{"id":307747,"date":"2025-10-16T09:57:22","date_gmt":"2025-10-16T09:57:22","guid":{"rendered":"https:\/\/www.europesays.com\/us\/307747\/"},"modified":"2025-10-16T09:57:22","modified_gmt":"2025-10-16T09:57:22","slug":"isolation-engineering-and-ecology-of-temperate-phages-from-the-human-gut","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/us\/307747\/","title":{"rendered":"Isolation, engineering and ecology of temperate phages from the human gut"},"content":{"rendered":"
  • \n

    Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. Massive expansion of human gut bacteriophage diversity. Cell 184<\/b>, 1098\u20131109 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nayfach, S. et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat. Microbiol. 6<\/b>, 960\u2013970 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gregory, A. C. et al. The Gut Virome Database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe 28<\/b>, 724\u2013740 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Clooney, A. G. et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe 26<\/b>, 764\u2013778 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gogokhia, L. et al. Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host Microbe 25<\/b>, 285\u2013299 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7<\/b>, 828\u2013836 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chevallereau, A., Pons, B. J., van Houte, S. & Westra, E. R. Interactions between bacterial and phage communities in natural environments. Nat. Rev. Microbiol. 20<\/b>, 49\u201362 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zuo, T. et al. Human-gut-DNA virome variations across geography, ethnicity, and urbanization. Cell Host Microbe 28<\/b>, 741\u2013751 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benler, S. et al. Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome 9<\/b>, 78 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Van Espen, L. et al. A previously undescribed highly prevalent phage identified in a Danish enteric virome catalog. mSystems 6<\/b>, e0038221 (2021).<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Govier, T. & Verwoerd, W. The promise and pitfalls of prophages. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.04.20.537752<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Anthenelli, M. et al. Phage and bacteria diversification through a prophage acquisition ratchet. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2020.04.08.028340<\/a> (2020).<\/p>\n<\/li>\n

  • \n

    Bobay, L. M., Touchon, M. & Rocha, E. P. C. Pervasive domestication of defective prophages by bacteria. Proc. Natl Acad. Sci. USA 111<\/b>, 12127\u201312132 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, X. et al. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1<\/b>, 147\u2013149 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Erez, Z. et al. Communication between viruses guides lysis-lysogeny decisions. Nature 541<\/b>, 488\u2013493 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Silpe, J. E., Duddy, O. P. & Bassler, B. L. Natural and synthetic inhibitors of a phage-encoded quorum-sensing receptor affect phage\u2013host dynamics in mixed bacterial communities. Proc. Natl Acad. Sci. USA 119<\/b>, e2217813119 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Browne, H. P. et al. Culturing of \u2018unculturable\u2019 human microbiota reveals novel taxa and extensive sporulation. Nature 533<\/b>, 543\u2013546 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Forster, S. C. et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat. Biotechnol. 37<\/b>, 186\u2013192 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Otsuji, N., Sekiguchi, M., Iijima, T. & Takagi, Y. Induction of phage formation in the lysogenic Escherichia coli K-12 by mitomycin C. Nature 184<\/b>, 1079\u20131080 (1959).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    \u0141o\u015b, J. M., \u0141o\u015b, M., W\u0229grzyn, A. & W\u0229grzyn, G. Hydrogen peroxide-mediated induction of the Shiga toxin-converting lambdoid prophage ST2-8624 in Escherichia coli O157:H7. FEMS Immunol. Med. Microbiol. 58<\/b>, 322\u2013329 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Oh, J.-H. et al. Dietary fructose and microbiota-derived short-chain fatty acids promote bacteriophage production in the gut symbiont Lactobacillus reuteri. Cell Host Microbe 25<\/b>, 273\u2013284 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morris, R. M., Cain, K. R., Hvorecny, K. L. & Kollman, J. M. Lysogenic host\u2013virus interactions in SAR11 marine bacteria. Nat. Microbiol. 5<\/b>, 1011\u20131015 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Boling, L. et al. Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. Gut Microbes 11<\/b>, 721\u2013734 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roux, S. et al. Minimum information about an uncultivated virus genome (MIUVIG). Nat. Biotechnol. 37<\/b>, 29\u201337 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lopez, J. A. et al. Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.09.27.614587<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Sutcliffe, S. G., Reyes, A. & Maurice, C. F. Bacteriophages playing nice: lysogenic bacteriophage replication stable in the human gut microbiota. iScience 26<\/b>, 106007 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shalon, D. et al. Profiling the human intestinal environment under physiological conditions. Nature 617<\/b>, 581\u2013591 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Adriaenssens, E. M. Phage diversity in the human gut microbiome: a taxonomist\u2019s perspective. mSystems 6<\/b>, e0079921 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bin Jang, H. et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37<\/b>, 632\u2013639 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benler, S. et al. A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. Microbiome 6<\/b>, 191 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yutin, N. et al. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat. Commun. 12<\/b>, 1044 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466<\/b>, 334\u2013338 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shkoporov, A. N. et al. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe 26<\/b>, 527\u2013541 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, M. et al. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295<\/b>, 2091\u20132094 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roux, S. et al. Ecology and molecular targets of hypermutation in the global microbiome. Nat. Commun. 12<\/b>, 3076 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Laurenceau, R. et al. Harnessing diversity generating retroelements for in vivo targeted hyper-mutagenesis. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.03.24.644984<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Dor\u00e9, H. et al. Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proc. Natl Acad. Sci. USA 121<\/b>, e2316469121 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Terzian, P. et al. PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genom. Bioinform. 3<\/b>, lqab067 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    O\u2019Brien, S., K\u00fcmmerli, R., Paterson, S., Winstanley, C. & Brockhurst, M. A. Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations. Proc. R. Soc. B 286<\/b>, 20191794 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Moreno-Gallego, J. L. et al. Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins. Cell Host Microbe 25<\/b>, 261\u2013272 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Silpe, J. E., Duddy, O. P. & Bassler, B. L. Induction mechanisms and strategies underlying interprophage competition during polylysogeny. PLoS Pathog. 19<\/b>, e1011363 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Refardt, D. Within-host competition determines reproductive success of temperate bacteriophages. ISME J. 5<\/b>, 1451\u20131460 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Azulay, G. et al. A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response. Cell Rep. 39<\/b>, 110723 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Guo, Y. et al. Control of lysogeny and antiphage defense by a prophage-encoded kinase-phosphatase module. Nat. Commun. 15<\/b>, 7244 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Song, S. et al. CRISPR-Cas controls cryptic prophages. Int. J. Mol. Sci. 23<\/b>, 16195 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Edgar, R. & Qimron, U. The Escherichia coli CRISPR system protects from \u03bb lysogenization, lysogens, and prophage induction. J. Bacteriol. 192<\/b>, 6291\u20136294 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Silpe, J. E. & Bassler, B. L. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell 176<\/b>, 268\u2013280 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Silpe, J. E. et al. Small protein modules dictate prophage fates during polylysogeny. Nature 620<\/b>, 625\u2013633 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mathieu, A. et al. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat. Commun. 11<\/b>, 378 (2020).<\/p>\n<\/li>\n

  • \n

    Lemire, S., Figueroa-Bossi, N. & Bossi, L. Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet. 7<\/b>, e1002149 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    D\u2019Adamo, G. L. et al. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Rep. Med. 4<\/b>, 101124 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stewart, C. S., Hold, G. L., Duncan, S. H., Flint, H. J. & Harmsen, H. J. M. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52<\/b>, 2141\u20132146 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mende, D. R. et al. ProGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res. 45<\/b>, D529\u2013D534 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. PLoS ONE 11<\/b>, e0163962 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30<\/b>, 772\u2013780 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Capella-Guti\u00e9rrez, S., Silla-Mart\u00ednez, J. M. & Gabald\u00f3n, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25<\/b>, 1972\u20131973 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30<\/b>, 1312\u20131313 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49<\/b>, W293\u2013W296 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11<\/b>, 2864\u20132868 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3<\/b>, e985 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8<\/b>, 90 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A. & Sun, F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 5<\/b>, 69 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39<\/b>, 578\u2013585 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9<\/b>, e1003118 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Alexeeva, S., Guerra Mart\u00ednez, J. A., Spus, M. & Smid, E. J. Spontaneously induced prophages are abundant in a naturally evolved bacterial starter culture and deliver competitive advantage to the host. BMC Microbiol. 18<\/b>, 120 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chantret, I. et al. Differential expression of sucrase-isomaltase in clones isolated from early and late passages of the cell line caco-2: evidence for glucose-dependent negative regulation. J. Cell Sci. 107<\/b>, 213\u2013225 (1994).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30<\/b>, 2114\u20132120 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9<\/b>, 357\u2013359 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25<\/b>, 2078\u20132079 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26<\/b>, 841\u2013842 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kieft, K. & Anantharaman, K. Deciphering active prophages from metagenomes. mSystems 7<\/b>, e00084-22 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Turkington, C. J. R., Abadi, N. N., Edwards, R. A. & Grasis, J. A. hafeZ: active prophage identification through read mapping. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.07.21.453177<\/a> (2021).<\/p>\n<\/li>\n

  • \n

    Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A. Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinformatics 36<\/b>, 4126\u20134129 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30<\/b>, 2068\u20132069 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tisza, M. J., Belford, A. K., Dominguez-Huerta, G., Bolduc, B. & Buck, C. B. Cenote-Taker 2 democratizes virus discovery and sequence annotation. Virus Evol. 7<\/b>, veaa100 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eddy, S. R. Accelerated profile HMM searches. PLoS Comp. Biol. 7<\/b>, e1002195 (2011).<\/p>\n<\/li>\n

  • \n

    Cook, R. et al. INfrastructure for a PHAge REference Database: identification of large-scale biases in the current collection of cultured phage genomes. Phage 2<\/b>, 214\u2013223 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, H. et al. Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae. Virus Evol. 5<\/b>, vez013 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ibrahim, B. et al. Bioinformatics meets virology: the European Virus Bioinformatics Center\u2019s second annual meeting. Viruses 10<\/b>, 256 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yutin, N., B\u00e4ckstr\u00f6m, D., Ettema, T. J. G., Krupovic, M. & Koonin, E. V. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis. Virol. J. 15<\/b>, 67 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roux, S., Krupovic, M., Daly, R.A. et al. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth\u2019s biomes. Nat. Microbiol. 4<\/b>, 1895\u20131906 (2019).<\/p>\n<\/li>\n

  • \n

    Breitwieser, F. P., Baker, D. N. & Salzberg, S. L. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biol. 19<\/b>, 198 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17<\/b>, 132 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Simonsen, M., Mailund, T. & Pedersen, C. N. S. in Algorithms in Bioinformatics (eds Crandall, K. A. & Lagergren, J.) 113\u2013122 (Springer, 2008).<\/p>\n<\/li>\n

  • \n

    Solari, S. M., Young, R. B., Marcelino, V. R. & Forster, S. C. Expam\u2014high-resolution analysis of metagenomes using distance trees. Bioinformatics 38<\/b>, 4814\u20134816 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ye, Y. Identification of diversity-generating retroelements in human microbiomes. Int. J. Mol. Sci. 15<\/b>, 14234\u201314246 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cobi\u00e1n G\u00fcemes, A. G. et al. Viruses as winners in the game of life. Annu. Rev. Virol. 3<\/b>, 197\u2013214 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    O\u2019Donnell, S. & Fischer, G. MUM&Co: accurate detection of all SV types through whole-genome alignment. Bioinformatics 36<\/b>, 3242\u20133243 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90\u2009K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9<\/b>, 5114 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Olm, M. R. et al. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 5<\/b>, e00731-19 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zheng, L. et al. CRISPR\/Cas-based genome editing for human gut commensal Bacteroides species. ACS Synth. Biol. 11<\/b>, 464\u2013472 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13<\/b>, e1005595 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 23<\/b>, 258 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dahlman, S. et al. Data and code for \u2018Isolation, engineering and ecological dynamics of temperate phages from the human gut\u2019. Figshare https:\/\/doi.org\/10.26180\/29946902.v1<\/a> (2025).<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. Massive expansion of human…\n","protected":false},"author":3,"featured_media":307748,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11],"tags":[155769,210,10046,20302,10047,159,67,132,68],"class_list":{"0":"post-307747","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-health","8":"tag-bacteriophages","9":"tag-health","10":"tag-humanities-and-social-sciences","11":"tag-microbiome","12":"tag-multidisciplinary","13":"tag-science","14":"tag-united-states","15":"tag-unitedstates","16":"tag-us"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@us\/115383255516798846","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/307747","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/comments?post=307747"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/posts\/307747\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media\/307748"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/media?parent=307747"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/categories?post=307747"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/us\/wp-json\/wp\/v2\/tags?post=307747"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}