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Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life

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  • Shimao Xiong

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Bing Xie

    (Peking University
    The Research Center of Female Pelvic Floor Disorder Disease of Peking University
    Joint International Research Center of Translational and Clinical Research)

  • Naiyi Yin

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Hongmei Zhu

    (Peking University
    The Research Center of Female Pelvic Floor Disorder Disease of Peking University)

  • Huimin Gao

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Xue Xu

    (Peking University)

  • Kang Xiao

    (University of Chinese Academy of Sciences)

  • Xiaolin Cai

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Guoxin Sun

    (Chinese Academy of Sciences)

  • Xiuli Sun

    (Peking University
    The Research Center of Female Pelvic Floor Disorder Disease of Peking University
    Joint International Research Center of Translational and Clinical Research)

  • Yanshan Cui

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Tom Wiele

    (Ghent University)

  • Yongguan Zhu

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

Abstract

Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.

Suggested Citation

  • Shimao Xiong & Bing Xie & Naiyi Yin & Hongmei Zhu & Huimin Gao & Xue Xu & Kang Xiao & Xiaolin Cai & Guoxin Sun & Xiuli Sun & Yanshan Cui & Tom Wiele & Yongguan Zhu, 2025. "Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60508-8
    DOI: 10.1038/s41467-025-60508-8
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    1. Marta Reyman & Marlies A. Houten & Debbie Baarle & Astrid A. T. M. Bosch & Wing Ho Man & Mei Ling J. N. Chu & Kayleigh Arp & Rebecca L. Watson & Elisabeth A. M. Sanders & Susana Fuentes & Debby Bogaer, 2019. "Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    2. Marta Reyman & Marlies A. Houten & Debbie Baarle & Astrid A. T. M. Bosch & Wing Ho Man & Mei Ling J. N. Chu & Kayleigh Arp & Rebecca L. Watson & Elisabeth A. M. Sanders & Susana Fuentes & Debby Bogaer, 2019. "Author Correction: Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life," Nature Communications, Nature, vol. 10(1), pages 1-1, December.
    3. Jakob Stokholm & Martin J. Blaser & Jonathan Thorsen & Morten A. Rasmussen & Johannes Waage & Rebecca K. Vinding & Ann-Marie M. Schoos & Asja Kunøe & Nadia R. Fink & Bo L. Chawes & Klaus Bønnelykke & , 2018. "Maturation of the gut microbiome and risk of asthma in childhood," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    4. Tanya Yatsunenko & Federico E. Rey & Mark J. Manary & Indi Trehan & Maria Gloria Dominguez-Bello & Monica Contreras & Magda Magris & Glida Hidalgo & Robert N. Baldassano & Andrey P. Anokhin & Andrew C, 2012. "Human gut microbiome viewed across age and geography," Nature, Nature, vol. 486(7402), pages 222-227, June.
    5. Fiona Fouhy & Claire Watkins & Cian J. Hill & Carol-Anne O’Shea & Brid Nagle & Eugene M. Dempsey & Paul W. O’Toole & R. Paul Ross & C. Anthony Ryan & Catherine Stanton, 2019. "Perinatal factors affect the gut microbiota up to four years after birth," Nature Communications, Nature, vol. 10(1), pages 1-10, 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. 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.
    8. Jakob Stokholm & Martin J. Blaser & Jonathan Thorsen & Morten A. Rasmussen & Johannes Waage & Rebecca K. Vinding & Ann-Marie M. Schoos & Asja Kunøe & Nadia R. Fink & Bo L. Chawes & Klaus Bønnelykke & , 2018. "Publisher Correction: Maturation of the gut microbiome and risk of asthma in childhood," Nature Communications, Nature, vol. 9(1), pages 1-2, December.
    9. Nhan T. Ho & Fan Li & Kathleen A. Lee-Sarwar & Hein M. Tun & Bryan P. Brown & Pia S. Pannaraj & Jeffrey M. Bender & Meghan B. Azad & Amanda L. Thompson & Scott T. Weiss & M. Andrea Azcarate-Peril & Au, 2018. "Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
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