{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:12:19Z","timestamp":1785420739056,"version":"3.56.0"},"posted":{"date-parts":[[2026,4,9]]},"group-title":"Microbiology","reference-count":15,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T00:00:00Z","timestamp":1775692800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"crossref","award":["2592104"],"award-info":[{"award-number":["2592104"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"award":["MR\/T030062\/1"],"award-info":[{"award-number":["MR\/T030062\/1"]}],"id":[{"id":"https:\/\/ror.org\/03x94j517","id-type":"ROR","asserted-by":"publisher"}]},{"award":["SSP 200580; NEOF\/NBAF"],"award-info":[{"award-number":["SSP 200580; NEOF\/NBAF"]}],"id":[{"id":"https:\/\/ror.org\/036g3b009","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Linking bacteriophages (phages) to their hosts remains a fundamental challenge to understanding microbial ecology, viral evolution, and horizontal gene transfer. Although phages are the most abundant biological entities on Earth, the majority of them remain uncharacterized due to the lack of efficient host-linking approaches. Traditional methods, such as plaque assays, have significant limitations as they depend on visible lysis and therefore fail to detect phages that do not form plaques. Conversely, shotgun metagenomics can recover viral genomes directly from environmental samples; however, it cannot directly link phages to their bacterial hosts. In this study, we addressed this limitation by tackling the critical question of \u201cwho infects whom?\u201d through the development of a novel, culture-independent approach that utilises an anucleate bacterial minicells-based platform to enrich for phages capable of infecting a target bacterial host. To validate our approach, purified\n                  <jats:italic>Escherichia coli<\/jats:italic>\n                  minicells were exposed to a concentrated viral fraction derived from sewage samples. Genomic DNA from phages that successfully infected and interacted with the\n                  <jats:italic>E. coli<\/jats:italic>\n                  minicells was isolated, amplified, and sequenced. Metagenomic analysis revealed a distinct\n                  <jats:italic>E. coli<\/jats:italic>\n                  -specific virome, including several putatively novel phage species and genera. This platform effectively bridges the gap between culture-dependent and metagenomic methods, providing a scalable, host-targeted tool for identifying phage-host pairs. Our approach also opens new opportunities for studying phage-host interaction networks in complex microbial ecosystems and enhances our ability to investigate viral diversity, host specificity, and the ecological roles of phages in natural environments.\n                <\/jats:p>","DOI":"10.64898\/2026.04.08.717211","type":"posted-content","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T07:30:20Z","timestamp":1775806220000},"source":"Crossref","is-referenced-by-count":0,"title":["Who Infects Whom? Exploiting Bacterial Minicells for Targeted Virome Enrichment and Phage-Host Interaction Analysis through an Integrated Metagenomic Approach"],"prefix":"10.64898","author":[{"given":"Arezoo","family":"Pedramfar","sequence":"first","affiliation":[{"name":"Becky Mayer Centre for Phage Research (BMCPR), Division of Microbiology and Infection, University of Leicester, Leicester LE1 7RH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Ensenat","sequence":"additional","affiliation":[{"name":"Becky Mayer Centre for Phage Research (BMCPR), Division of Microbiology and Infection, University of Leicester, Leicester LE1 7RH, UK"},{"name":"ESTBB, Facult\u00e9 des Sciences, Universit\u00e9 Catholique de Lyon, 10 Place des Archives, 69002 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie S.","family":"Allcock","sequence":"additional","affiliation":[{"name":"Electron Microscopy Facility Core Biotechnology Services, College of Life Sciences, University of Leicester, Leicester, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew D.","family":"Millard","sequence":"additional","affiliation":[{"name":"Becky Mayer Centre for Phage Research (BMCPR), Division of Microbiology and Infection, University of Leicester, Leicester LE1 7RH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard E.","family":"Galyov","sequence":"additional","affiliation":[{"name":"Becky Mayer Centre for Phage Research (BMCPR), Division of Microbiology and Infection, University of Leicester, Leicester LE1 7RH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041306150564000_2026.04.08.717211v1.1","doi-asserted-by":"publisher","DOI":"10.3390\/v17010065"},{"key":"2026041306150564000_2026.04.08.717211v1.2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1659093"},{"key":"2026041306150564000_2026.04.08.717211v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nature19094"},{"key":"2026041306150564000_2026.04.08.717211v1.4","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.08490"},{"key":"2026041306150564000_2026.04.08.717211v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0190-y"},{"key":"2026041306150564000_2026.04.08.717211v1.6","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1760-x"},{"key":"2026041306150564000_2026.04.08.717211v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0526-2"},{"key":"2026041306150564000_2026.04.08.717211v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/nature13459"},{"key":"2026041306150564000_2026.04.08.717211v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.101439"},{"key":"2026041306150564000_2026.04.08.717211v1.10","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-50112-8_1"},{"key":"2026041306150564000_2026.04.08.717211v1.11","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00901-15"},{"key":"2026041306150564000_2026.04.08.717211v1.12","doi-asserted-by":"publisher","DOI":"10.1089\/phage.2021.0007"},{"key":"2026041306150564000_2026.04.08.717211v1.13","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01340-15"},{"key":"2026041306150564000_2026.04.08.717211v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-50777-0"},{"key":"2026041306150564000_2026.04.08.717211v1.15","doi-asserted-by":"publisher","DOI":"10.1098\/rsob.210188"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.04.08.717211","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T13:15:14Z","timestamp":1776086114000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.04.08.717211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,9]]},"references-count":15,"URL":"https:\/\/doi.org\/10.64898\/2026.04.08.717211","relation":{},"subject":[],"published":{"date-parts":[[2026,4,9]]},"subtype":"preprint"}}