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

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Date
2023
Authors
Feehily, Conor
O’Neill, Ian J.
Walsh, Calum J.
Moore, Rebecca L.
Killeen, Sarah Louise
Geraghty, Aisling A.
Lawton, Elaine M.
Byrne, David F.
Sanchez-Gallardo, Rocio
Nori, Sai Ravi Chandra
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Nature Research
Published Version
10.1038/s41467-023-38694-0
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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.
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Keywords
Infant gut microbiome , Mother-infant , Bifidobacterial strains , Metagenomic sequencing , Metagenomic approach
Citation
Feehily, C., O’Neill, I.J., Walsh, C.J., Moore, R.L., Killeen, S.L., Geraghty, A.A., Lawton, E.M., Byrne, D., Sanchez-Gallardo, R., Nori, S.R.C., Nielsen, I.B., Wortmann, E., Matthews, E., O’Flaherty, R., Rudd, P.M., Groeger, D., Shanahan, F., Saldova, R., McAuliffe, F.M., Van Sinderen, D. and Cotter, P.D. (2023) ‘Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach’, Nature Communications, 14(1), 3015 (14pp). doi: 10.1038/s41467-023-38694-0
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https://hdl.handle.net/10468/15305
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APC Microbiome Ireland - Journal Articles
Microbiology - Journal Articles
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© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.