Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome
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 (...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61154-w |
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| author | Anna Samarra Alejandro J. Alcañiz Cecilia Martínez-Costa Alberto Marina Iñaki Comas Nicola Segata Narciso M. Quijada Maria Carmen Collado |
| author_facet | Anna Samarra Alejandro J. Alcañiz Cecilia Martínez-Costa Alberto Marina Iñaki Comas Nicola Segata Narciso M. Quijada Maria Carmen Collado |
| author_sort | Anna Samarra |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e9afdec0872848c19a299779f711b8e5 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-e9afdec0872848c19a299779f711b8e52025-08-20T03:37:37ZengNature PortfolioNature Communications2041-17232025-07-0116111410.1038/s41467-025-61154-wBreastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistomeAnna Samarra0Alejandro J. Alcañiz1Cecilia Martínez-Costa2Alberto Marina3Iñaki Comas4Nicola Segata5Narciso M. Quijada6Maria Carmen Collado7Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)Department of Pediatrics, School of Medicine, University of ValenciaBiomedicine Institute of Valencia- National Research Council (IBV-CSIC), Valencia, Spain and CIBER de Enfermedades Raras (CIBERER)-ISCIIIBiomedicine Institute of Valencia-National Research Council (IBV-CSIC), Valencia, and CIBER de Epidemiología y Salud Pública (CIBERESP) -ISCIIIDepartment Cellular, Computational and Integrative Biology (CIBIO)-, University of TrentoInstitute of Functional Biology and Genomics (IBFG), CSIC - University of SalamancaDepartment of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC)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.https://doi.org/10.1038/s41467-025-61154-w |
| spellingShingle | Anna Samarra Alejandro J. Alcañiz Cecilia Martínez-Costa Alberto Marina Iñaki Comas Nicola Segata Narciso M. Quijada Maria Carmen Collado Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome Nature Communications |
| title | Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome |
| title_full | Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome |
| title_fullStr | Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome |
| title_full_unstemmed | Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome |
| title_short | Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome |
| title_sort | breastfeeding and early bifidobacterium driven microbial colonization shape the infant gut resistome |
| url | https://doi.org/10.1038/s41467-025-61154-w |
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