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Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk

Lookup NU author(s): Dr Greg YoungORCiD, Professor Janet Berrington

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2025 The AuthorsBacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.1

Publication metadata

Author(s): Yew WC, Young GR, Cheung W, Nelson A, Berrington JE, Smith DL

Publication type: Article

Publication status: Published

Journal: STAR Protocols

Year: 2025

Volume: 6

Issue: 3

Print publication date: 19/09/2025

Online publication date: 21/06/2025

Acceptance date: 02/04/2018

Date deposited: 09/07/2025

ISSN (electronic): 2666-1667

Publisher: Cell Press

URL: https://doi.org/10.1016/j.xpro.2025.103917

DOI: 10.1016/j.xpro.2025.103917

Data Access Statement: The raw metagenomics data generated during this study are available at ENA (PRJEB58774): https://www.ebi.ac.uk/ena/ browser/view/PRJEB58774. This publication did not generate any original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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