{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T10:36:00Z","timestamp":1793270160110,"version":"4.5.0"},"reference-count":90,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T00:00:00Z","timestamp":1793232000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T00:00:00Z","timestamp":1793232000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["ERC-AdG 787514"],"award-info":[{"award-number":["ERC-AdG 787514"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["2016-03686"],"award-info":[{"award-number":["2016-03686"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-026-02480-7","type":"journal-article","created":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T10:02:50Z","timestamp":1793268170000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5831-5895","authenticated-orcid":false,"given":"Simon","family":"Roux","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uri","family":"Neri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8140-0131","authenticated-orcid":false,"given":"Brian","family":"Bushnell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brayon J.","family":"Fremin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikhil A.","family":"George","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5129-5652","authenticated-orcid":false,"given":"Uri","family":"Gophna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5974-9428","authenticated-orcid":false,"given":"Laura A.","family":"Hug","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3913-2484","authenticated-orcid":false,"given":"Antonio Pedro","family":"Camargo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongying","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5802-9485","authenticated-orcid":false,"given":"Natalia","family":"Ivanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6131-0462","authenticated-orcid":false,"given":"Nikos C.","family":"Kyrpides","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8162-1276","authenticated-orcid":false,"given":"Emiley A.","family":"Eloe-Fadrosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,29]]},"reference":[{"key":"2480_CR1","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1126\/science.1153213","volume":"320","author":"PG Falkowski","year":"2008","unstructured":"Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth\u2019s biogeochemical cycles. Science 320, 1034\u20131039 https:\/\/doi.org\/10.1126\/science.1153213 (2008).","journal-title":"Science"},{"key":"2480_CR2","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/nm.4517","volume":"24","author":"JA Gilbert","year":"2018","unstructured":"Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392\u2013400 https:\/\/doi.org\/10.1038\/nm.4517 (2018).","journal-title":"Nat. Med."},{"key":"2480_CR3","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2012.0383","author":"JL Macalady","year":"2013","unstructured":"Macalady, J. L. et al. Energy, ecology and the distribution of microbial life. Phil. Trans. R. Soc. B https:\/\/doi.org\/10.1098\/rstb.2012.0383 (2013).","journal-title":"Phil. Trans. R. Soc. B"},{"key":"2480_CR4","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1146\/annurev.ecolsys.38.091206.095740","volume":"38","author":"SA West","year":"2007","unstructured":"West, S. A., Diggle, S. P., Buckling, A., Gardner, A. & Griffin, A. S. The social lives of microbes. Annu. Rev. Ecol. Evol. Syst. 38, 53\u201377 https:\/\/doi.org\/10.1146\/annurev.ecolsys.38.091206.095740 (2007).","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"2480_CR5","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2022.102152","volume":"68","author":"MJ Bottery","year":"2022","unstructured":"Bottery, M. J. Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr. Opin. Microbiol. 68, 102152 https:\/\/doi.org\/10.1016\/j.mib.2022.102152 (2022).","journal-title":"Curr. Opin. Microbiol."},{"key":"2480_CR6","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/s41564-018-0166-y","volume":"3","author":"M Breitbart","year":"2018","unstructured":"Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. Nat. Microbiol. 3, 754\u2013766 https:\/\/doi.org\/10.1038\/s41564-018-0166-y (2018).","journal-title":"Nat. Microbiol."},{"key":"2480_CR7","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.chom.2019.01.017","volume":"25","author":"AN Shkoporov","year":"2019","unstructured":"Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the \u2018known unknown\u2019 of the microbiome. Cell Host Microbe 25, 195\u2013209 https:\/\/doi.org\/10.1016\/j.chom.2019.01.017 (2019).","journal-title":"Cell Host Microbe"},{"key":"2480_CR8","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1146\/annurev-virology-101416-041639","volume":"4","author":"KE Williamson","year":"2017","unstructured":"Williamson, K. E., Fuhrmann, J. J., Wommack, K. E. & Radosevich, M. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu. Rev. Virol. 4, 201\u2013219 https:\/\/doi.org\/10.1146\/annurev-virology-101416-041639 (2017).","journal-title":"Annu. Rev. Virol."},{"key":"2480_CR9","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41579-019-0299-x","volume":"18","author":"KS Makarova","year":"2020","unstructured":"Makarova, K. S. et al. Evolutionary classification of CRISPR\u2013Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67\u201383 https:\/\/doi.org\/10.1038\/s41579-019-0299-x (2020).","journal-title":"Nat. Rev. Microbiol."},{"key":"2480_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2017.92","volume":"2","author":"R Barrangou","year":"2017","unstructured":"Barrangou, R. & Horvath, P. A decade of discovery: CRISPR functions and applications. Nat. Microbiol. 2, 17092 https:\/\/doi.org\/10.1038\/nmicrobiol.2017.92 (2017).","journal-title":"Nat. Microbiol."},{"key":"2480_CR11","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258096","volume":"346","author":"JA Doudna","year":"2014","unstructured":"Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR\u2013Cas9. Science 346, 1258096 https:\/\/doi.org\/10.1126\/science.1258096 (2014).","journal-title":"Science"},{"key":"2480_CR12","doi-asserted-by":"publisher","DOI":"10.1126\/science.add8643","volume":"379","author":"JY Wang","year":"2023","unstructured":"Wang, J. Y. & Doudna, J. A. CRISPR technology: a decade of genome editing is only the beginning. Science 379, eadd8643 https:\/\/doi.org\/10.1126\/science.add8643 (2023).","journal-title":"Science"},{"key":"2480_CR13","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nrmicro.2015.14","volume":"14","author":"G Amitai","year":"2016","unstructured":"Amitai, G. & Sorek, R. CRISPR\u2013Cas adaptation: insights into the mechanism of action. Nat. Rev. Microbiol. 14, 67\u201376 https:\/\/doi.org\/10.1038\/nrmicro.2015.14 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"2480_CR14","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1126\/science.1138140","volume":"315","author":"R Barrangou","year":"2007","unstructured":"Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709\u20131712 https:\/\/doi.org\/10.1126\/science.1138140 (2007).","journal-title":"Science"},{"key":"2480_CR15","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1146\/annurev.micro.112408.134123","volume":"64","author":"H Deveau","year":"2010","unstructured":"Deveau, H., Garneau, J. E. & Moineau, S. CRISPR\/Cas system and its role in phage\u2013bacteria interactions. Annu. Rev. Microbiol. 64, 475\u2013493 https:\/\/doi.org\/10.1146\/annurev.micro.112408.134123 (2010).","journal-title":"Annu. Rev. Microbiol."},{"key":"2480_CR16","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1146\/annurev-ecolsys-121415-032428","volume":"47","author":"ER Westra","year":"2016","unstructured":"Westra, E. R., Dowling, A. J., Broniewski, J. M. & van Houte, S. Evolution and ecology of CRISPR. Annu. Rev. Ecol. Evol. Syst. 47, 307\u2013331 https:\/\/doi.org\/10.1146\/annurev-ecolsys-121415-032428 (2016).","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"2480_CR17","doi-asserted-by":"publisher","first-page":"3346","DOI":"10.1038\/s41564-025-02180-8","volume":"10","author":"KS Makarova","year":"2025","unstructured":"Makarova, K. S. et al. An updated evolutionary classification of CRISPR\u2013Cas systems including rare variants. Nat. Microbiol. 10, 3346\u20133361 https:\/\/doi.org\/10.1038\/s41564-025-02180-8 (2025).","journal-title":"Nat. Microbiol."},{"key":"2480_CR18","doi-asserted-by":"publisher","first-page":"10862","DOI":"10.1093\/nar\/gkae772","volume":"52","author":"A Fehrenbach","year":"2024","unstructured":"Fehrenbach, A., Mitrofanov, A., Alkhnbashi, O. S., Backofen, R. & Baumdicker, F. SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions. Nucleic Acids Res. 52, 10862\u201310878 https:\/\/doi.org\/10.1093\/nar\/gkae772 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR19","doi-asserted-by":"publisher","first-page":"664299","DOI":"10.3389\/fmicb.2021.664299","volume":"12","author":"SC Garrett","year":"2021","unstructured":"Garrett, S. C. Pruning and tending immune memories: spacer dynamics in the CRISPR array. Front. Microbiol. 12, 664299 https:\/\/doi.org\/10.3389\/fmicb.2021.664299 (2021).","journal-title":"Front. Microbiol."},{"key":"2480_CR20","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1016\/j.chom.2021.03.018","volume":"29","author":"BNJ Watson","year":"2021","unstructured":"Watson, B. N. J., Steens, J. A., Staals, R. H. J., Westra, E. R. & van Houte, S. Coevolution between bacterial CRISPR\u2013Cas systems and their bacteriophages. Cell Host Microbe 29, 715\u2013725 https:\/\/doi.org\/10.1016\/j.chom.2021.03.018 (2021).","journal-title":"Cell Host Microbe"},{"key":"2480_CR21","doi-asserted-by":"publisher","unstructured":"Zhang, A.-N. et al. CRISPR\u2013Cas spacer acquisition is a rare event in human gut microbiome. Cell Genom. 5, 100725 https:\/\/doi.org\/10.1016\/j.xgen.2024.100725 (2024).","DOI":"10.1016\/j.xgen.2024.100725"},{"key":"2480_CR22","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1126\/science.1157358","volume":"320","author":"AF Andersson","year":"2008","unstructured":"Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047\u20131050 https:\/\/doi.org\/10.1126\/science.1157358 (2008).","journal-title":"Science"},{"key":"2480_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms10613","volume":"7","author":"D Burstein","year":"2016","unstructured":"Burstein, D. et al. Major bacterial lineages are essentially devoid of CRISPR\u2013Cas viral defence systems. Nat. Commun. 7, 10613 https:\/\/doi.org\/10.1038\/ncomms10613 (2016).","journal-title":"Nat. Commun."},{"key":"2480_CR24","doi-asserted-by":"publisher","first-page":"370871","DOI":"10.1155\/2013\/370871","volume":"2013","author":"JB Emerson","year":"2013","unstructured":"Emerson, J. B. et al. Virus\u2013host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea 2013, 370871 https:\/\/doi.org\/10.1155\/2013\/370871 (2013).","journal-title":"Archaea"},{"key":"2480_CR25","doi-asserted-by":"publisher","first-page":"e00075","DOI":"10.1128\/msystems.00075-18","volume":"3","author":"WE England","year":"2018","unstructured":"England, W. E., Kim, T. & Whitaker, R. J. Metapopulation structure of CRISPR\u2013Cas immunity in Pseudomonas aeruginosa and its viruses. mSystems 3, e00075\u201318 https:\/\/doi.org\/10.1128\/msystems.00075-18 (2018).","journal-title":"mSystems"},{"key":"2480_CR26","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1038\/ismej.2015.162","volume":"10","author":"CL Sun","year":"2016","unstructured":"Sun, C. L., Thomas, B. C., Barrangou, R. & Banfield, J. F. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J. 10, 858\u2013870 https:\/\/doi.org\/10.1038\/ismej.2015.162 (2016).","journal-title":"ISME J"},{"key":"2480_CR27","doi-asserted-by":"publisher","unstructured":"Amundson, K. K., Roux, S., Shelton, J. L. & Wilkins, M. J. Long-term CRISPR locus dynamics and stable host\u2013virus co-existence in subsurface fractured shales. Curr. Biol. 33, 3125\u20133135.e4 https:\/\/doi.org\/10.1016\/j.cub.2023.06.033 (2023).","DOI":"10.1016\/j.cub.2023.06.033"},{"key":"2480_CR28","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/s41564-018-0190-y","volume":"3","author":"JB Emerson","year":"2018","unstructured":"Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870\u2013880 https:\/\/doi.org\/10.1038\/s41564-018-0190-y (2018).","journal-title":"Nat. Microbiol."},{"key":"2480_CR29","doi-asserted-by":"publisher","DOI":"10.1128\/aem.00177-23","volume":"89","author":"JC Kosmopoulos","year":"2023","unstructured":"Kosmopoulos, J. C., Campbell, D. E., Whitaker, R. J. & Wilbanks, E. G. Horizontal gene transfer and CRISPR targeting drive phage\u2013bacterial host interactions and coevolution in \u2018pink berry\u2019 marine microbial aggregates. Appl. Environ. Microbiol. 89, e00177-23 https:\/\/doi.org\/10.1128\/aem.00177-23 (2023).","journal-title":"Appl. Environ. Microbiol."},{"key":"2480_CR30","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wrae134","volume":"18","author":"A L\u00f3pez-Beltr\u00e1n","year":"2024","unstructured":"L\u00f3pez-Beltr\u00e1n, A., Botelho, J. & Iranzo, J. Dynamics of CRISPR-mediated virus\u2013host interactions in the human gut microbiome. ISME J. 18, wrae134 https:\/\/doi.org\/10.1093\/ismejo\/wrae134 (2024).","journal-title":"ISME J"},{"key":"2480_CR31","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1038\/s41564-022-01203-y","volume":"7","author":"AR Nelson","year":"2022","unstructured":"Nelson, A. R. et al. Wildfire-dependent changes in soil microbiome diversity and function. Nat. Microbiol. 7, 1419\u20131430 https:\/\/doi.org\/10.1038\/s41564-022-01203-y (2022).","journal-title":"Nat. Microbiol."},{"key":"2480_CR32","doi-asserted-by":"publisher","first-page":"i520","DOI":"10.1093\/bioinformatics\/btw456","volume":"32","author":"J Lei","year":"2016","unstructured":"Lei, J. & Sun, Y. Assemble CRISPRs from metagenomic sequencing data. Bioinformatics 32, i520\u2013i528 https:\/\/doi.org\/10.1093\/bioinformatics\/btw456 (2016).","journal-title":"Bioinformatics"},{"key":"2480_CR33","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.3788","volume":"5","author":"AG Moller","year":"2017","unstructured":"Moller, A. G. & Liang, C. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5, e3788 https:\/\/doi.org\/10.7717\/peerj.3788 (2017).","journal-title":"PeerJ"},{"key":"2480_CR34","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaa063","volume":"2","author":"JD Podlevsky","year":"2020","unstructured":"Podlevsky, J. D., Hudson, C. M., Timlin, J. A. & Williams, K. P. CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. NAR Genom. Bioinform. 2, lqaa063 https:\/\/doi.org\/10.1093\/nargab\/lqaa063 (2020).","journal-title":"NAR Genom. Bioinform."},{"key":"2480_CR35","doi-asserted-by":"publisher","first-page":"e105","DOI":"10.1093\/nar\/gkt183","volume":"41","author":"CT Skennerton","year":"2013","unstructured":"Skennerton, C. T., Imelfort, M. & Tyson, G. W. Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res. 41, e105 https:\/\/doi.org\/10.1093\/nar\/gkt183 (2013).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR36","doi-asserted-by":"publisher","first-page":"e00897-17","DOI":"10.1128\/mBio.00897-17","volume":"8","author":"S Silas","year":"2017","unstructured":"Silas, S. et al. On the origin of reverse transcriptase- using CRISPR\u2013Cas systems and their hyperdiverse, enigmatic spacer repertoires. mBio 8, e00897-17 https:\/\/doi.org\/10.1128\/mBio.00897-17 (2017).","journal-title":"mBio"},{"key":"2480_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-32078-6","volume":"13","author":"NA George","year":"2023","unstructured":"George, N. A. & Hug, L. A. CRISPR-resolved virus\u2013host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts. Sci. Rep. 13, 5611 https:\/\/doi.org\/10.1038\/s41598-023-32078-6 (2023).","journal-title":"Sci. Rep."},{"key":"2480_CR38","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1038\/s41564-023-01347-5","volume":"8","author":"Y Hwang","year":"2023","unstructured":"Hwang, Y., Roux, S., Coclet, C., Krause, S. J. E. & Girguis, P. R. Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nat. Microbiol. 8, 946\u2013957 https:\/\/doi.org\/10.1038\/s41564-023-01347-5 (2023).","journal-title":"Nat. Microbiol."},{"key":"2480_CR39","doi-asserted-by":"publisher","first-page":"e01766","DOI":"10.1128\/mbio.01766-23","volume":"14","author":"J Liu","year":"2023","unstructured":"Liu, J., Jaffe, A. L., Chen, L., Bor, B. & Banfield, J. F. Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria. mBio 14, e01766\u201323 https:\/\/doi.org\/10.1128\/mbio.01766-23 (2023).","journal-title":"mBio"},{"key":"2480_CR40","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1089\/crispr.2020.0059","volume":"3","author":"J Russel","year":"2020","unstructured":"Russel, J., Pinilla-Redondo, R., Mayo-Mu\u00f1oz, D., Shah, S. A. & S\u00f8rensen, S. J. CRISPRCasTyper: automated identification, annotation, and classification of CRISPR\u2013Cas loci. CRISPR J.3, 462\u2013469 https:\/\/doi.org\/10.1089\/crispr.2020.0059 (2020).","journal-title":"CRISPR J."},{"key":"2480_CR41","doi-asserted-by":"publisher","unstructured":"Arita, M., Karsch-Mizrachi, I. & Cochrane, G. on behalf of the International Nucleotide Sequence Database Collaboration. The international nucleotide sequence database collaboration. Nucleic Acids Res. 49, D121\u2013D124 https:\/\/doi.org\/10.1093\/nar\/gkaa967 (2021).","DOI":"10.1093\/nar\/gkaa967"},{"key":"2480_CR42","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/s41564-018-0312-6","volume":"4","author":"RA Daly","year":"2019","unstructured":"Daly, R. A. et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat. Microbiol. 4, 352\u2013361 https:\/\/doi.org\/10.1038\/s41564-018-0312-6 (2019).","journal-title":"Nat. Microbiol."},{"key":"2480_CR43","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1038\/nrg3425","volume":"14","author":"AD Cutter","year":"2013","unstructured":"Cutter, A. D. & Payseur, B. A. Genomic signatures of selection at linked sites: unifying the disparity among species. Nat. Rev. Genet. 14, 262\u2013274 https:\/\/doi.org\/10.1038\/nrg3425 (2013).","journal-title":"Nat. Rev. Genet."},{"key":"2480_CR44","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41564-017-0096-0","volume":"3","author":"RS Mehta","year":"2018","unstructured":"Mehta, R. S. et al. Stability of the human faecal microbiome in a cohort of adult men. Nat. Microbiol. 3, 347\u2013355 https:\/\/doi.org\/10.1038\/s41564-017-0096-0 (2018).","journal-title":"Nat. Microbiol."},{"key":"2480_CR45","doi-asserted-by":"publisher","first-page":"900","DOI":"10.4161\/rna.23929","volume":"10","author":"E Mick","year":"2013","unstructured":"Mick, E., Stern, A. & Sorek, R. Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes. RNA Biol. 10, 900\u2013906 https:\/\/doi.org\/10.4161\/rna.23929 (2013).","journal-title":"RNA Biol."},{"key":"2480_CR46","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.molcel.2016.02.031","volume":"62","author":"RT Leenay","year":"2016","unstructured":"Leenay, R. T. et al. Identifying and visualizing functional PAM diversity across CRISPR\u2013Cas systems. Mol. Cell 62, 137\u2013147 https:\/\/doi.org\/10.1016\/j.molcel.2016.02.031 (2016).","journal-title":"Mol. Cell"},{"key":"2480_CR47","doi-asserted-by":"publisher","first-page":"3523","DOI":"10.1093\/nar\/gkac142","volume":"50","author":"GA Rybnicky","year":"2022","unstructured":"Rybnicky, G. A., Fackler, N. A., Karim, A. S., K\u00f6pke, M. & Jewett, M. C. Spacer2PAM: a computational framework to guide experimental determination of functional CRISPR\u2013Cas system PAM sequences. Nucleic Acids Res. 50, 3523\u20133534 https:\/\/doi.org\/10.1093\/nar\/gkac142 (2022).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR48","doi-asserted-by":"publisher","unstructured":"Neri, U., Camargo, A. P., Bushnell, B., Beeloo, R. & Roux, S. Computational tool choice impacts CRISPR spacer-protospacer detection. Bioinformatics. 42, btag394 https:\/\/doi.org\/10.1093\/bioinformatics\/btag394 (2025).","DOI":"10.1093\/bioinformatics\/btag394"},{"key":"2480_CR49","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaf201","volume":"17","author":"K Sures","year":"2025","unstructured":"Sures, K. et al. Acquisition of spacers from foreign prokaryotic genomes by CRISPR\u2013Cas systems in natural environments. Genome Biol. Evol. 17, evaf201 https:\/\/doi.org\/10.1093\/gbe\/evaf201 (2025).","journal-title":"Genome Biol. Evol."},{"key":"2480_CR50","doi-asserted-by":"publisher","unstructured":"Hyman, P. & Abedon, S. T. Bacteriophage host range and bacterial resistance. In Advances in Applied Microbiology (eds Laskin, A. I. et al.), Ch. 7, 217\u2013248 https:\/\/doi.org\/10.1016\/S0065-2164(10)70007-1 (Academic Press, 2010).","DOI":"10.1016\/S0065-2164(10)70007-1"},{"key":"2480_CR51","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1146\/annurev-micro-030322-040423","volume":"76","author":"BR Macadangdang","year":"2022","unstructured":"Macadangdang, B. R., Makanani, S. K. & Miller, J. F. Accelerated evolution by diversity-generating retroelements. Annu. Rev. Microbiol. 76, 389\u2013411 https:\/\/doi.org\/10.1146\/annurev-micro-030322-040423 (2022).","journal-title":"Annu. Rev. Microbiol."},{"key":"2480_CR52","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1038\/s41564-021-00928-6","volume":"6","author":"S Nayfach","year":"2021","unstructured":"Nayfach, S. et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat. Microbiol. 6, 960\u2013970 https:\/\/doi.org\/10.1038\/s41564-021-00928-6 (2021).","journal-title":"Nat. Microbiol."},{"key":"2480_CR53","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/s41564-018-0302-8","volume":"4","author":"I Turgeman-Grott","year":"2019","unstructured":"Turgeman-Grott, I. et al. Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nat. Microbiol. 4, 177\u2013186 https:\/\/doi.org\/10.1038\/s41564-018-0302-8 (2019).","journal-title":"Nat. Microbiol."},{"key":"2480_CR54","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/nature19094","volume":"536","author":"D P\u00e1ez-Espino","year":"2016","unstructured":"P\u00e1ez-Espino, D. et al. Uncovering Earth\u2019s virome. Nature 536, 425\u2013430 https:\/\/doi.org\/10.1038\/nature19094 (2016).","journal-title":"Nature"},{"key":"2480_CR55","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.1111","volume":"9","author":"N Ikeyama","year":"2020","unstructured":"Ikeyama, N. et al. Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron. MicrobiologyOpen 9, e1111 https:\/\/doi.org\/10.1002\/mbo3.1111 (2020).","journal-title":"MicrobiologyOpen"},{"key":"2480_CR56","doi-asserted-by":"publisher","DOI":"10.1038\/srep33665","volume":"6","author":"N Nallabelli","year":"2016","unstructured":"Nallabelli, N. et al. Biochemical and genome sequence analyses of Megasphaera sp. strain DISK18 from dental plaque of a healthy individual reveals commensal lifestyle. Sci. Rep. 6, 33665 https:\/\/doi.org\/10.1038\/srep33665 (2016).","journal-title":"Sci. Rep."},{"key":"2480_CR57","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/nrmicro.2017.120","volume":"16","author":"A Pawluk","year":"2018","unstructured":"Pawluk, A., Davidson, A. R. & Maxwell, K. L. Anti-CRISPR: discovery, mechanism and function. Nat. Rev. Microbiol. 16, 12\u201317 https:\/\/doi.org\/10.1038\/nrmicro.2017.120 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"2480_CR58","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5922-8","volume":"20","author":"TJ Lam","year":"2019","unstructured":"Lam, T. J. & Ye, Y. Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes. BMC Genomics 20, 567 https:\/\/doi.org\/10.1186\/s12864-019-5922-8 (2019).","journal-title":"BMC Genomics"},{"key":"2480_CR59","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1007\/s00239-005-0223-z","volume":"62","author":"JS Godde","year":"2006","unstructured":"Godde, J. S. & Bickerton, A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62, 718\u2013729 https:\/\/doi.org\/10.1007\/s00239-005-0223-z (2006).","journal-title":"J. Mol. Evol."},{"key":"2480_CR60","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/S0958-1669(03)00036-3","volume":"14","author":"S Molin","year":"2003","unstructured":"Molin, S. & Tolker-Nielsen, T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14, 255\u2013261 https:\/\/doi.org\/10.1016\/S0958-1669(03)00036-3 (2003).","journal-title":"Curr. Opin. Biotechnol."},{"key":"2480_CR61","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1016\/j.mib.2007.06.004","volume":"10","author":"B Medhekar","year":"2007","unstructured":"Medhekar, B. & Miller, J. F. Diversity-generating retroelements. Curr. Opin. Microbiol. 10, 388\u2013395 https:\/\/doi.org\/10.1016\/j.mib.2007.06.004 (2007).","journal-title":"Curr. Opin. Microbiol."},{"key":"2480_CR62","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1038\/s41564-025-02203-4","volume":"11","author":"A Perfilyev","year":"2026","unstructured":"Perfilyev, A. et al. Large-scale analysis of bacterial genomes reveals thousands of lytic phages. Nat. Microbiol. 11, 42\u201352 https:\/\/doi.org\/10.1038\/s41564-025-02203-4 (2026).","journal-title":"Nat. Microbiol."},{"key":"2480_CR63","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/s41564-025-02207-0","volume":"11","author":"PE Dougherty","year":"2026","unstructured":"Dougherty, P. E. et al. Persistent virulent phages exist across bacterial isolates. Nat. Microbiol. 11, 31\u201341 https:\/\/doi.org\/10.1038\/s41564-025-02207-0 (2026).","journal-title":"Nat. Microbiol."},{"key":"2480_CR64","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1038\/ismej.2017.16","volume":"11","author":"C Howard-Varona","year":"2017","unstructured":"Howard-Varona, C., Hargreaves, K. R., Abedon, S. T. & Sullivan, M. B. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11, 1511\u20131520 https:\/\/doi.org\/10.1038\/ismej.2017.16 (2017).","journal-title":"ISME J"},{"key":"2480_CR65","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1038\/s41396-020-00870-1","volume":"15","author":"M Berg","year":"2021","unstructured":"Berg, M. et al. Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus\u2013host interactions. ISME J. 15, 1569\u20131584 https:\/\/doi.org\/10.1038\/s41396-020-00870-1 (2021).","journal-title":"ISME J."},{"key":"2480_CR66","doi-asserted-by":"publisher","first-page":"D134","DOI":"10.1093\/nar\/gkad903","volume":"52","author":"EW Sayers","year":"2024","unstructured":"Sayers, E. W. et al. GenBank 2024 update. Nucleic Acids Res. 52, D134\u2013D137 https:\/\/doi.org\/10.1093\/nar\/gkad903 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR67","doi-asserted-by":"publisher","first-page":"D723","DOI":"10.1093\/nar\/gkac976","volume":"51","author":"I-MA Chen","year":"2023","unstructured":"Chen, I.-M. A. et al. The IMG\/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res. 51, D723\u2013D732 https:\/\/doi.org\/10.1093\/nar\/gkac976 (2023).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR68","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1186\/1471-2105-8-209","volume":"8","author":"C Bland","year":"2007","unstructured":"Bland, C. et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinf. 8, 209 https:\/\/doi.org\/10.1186\/1471-2105-8-209 (2007).","journal-title":"BMC Bioinf."},{"key":"2480_CR69","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150\u20133152 https:\/\/doi.org\/10.1093\/bioinformatics\/bts565 (2012).","journal-title":"Bioinformatics"},{"key":"2480_CR70","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkz915","volume":"48","author":"C Pourcel","year":"2020","unstructured":"Pourcel, C. et al. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. Nucleic Acids Res. 48, D535\u2013D544 https:\/\/doi.org\/10.1093\/nar\/gkz915 (2020).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR71","doi-asserted-by":"publisher","unstructured":"Woodcroft, B. J., Cunningham, M., Gans, J. D., Bolduc, B. B. & Hodgkins, S. B. Kingfisher: a utility for procurement of public sequencing data. Version v0.4.0. Zenodo https:\/\/doi.org\/10.5281\/zenodo.10525086 (2024).","DOI":"10.5281\/zenodo.10525086"},{"key":"2480_CR72","doi-asserted-by":"publisher","first-page":"D957","DOI":"10.1093\/nar\/gkac974","volume":"51","author":"S Mukherjee","year":"2023","unstructured":"Mukherjee, S. et al. Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. Nucleic Acids Res. 51, D957\u2013D963 https:\/\/doi.org\/10.1093\/nar\/gkac974 (2023).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR73","doi-asserted-by":"publisher","first-page":"D753","DOI":"10.1093\/nar\/gkac1080","volume":"51","author":"L Richardson","year":"2022","unstructured":"Richardson, L. et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 51, D753\u2013D759 https:\/\/doi.org\/10.1093\/nar\/gkac1080 (2022).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR74","doi-asserted-by":"crossref","unstructured":"Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag New York, 2016).","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"2480_CR75","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583 https:\/\/doi.org\/10.1038\/nmeth.3869 (2016).","journal-title":"Nat. Methods"},{"key":"2480_CR76","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593\u2013594 https:\/\/doi.org\/10.1093\/bioinformatics\/btr708 (2012).","journal-title":"Bioinformatics"},{"key":"2480_CR77","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25 (2009).","journal-title":"Genome Biol"},{"key":"2480_CR78","doi-asserted-by":"publisher","first-page":"D733","DOI":"10.1093\/nar\/gkac1037","volume":"51","author":"AP Camargo","year":"2023","unstructured":"Camargo, A. P. et al. IMG\/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res. 51, D733\u2013D743 https:\/\/doi.org\/10.1093\/nar\/gkac1037 (2023).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR79","doi-asserted-by":"publisher","first-page":"D164","DOI":"10.1093\/nar\/gkad964","volume":"52","author":"AP Camargo","year":"2024","unstructured":"Camargo, A. P. et al. IMG\/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Res. 52, D164\u2013D173 https:\/\/doi.org\/10.1093\/nar\/gkad964 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR80","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 421 https:\/\/doi.org\/10.1186\/1471-2105-10-421 (2009).","journal-title":"BMC Bioinf."},{"key":"2480_CR81","doi-asserted-by":"publisher","first-page":"3155","DOI":"10.1093\/nar\/gkac163","volume":"50","author":"S Khedkar","year":"2022","unstructured":"Khedkar, S. et al. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. Nucleic Acids Res. 50, 3155\u20133168 https:\/\/doi.org\/10.1093\/nar\/gkac163 (2022).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR82","doi-asserted-by":"publisher","first-page":"lqab067","DOI":"10.1093\/nargab\/lqab067","volume":"3","author":"P Terzian","year":"2021","unstructured":"Terzian, P. et al. PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genom. Bioinform. 3, lqab067 https:\/\/doi.org\/10.1093\/nargab\/lqab067 (2021).","journal-title":"NAR Genom. Bioinform."},{"key":"2480_CR83","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 https:\/\/doi.org\/10.1371\/journal.pcbi.1002195 (2011).","journal-title":"PLoS Comput. Biol."},{"key":"2480_CR84","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23402-7","volume":"12","author":"S Roux","year":"2021","unstructured":"Roux, S. et al. Ecology and molecular targets of hypermutation in the global microbiome. Nat. Commun. 12, 3076 https:\/\/doi.org\/10.1038\/s41467-021-23402-7 (2021).","journal-title":"Nat. Commun."},{"key":"2480_CR85","doi-asserted-by":"publisher","first-page":"D419","DOI":"10.1093\/nar\/gkad932","volume":"52","author":"Y Yan","year":"2024","unstructured":"Yan, Y., Zheng, J., Zhang, X. & Yin, Y. dbAPIS: a database of anti-prokaryotic immune system genes. Nucleic Acids Res. 52, D419\u2013D425 https:\/\/doi.org\/10.1093\/nar\/gkad932 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2480_CR86","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59\u201360 https:\/\/doi.org\/10.1038\/nmeth.3176 (2015).","journal-title":"Nat. Methods"},{"key":"2480_CR87","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","volume":"35","author":"M Steinegger","year":"2017","unstructured":"Steinegger, M. & S\u00f6ding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026\u20131028 https:\/\/doi.org\/10.1038\/nbt.3988 (2017).","journal-title":"Nat. Biotechnol."},{"key":"2480_CR88","doi-asserted-by":"publisher","unstructured":"Zielezinski, A. et al. Ultrafast and accurate sequence alignment and clustering of viral genomes. Nat. Methods 22, 1191\u20131194, https:\/\/doi.org\/10.1038\/s41592-025-02701-7 (2025).","DOI":"10.1038\/s41592-025-02701-7"},{"key":"2480_CR89","doi-asserted-by":"publisher","first-page":"151","DOI":"10.12688\/f1000research.4492.2","volume":"3","author":"B Demchak","year":"2014","unstructured":"Demchak, B. et al. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 3, 151 https:\/\/doi.org\/10.12688\/f1000research.4492.2 (2014).","journal-title":"F1000Res."},{"key":"2480_CR90","doi-asserted-by":"publisher","unstructured":"Roux, S. Supplementary files for \u2018Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems\u2019. figshare https:\/\/doi.org\/10.6084\/m9.figshare.33089930 (2026).","DOI":"10.6084\/m9.figshare.33089930"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02480-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02480-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02480-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T10:02:52Z","timestamp":1793268172000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02480-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,29]]},"references-count":90,"alternative-id":["2480"],"URL":"https:\/\/doi.org\/10.1038\/s41564-026-02480-7","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,29]]},"assertion":[{"value":"22 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}