{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T20:56:13Z","timestamp":1781816173675,"version":"3.54.5"},"reference-count":25,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,6,4]],"date-time":"2025-06-04T00:00:00Z","timestamp":1748995200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000317","name":"Action Medical Research","doi-asserted-by":"publisher","award":["GN2730"],"award-info":[{"award-number":["GN2730"]}],"id":[{"id":"10.13039\/501100000317","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.xpro.2025.103917","type":"journal-article","created":{"date-parts":[[2025,6,21]],"date-time":"2025-06-21T04:48:54Z","timestamp":1750481334000},"page":"103917","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk"],"prefix":"10.1016","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7977-9720","authenticated-orcid":false,"given":"Wen C.","family":"Yew","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory R.","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Cheung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet E.","family":"Berrington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4925-467X","authenticated-orcid":false,"given":"Darren L.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2025.103917_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113373","article-title":"The core phageome and its interrelationship with preterm human milk lipids","volume":"42","author":"Yew","year":"2023","journal-title":"Cell Rep."},{"key":"10.1016\/j.xpro.2025.103917_bib2","doi-asserted-by":"crossref","DOI":"10.3389\/fped.2022.856520","article-title":"Optimisation and application of a novel method to identify bacteriophages in maternal milk and infant stool identifies host-phage communities within preterm infant gut","volume":"10","author":"Young","year":"2022","journal-title":"Front. Pediatr."},{"key":"10.1016\/j.xpro.2025.103917_bib3","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1016\/j.bbamem.2017.04.006","article-title":"The critical role of phosphatidylcholine and phosphatidylethanolamine metabolism in health and disease","volume":"1859","author":"van der Veen","year":"2017","journal-title":"Biochim. Biophys. Acta. Biomembr."},{"key":"10.1016\/j.xpro.2025.103917_bib4","author":"Bushnell"},{"key":"10.1016\/j.xpro.2025.103917_bib5","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-inone FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.103917_bib6","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1093\/bioinformatics\/btx754","article-title":"BioBakery: a meta\u2019omic analysis environment","volume":"34","author":"McIver","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.103917_bib7","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res."},{"key":"10.1016\/j.xpro.2025.103917_bib8","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.103917_bib9","author":"Li"},{"key":"10.1016\/j.xpro.2025.103917_bib10","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.103917_bib11","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.103917_bib12","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.xpro.2025.103917_bib13","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2025.103917_bib14","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.xpro.2025.103917_bib15","doi-asserted-by":"crossref","DOI":"10.7717\/peerj-cs.104","article-title":"Bracken: estimating species abundance in metagenomics data","volume":"3","author":"Lu","year":"2017","journal-title":"PeerJ Comput. Sci."},{"key":"10.1016\/j.xpro.2025.103917_bib16","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.xpro.2025.103917_bib17","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4","volume":"41","author":"Blanco-Miguez","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2025.103917_bib18","author":"Oksanen"},{"key":"10.1016\/j.xpro.2025.103917_bib19","doi-asserted-by":"crossref","first-page":"378","DOI":"10.32614\/RJ-2017-066","article-title":"glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling","volume":"9","author":"Brooks","year":"2017","journal-title":"R J."},{"key":"10.1016\/j.xpro.2025.103917_bib20","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1080\/00031305.1980.10483031","article-title":"Population marginal means in the linear model: An alternative to least squares means","volume":"34","author":"Searle","year":"1980","journal-title":"Am. Stat."},{"key":"10.1016\/j.xpro.2025.103917_bib21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.xpro.2025.103917_bib22","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005752","article-title":"MixOmics: an R package for \u2018omics feature selection and multiple data integration","volume":"13","author":"Rohart","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.xpro.2025.103917_bib23","doi-asserted-by":"crossref","first-page":"e00073-17","DOI":"10.1128\/mSphereDirect.00073-17","article-title":"OptiClust, an improved method for assigning amplicon-based sequence data to operational taxonomic units","volume":"2","author":"Westcott","year":"2017","journal-title":"mSphere"},{"key":"10.1016\/j.xpro.2025.103917_bib25","doi-asserted-by":"crossref","first-page":"3375","DOI":"10.3168\/jds.2015-9655","article-title":"Short communication: improved method for centrifugal recovery of bacteria from raw milk applied to sensitive real-time quantitative PCR detection of Salmonella spp","volume":"99","author":"Brewster","year":"2016","journal-title":"J. Dairy Sci."},{"key":"10.1016\/j.xpro.2025.103917_bib26","doi-asserted-by":"crossref","first-page":"2879","DOI":"10.3168\/jds.2018-15044","article-title":"The simulated in vitro infant gastrointestinal digestion of droplets covered with milk fat globule membrane polar lipids concentrate","volume":"102","author":"Luo","year":"2019","journal-title":"J. Dairy Sci."}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166725003235?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166725003235?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T20:21:24Z","timestamp":1781814084000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166725003235"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":25,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["S2666166725003235"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2025.103917","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2025.103917","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2023.113373","name":"associatedlink","label":"CrossRef DOI link to the associated document"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"103917"}}