dc.contributor.author	Pan, Zhe	en
dc.contributor.author	Walsh, Calum J.	en
dc.contributor.author	Feehily, Conor	en
dc.contributor.author	Nori, Sai Ravi Chandra	en
dc.contributor.author	McAuliffe, Fionnuala M.	en
dc.contributor.author	Cotter, Paul D.	en
dc.contributor.author	MacSharry, John	en
dc.contributor.author	van Sinderen, Douwe	en
dc.date.accessioned	2025-08-22T15:57:02Z
dc.date.available	2025-08-22T15:57:02Z
dc.date.issued	2025-08-04	en
dc.description.abstract	The infant resistome, the collection of antibiotic resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week, n = 119; 1-month, n = 119), maternal stools (1-month postpartum, n = 120), and breastmilk (1-month postpartum, n = 73). Breastfeeding correlated with increased functional redundancy and altered bacterial-ARG co-occurrence networks in the infant resistome. Escherichia coli dominated early resistome dynamics with a higher abundance correlating with reduced functional redundancy. Bifidobacterium longum exhibited a consistent negative association with 21 ARGs at one-month in breastfed infants, while four negative relationships between ARGs and Bifidobacterium bifidum were observed in formula-fed infants. ARG transmission via breastmilk appears to be gene-specific, with the quinolone resistance gene sdrM likely transmitted under maternal antibiotic use. Delivery mode modulated the microbial environment in ways that interact with resistome structure and changing functional redundancy, particularly through genera like Staphylococcus and Streptococcus. These findings highlight the role of early feeding practices in resistome development and propose functional redundancy as a key ecological framework for understanding infant gut resistome dynamics.	en
dc.description.sponsorship	European Union’s Horizon 2020
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Pan, Z., Walsh, C.J., Feehily, C., Nori, S.R.C., McAuliffe, F.M., Cotter, P.D., MacSharry, J. and Van Sinderen, D. (2025) ‘Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome’, Gut Microbes, 17(1), 2541033. https://doi.org/10.1080/19490976.2025.2541033	en
dc.identifier.doi	10.1080/19490976.2025.2541033	en
dc.identifier.eissn	1949-0984	en
dc.identifier.issn	1949-0976	en
dc.identifier.issued	1	en
dc.identifier.journaltitle	Gut Microbes	en
dc.identifier.uri	https://hdl.handle.net/10468/17799
dc.identifier.volume	17	en
dc.language.iso	en	en
dc.publisher	Taylor & Francis	en
dc.relation.project	101034270
dc.rights	© 2025, University College Cork. Published with license by Taylor & Francis Group, LLC. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permitsunrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allowthe posting of the Accepted Manuscript in a repository by the author(s) or with their consent.	en
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	en
dc.subject	Infant resistome	en
dc.subject	Early resistome	en
dc.subject	Breastfeeding	en
dc.subject	Bifidobacterium	en
dc.subject	Resistome transmission	en
dc.subject	Delivery mode	en
dc.subject	Functional redundancy	en
dc.title	Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome	en
dc.type	Article (peer-reviewed)	en

Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome

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