Giant oversights in the human gut virome

• Published in: Gut Vol. 69; no. 7; pp. 1357 - 1358
• Main Authors: Sutton, Thomas D S, Clooney, Adam G, Hill, Colin
• Format: Journal Article
• Language: English
• Published: England BMJ Publishing Group LTD 01.07.2020
• Subjects: Biodegradation; Capsids; Colitis, Ulcerative; Deoxyribonucleic acid; DNA; DNA sequencing; Gastrointestinal Microbiome; Genomes; Humans; Inflammatory bowel disease; Inflammatory Bowel Diseases; Mucous Membrane; Proteins; Taxonomy; tRNA; Virome; Viruses; Ireland; IBD basic research; IBD; inflammatory bowel disease; IBD clinical
• ISSN: 0017-5749; 1468-3288
• DOI: 10.1136/gutjnl-2019-319067

[...]the DNA extraction method states that 0.22 µm filters were used to remove bacterial and eukaryotic cells, followed by chemical and enzymatic degradation of DNA unprotected by viral capsids. [...]we aligned sequencing reads provided by the authors to a database of all representative Mimivirus and C. ericina virus sequences present in the UniProt TrEMBL database (228 as of April 2019; see online supplementary methods). The only alignments of contigs classified as Mimivirus and C. ericina virus to the Mimivirus and C. ericina virus database were short (4.3% of the query contig length on average), low identity hits to proteins such as heat-shock protein and tRNA synthetase (figure 1A–D), which are conserved across domains of life.3 4 When aligned to the NT database, these same contigs displayed high identity and often full-length alignments to bacterial and fungal sequences and none to C. ericina or Mimivirus genomes.