{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T23:41:51Z","timestamp":1792626111581,"version":"4.5.0"},"reference-count":86,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T00:00:00Z","timestamp":1614816000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["12\/RC\/2273_P2"],"award-info":[{"award-number":["12\/RC\/2273_P2"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.<\/jats:p>","DOI":"10.3390\/microorganisms9030524","type":"journal-article","created":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T21:58:07Z","timestamp":1614895087000},"page":"524","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2222-2344","authenticated-orcid":false,"given":"Julie","family":"Callanan","sequence":"first","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0044-3878","authenticated-orcid":false,"given":"Stephen R.","family":"Stockdale","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5547-8672","authenticated-orcid":false,"given":"Andrey","family":"Shkoporov","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorraine A.","family":"Draper","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. Paul","family":"Ross","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8527-1445","authenticated-orcid":false,"given":"Colin","family":"Hill","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.chom.2019.01.017","article-title":"Bacteriophages of the Human Gut: The \u201cKnown Unknown\u201d of the Microbiome","volume":"25","author":"Shkoporov","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6220","DOI":"10.1128\/JB.185.20.6220-6223.2003","article-title":"Metagenomic Analyses of an Uncultured Viral Community from Human Feces","volume":"185","author":"Breitbart","year":"2003","journal-title":"J. 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