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

Author

Listed:
  • 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
    INCLIVA)

  • 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))

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.

Suggested Citation

  • Anna Samarra & Alejandro J. Alcañiz & Cecilia Martínez-Costa & Alberto Marina & Iñaki Comas & Nicola Segata & Narciso M. Quijada & Maria Carmen Collado, 2025. "Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61154-w
    DOI: 10.1038/s41467-025-61154-w
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    1. Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Je, 2021. "Multivariable association discovery in population-scale meta-omics studies," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-27, November.
    2. Kuhn, Max, 2008. "Building Predictive Models in R Using the caret Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 28(i05).
    3. Yan Shao & Samuel C. Forster & Evdokia Tsaliki & Kevin Vervier & Angela Strang & Nandi Simpson & Nitin Kumar & Mark D. Stares & Alison Rodger & Peter Brocklehurst & Nigel Field & Trevor D. Lawley, 2019. "Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth," Nature, Nature, vol. 574(7776), pages 117-121, October.
    4. Christopher J. Stewart & Nadim J. Ajami & Jacqueline L. O’Brien & Diane S. Hutchinson & Daniel P. Smith & Matthew C. Wong & Matthew C. Ross & Richard E. Lloyd & HarshaVardhan Doddapaneni & Ginger A. M, 2018. "Temporal development of the gut microbiome in early childhood from the TEDDY study," Nature, Nature, vol. 562(7728), pages 583-588, October.
    5. Wanli He & Jakob Russel & Franziska Klincke & Joseph Nesme & Søren Johannes Sørensen, 2024. "Insights into the ecology of the infant gut plasmidome," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Xuanji Li & Asker Brejnrod & Jonathan Thorsen & Trine Zachariasen & Urvish Trivedi & Jakob Russel & Gisle Alberg Vestergaard & Jakob Stokholm & Morten Arendt Rasmussen & Søren Johannes Sørensen, 2023. "Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Daphna Rothschild & Omer Weissbrod & Elad Barkan & Alexander Kurilshikov & Tal Korem & David Zeevi & Paul I. Costea & Anastasia Godneva & Iris N. Kalka & Noam Bar & Smadar Shilo & Dar Lador & Arnau Vi, 2018. "Environment dominates over host genetics in shaping human gut microbiota," Nature, Nature, vol. 555(7695), pages 210-215, March.
    Full references (including those not matched with items on IDEAS)

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