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

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 Busch Nielsen, Esther Wortmann, Elizabeth Matthews, Roisin O’Flaherty, Pauline M. Rudd, David Groeger, Fergus Shanahan, Radka Saldova, Fionnuala M. McAuliffe, Douwe Sinderen () and Paul D. Cotter
Additional contact information
Conor Feehily: Teagasc Food Research Centre, Fermoy, Co
Ian J. O’Neill: National University of Ireland
Calum J. Walsh: Teagasc Food Research Centre, Fermoy, Co
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
David Byrne: University College Dublin, National Maternity Hospital
Rocio Sanchez-Gallardo: National University of Ireland
Sai Ravi Chandra Nori: Teagasc Food Research Centre, Fermoy, Co
Ida Busch Nielsen: National University of Ireland
Esther Wortmann: National University of Ireland
Elizabeth Matthews: National Institute for Bioprocessing Research and Training, Co
Roisin O’Flaherty: National Institute for Bioprocessing Research and Training, Co
Pauline M. Rudd: National Institute for Bioprocessing Research and Training, Co
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
Fionnuala M. McAuliffe: University College Dublin, National Maternity Hospital
Douwe Sinderen: National University of Ireland
Paul D. Cotter: Teagasc Food Research Centre, Fermoy, Co

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-38694-0

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