The research from the Institute of Agrochemistry and Food Technology in Valencia, Spain, found that birth modes (vaginal vs caesarean) and feeding methods (breastmilk vs formula) also play a key role.
It suggests that breastfeeding can counteract early-life antibiotic exposure and promote Bifidobacterium dominance in the infant gut.
“Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome,” the researchers wrote in Nature Communications. “Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.”
But could Bifidobacterium probiotics also help to reduce antimicrobial resistance?
The crucial role of Bifidobacterium in the infant gut
Bifidobacterium is a keystone of the infant gut microbiome. However, research shows that levels of this key gut bacteria are declining in modern infant populations.
A recent large-scale study from Persephone Biosciences revealed that 76% of U.S. infants are deficient in Bifidobacterium, with 25% having none at all.
“Our data demonstrates that Bifidobacterium have numerous positive effects on infant health, including reduction of risk for chronic disease and suppression of deleterious genes like ARGs,” Stephanie Culler, co-founder and CEO of Persephone Biosciences and an author on that study, told NutraIngredients.
“In our study, a quarter of infants were missing these critical infant Bifidobacterium, putting them at risk. This recent publication by Samarra et al. expands upon our findings that Bifidobacterium suppress ARGs in the infant gut, characterizing the ARGs in depth and demonstrating a critical role for breastmilk.”
With research in this area still fairly limited, Samarra et al. explored the factors that shape the dynamics of the infant gut resistome (the collection of antibiotic resistance genes) and provide strategies to ameliorate the spread of antimicrobial resistance in early life.
Bifidobacterium may help to suppress ARG-carrying bacteria
In this latest study, the researchers analyzed 265 gut metagenomes from stool samples from 66 mother-infant pairs. They identified 208 different antibiotic resistance genes in infants and 134 in the mothers, with 122 ARGs shared among them.
They highlighted that the total load of antibiotic resistance genes significantly decreases during the first year of life, with an infant’s resistome diversity increasing over time to resemble the mother’s.
In addition to the finding that high levels of Bifidobacterium were linked to a lower loads of antimicrobial resistance genes, the researchers also noted that specific species B. longum and B. bifidum were consistently more abundant in high-Bifidobacterium infants across all timepoints, with B. breve more abundant during early infancy and at one year.
Infant with a low abundance of Bifidobacterium tended to be heavily populated with other types of bacteria such as E. coli, Clostridium perfringens, Klebsiella pneumoniae and Staphylococcus aureus.
These types of bacteria are known to carry a significant number of antibiotic resistance genes, supporting the idea that Bifidobacterium may help to suppress ARG-carrying bacteria, reducing the risk of antibiotic resistance.
Could probiotics help to protect infants from antibiotic resistance?
The researchers then analyzed whether babies born vaginally or via caesarean section had differing levels of key gut bacteria. They found that C-section born infants had higher levels of antibiotic resistance genes, as did formula-fed infants.
However, breastfeeding was found to lower the load of antibiotic resistance genes and even mitigate the impact of cesarean-associated antimicrobial exposure.
“We identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition,” they wrote.
While the study itself makes no reference to the potential role of probiotics in preventing antibiotic resistance, Dr. Culler says the results suggest infant pre and probiotics could be a useful tool in babies who are unable to breastfeed.
“Probiotics can help infants by replenishing missing bacteria, specifically those rich in infant Bifidobacterium," she said.
“Importantly, for infants unable to breastfeed, it is not just the probiotics that matter but also the prebiotics, what the bacteria feed on. A product containing both infant Bifidobacterium—such as B. infantis, B. breve and B. longum—and HMOs is ideal for supporting an infant who cannot breastfeed.”
Source: Nature Communications. doi: 10.1038/s41467-025-61154-w. “Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome". Authors: A. Samarra, et al.