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

Wen C. Yew; Gregory R. Young; William Cheung; Andrew Nelson; Janet E. Berrington; Darren L. Smith

doi:10.1016/j.xpro.2025.103917

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

Wen C. Yew, Gregory R. Young, William Cheung, Andrew Nelson, Janet E. Berrington, Darren L. Smith^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Downloads (Pure)

Abstract

Bacteriophages 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

Original language	English
Article number	103917
Number of pages	33
Journal	STAR Protocols
Volume	6
Issue number	3
Early online date	21 Jun 2025
DOIs	https://doi.org/10.1016/j.xpro.2025.103917
Publication status	Published - 19 Sept 2025

Keywords

Bioinformatics
Microbiology
Molecular Biology
Systems biology

Access to Document

10.1016/j.xpro.2025.103917Licence: CC BY

1-s2.0-S2666166725003235-mainFinal published version, 5.52 MBLicence: CC BY

Cite this

@article{4fea6abe8cdc45818099627714903faf,

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

abstract = "Bacteriophages 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",

keywords = "Bioinformatics, Microbiology, Molecular Biology, Systems biology",

author = "Yew, \{Wen C.\} and Young, \{Gregory R.\} and William Cheung and Andrew Nelson and Berrington, \{Janet E.\} and Smith, \{Darren L.\}",

year = "2025",

month = sep,

day = "19",

doi = "10.1016/j.xpro.2025.103917",

language = "English",

volume = "6",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "3",

}

TY - JOUR

T1 - Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk

AU - Yew, Wen C.

AU - Young, Gregory R.

AU - Cheung, William

AU - Nelson, Andrew

AU - Berrington, Janet E.

AU - Smith, Darren L.

PY - 2025/9/19

Y1 - 2025/9/19

N2 - Bacteriophages 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

AB - Bacteriophages 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

KW - Bioinformatics

KW - Microbiology

KW - Molecular Biology

KW - Systems biology

UR - https://www.scopus.com/pages/publications/105008582616

U2 - 10.1016/j.xpro.2025.103917

DO - 10.1016/j.xpro.2025.103917

M3 - Article

AN - SCOPUS:105008582616

SN - 2666-1667

VL - 6

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 103917

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this