Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome

Anna Samarra, Alejandro J. Alcañiz, Cecilia Martínez-Costa, Alberto Marina, Iñaki Comas, Nicola Segata, Narciso M. Quijada () and Maria Carmen Collado ()
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Anna Samarra: Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)
Alejandro J. Alcañiz: Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)
Cecilia Martínez-Costa: University of Valencia
Alberto Marina: Spain and CIBER de Enfermedades Raras (CIBERER)-ISCIII
Iñaki Comas: and CIBER de Epidemiología y Salud Pública (CIBERESP) -ISCIII
Nicola Segata: University of Trento
Narciso M. Quijada: CSIC - University of Salamanca
Maria Carmen Collado: Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, 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. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.

Date: 2025
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DOI: 10.1038/s41467-025-61154-w

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