Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome
Open accessAbstract
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.
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Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts.
“Bifidobacterium, and Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts56–59.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [59]
The Results section reports significantly lower ARG loads in infants with high Bifidobacterium abundance, and the Discussion suggests Bifidobacterium may suppress AMR-carrying taxa. The paper does not establish that Bifidobacterium supplementation lowers ARG abundance or demonstrate competitive exclusion as the mechanism. (LLM, conf=0.87)
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- Authors
- Samarra, A., Alcañiz, A. J., Martínez-Costa, C., Marina, A., Comas, I., Segata, N., Quijada, N. M., & Collado, M. C.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- University of Trento (IT)
- Universidad de Salamanca (ES)
- Corresponding author
- Quijada, Narciso M.
- ORCID
- Venue
- Nature Communications
- Published
- 2025-07-02
- Volume
- 16
- Issue
- 1
- Pages
- 6099-6099
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC12222458
- OpenAlex
- W4411947467
- Cited by
- 32
- References
- 74
- Citations by year
- 2026: 27 · 2025: 5
- FWCI
- 9.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Iris (University of Trento) (submittedVersion, cc-by-nc-nd)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
- Funders
- American Concrete Institute Foundation
- European Commission (MAMI-639226 project, 639226, 13039/501100011033, 501100011033, H2020, 101094099)
- Generalitat Valenciana (501100011033, PROMETEO2020/12, CIPROM2023/030, ACIF/2021)
- Ministerio de Ciencia e Innovación (MCIN/AEI/10, .13039/501100011033, CEX 2021-001189-S, / AEI/10, PID2022-139475OB-I00, 501100011033, PID2022)
- Horizon 2020 Framework Programme
- HORIZON EUROPE Framework Programme (101094099)
- Agencia Estatal de Investigación (501100011033, 13039, .13039/501100011033, CEX2021-001189 -S, H2020, AEI/10)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- breastfeeding, Bifidobacterium, infant gut microbiota, antimicrobial resistance genes, resistome, cesarean section, antibiotic exposure, exclusive breastfeeding, breastfeeding cessation, perinatal factors, mother-infant dyads, early-life microbial colonization
- MeSH terms
- Gastrointestinal Microbiome, Adult, Anti-Bacterial Agents, Bifidobacterium, Breast Feeding, Cesarean Section, Feces, Female, Humans, Infant, Infant, Newborn, Male, Milk, Human, Drug Resistance, Bacterial, Metagenome
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