work
The results show that lactation favors the presence of bacteria of the genus Bifidobacterium, which play a key role in protecting the child’s intestine against the appearance of bacteria with genes related to antibiotic resistance. "A high presence of bifidobacteria in the child’s intestine is associated with a set of microbiome genes that confer resistance to antimicrobials, what we call resistome, less diverse and with less load of resistance genes," says Ma Carmen Collado, researcher at IATA-CSIC that leads the work. "On the other hand, a lower abundance of these bacteria is associated with a more diverse microbiome, and with the presence of potentially pathogenic microorganisms that have a higher load of resistance genes," she warns.
Shield against the impact of cesarean section on microbiota
Another important finding of the study is that the growth of bifidobacteria associated with exclusive breastfeeding could mitigate adverse effects of cesarean delivery, that interferes with the natural transfer of beneficial bacteria during delivery and involves early exposure to antibiotics. This can alter microbial colonization of the intestine and promote the appearance of treatment-resistant bacteria. The team found that babies born by cesarean section and exclusively breastfed during the first month had a much lower load of AMR-associated genes than those who were not breastfed, and similar to vaginal births.
On the other hand, discontinuing breastfeeding before six months of age, the minimum period recommended by the WHO to maintain this practice, was associated with a sustained increase in antibiotic resistance genes, which could make it difficult to treat future infections. "Our results show that exclusive breastfeeding not only benefits the baby today, but also has lasting long-term implications for their intestinal health," explains Anna Samarra, IATA-CSIC pre-doctoral researcher in the MAINBIOTICS group and first author.
Early prevention from lactation
"These findings provide scientific evidence on the importance of breastfeeding in the health of the lactating baby in the short and long term," says Cecilia Martínez Costa, head of the Paediatric Service at the University Clinical Hospital of Valencia and co-author of the study. "In addition, these strategies will also contribute to reducing antibiotic resistance, one of the major public health challenges facing our society," she concludes. Thus, encouraging breastfeeding not only protects the health of the baby, but can also help reduce the transmission of resistant genes in the population, the researchers say.
The research team has used metagenomic analyses, which study both bacterial composition and genes related to antibiotic resistance, with clinical information and infant growth data. "This work combines for the first time clinical, anthropometric and metagenomic data in a well-characterized cohort to study how child resistome is configured in real life conditions. The integration of all these layers of information has allowed us to understand more precisely the role of breastfeeding in the early modulation of the microbiome," describes Narciso M. Quijada, a researcher at the IBFG and one of the main authors of the study.
"Our results show that exclusive breastfeeding not only benefits the baby today, but also has lasting long-term implications for their intestinal health," said Anna Samarra, MAINBIOTICS pre-doctoral researcher at IATA and first author
This research has been made possible thanks to European, national and within the framework of NeoHealth and Microglocal projects under the call for projects Prometeo- Research Groups of Excellence of the Generalitat Valenciana. These projects aim to study the spread of antibiotic resistance in the mother-child environment, and have the collaboration of CSIC researchers Iñaki Comas and Alberto Marina, both at the Valencia Institute of Biomedicine (IBV-CSIC).
Don’t miss the interview with María Carmen Collado in our section of Europark
Source: Delegation CSIC Comunitat Valenciana
Samarra, A. et al. Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome. Nature Communications 16, 6099 (2025). https://doi.org/10.1038/s41467-025-61154-w
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