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Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach

Author

Listed:
  • Conor Feehily

    (Teagasc Food Research Centre, Fermoy, Co
    National University of Ireland
    University of Oxford, John Radcliffe Hospital)

  • Ian J. O’Neill

    (National University of Ireland
    University College Cork)

  • Calum J. Walsh

    (Teagasc Food Research Centre, Fermoy, Co
    National University of Ireland)

  • Rebecca L. Moore

    (University College Dublin, National Maternity Hospital)

  • Sarah Louise Killeen

    (University College Dublin, National Maternity Hospital)

  • Aisling A. Geraghty

    (University College Dublin, National Maternity Hospital)

  • Elaine M. Lawton

    (Teagasc Food Research Centre, Fermoy, Co
    National University of Ireland)

  • David Byrne

    (University College Dublin, National Maternity Hospital)

  • Rocio Sanchez-Gallardo

    (National University of Ireland
    University College Cork)

  • Sai Ravi Chandra Nori

    (Teagasc Food Research Centre, Fermoy, Co
    National University of Ireland
    School of Mathematics, Statistics & Applied Mathematics, University of Galway)

  • Ida Busch Nielsen

    (National University of Ireland
    University College Cork)

  • Esther Wortmann

    (National University of Ireland
    University College Cork)

  • Elizabeth Matthews

    (National Institute for Bioprocessing Research and Training, Co)

  • Roisin O’Flaherty

    (National Institute for Bioprocessing Research and Training, Co
    Maynooth University, Maynooth, Co)

  • Pauline M. Rudd

    (National Institute for Bioprocessing Research and Training, Co
    Bioprocessing Technology Institute, AStar)

  • David Groeger

    (PrecisionBiotics Group Ltd. (Novozymes Cork), Cork Airport Business Park)

  • Fergus Shanahan

    (National University of Ireland)

  • Radka Saldova

    (National Institute for Bioprocessing Research and Training, Co
    University College Dublin (UCD))

  • Fionnuala M. McAuliffe

    (University College Dublin, National Maternity Hospital)

  • Douwe Sinderen

    (National University of Ireland
    University College Cork)

  • Paul D. Cotter

    (Teagasc Food Research Centre, Fermoy, Co
    National University of Ireland)

Abstract

A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.

Suggested Citation

  • Conor Feehily & Ian J. O’Neill & Calum J. Walsh & Rebecca L. Moore & Sarah Louise Killeen & Aisling A. Geraghty & Elaine M. Lawton & David Byrne & Rocio Sanchez-Gallardo & Sai Ravi Chandra Nori & Ida , 2023. "Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38694-0
    DOI: 10.1038/s41467-023-38694-0
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    References listed on IDEAS

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    1. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    2. Eric J. Muinck & Pål Trosvik, 2018. "Individuality and convergence of the infant gut microbiota during the first year of life," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    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.
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