{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T19:19:49Z","timestamp":1788808789919,"version":"build-2803163510"},"reference-count":80,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM131738"],"award-info":[{"award-number":["R35GM131738"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. Department of Health & Human Services | National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM158145"],"award-info":[{"award-number":["R35GM158145"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000183","name":"United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office","doi-asserted-by":"publisher","award":["W911NF-20-1-0195"],"award-info":[{"award-number":["W911NF-20-1-0195"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-026-02438-9","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:04:05Z","timestamp":1787562245000},"page":"2408-2422","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Colibactin produced by a honeybee gut symbiont mediates pathogen defence"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9318-8158","authenticated-orcid":false,"given":"Yulin","family":"Song","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Elijah","family":"Powell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4627-4878","authenticated-orcid":false,"given":"Joel W. H.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunxi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2537-8371","authenticated-orcid":false,"given":"Miguel A.","family":"Aguilar Ramos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"De Jong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8427-3879","authenticated-orcid":false,"given":"Patrick J.","family":"Lariviere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayaditya","family":"Maganti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5985-5714","authenticated-orcid":false,"given":"Emily P.","family":"Balskus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2983-9769","authenticated-orcid":false,"given":"Nancy A.","family":"Moran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"2438_CR1","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1152\/physrev.00045.2009","volume":"90","author":"I Sekirov","year":"2010","unstructured":"Sekirov, I., Russell, S. L., Antunes, L. C. & Finlay, B. B. Gut microbiota in health and disease. Physiol. Rev. 90, 859\u2013904 (2010).","journal-title":"Physiol. Rev."},{"key":"2438_CR2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat2456","volume":"361","author":"L Garcia-Bayona","year":"2018","unstructured":"Garcia-Bayona, L. & Comstock, L. E. Bacterial antagonism in host-associated microbial communities. Science 361, eaat2456 (2018).","journal-title":"Science"},{"key":"2438_CR3","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41579-023-00990-3","volume":"22","author":"EVS Motta","year":"2024","unstructured":"Motta, E. V. S. & Moran, N. A. The honeybee microbiota and its impact on health and disease. Nat. Rev. Microbiol. 22, 122\u2013137 (2024).","journal-title":"Nat. Rev. Microbiol."},{"key":"2438_CR4","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1038\/nrmicro.2016.43","volume":"14","author":"WK Kwong","year":"2016","unstructured":"Kwong, W. K. & Moran, N. A. Gut microbial communities of social bees. Nat. Rev. Microbiol. 14, 374\u2013384 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"2438_CR5","doi-asserted-by":"publisher","first-page":"11509","DOI":"10.1073\/pnas.1405838111","volume":"111","author":"WK Kwong","year":"2014","unstructured":"Kwong, W. K., Engel, P., Koch, H. & Moran, N. A. Genomics and host specialization of honey bee and bumble bee gut symbionts. Proc. Natl Acad. Sci. USA 111, 11509\u201311514 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2115013119","volume":"119","author":"Y Li","year":"2022","unstructured":"Li, Y., Leonard, S. P., Powell, J. E. & Moran, N. A. Species divergence in gut-restricted bacteria of social bees. Proc. Natl Acad. Sci. USA 119, e2115013119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR7","doi-asserted-by":"publisher","first-page":"e00193-15","DOI":"10.1128\/mBio.00193-15","volume":"6","author":"P Engel","year":"2015","unstructured":"Engel, P., Bartlett, K. D. & Moran, N. A. The bacterium Frischella perrara causes scab formation in the gut of its honeybee host. mBio 6, e00193-15 (2015).","journal-title":"mBio"},{"key":"2438_CR8","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01649-18","volume":"9","author":"K Raymann","year":"2018","unstructured":"Raymann, K., Coon, K. L., Shaffer, Z., Salisbury, S. & Moran, N. A. Pathogenicity of Serratia marcescens strains in honey bees. mBio 9, e01649-18 (2018).","journal-title":"mBio"},{"key":"2438_CR9","doi-asserted-by":"publisher","first-page":"2576","DOI":"10.1111\/mec.14058","volume":"26","author":"O Emery","year":"2017","unstructured":"Emery, O., Schmidt, K. & Engel, P. Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera). Mol. Ecol. 26, 2576\u20132590 (2017).","journal-title":"Mol. Ecol."},{"key":"2438_CR10","doi-asserted-by":"publisher","first-page":"1502","DOI":"10.1128\/AEM.03283-14","volume":"81","author":"P Engel","year":"2015","unstructured":"Engel, P., Vizcaino, M. I. & Crawford, J. M. Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthesis pathways. Appl. Environ. Microbiol. 81, 1502\u20131512 (2015).","journal-title":"Appl. Environ. Microbiol."},{"key":"2438_CR11","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1126\/science.1127059","volume":"313","author":"JP Nougayrede","year":"2006","unstructured":"Nougayrede, J. P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848\u2013851 (2006).","journal-title":"Science"},{"key":"2438_CR12","doi-asserted-by":"publisher","first-page":"4696","DOI":"10.1128\/IAI.00522-09","volume":"77","author":"J Putze","year":"2009","unstructured":"Putze, J. et al. Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae. Infect. Immun. 77, 4696\u20134703 (2009).","journal-title":"Infect. Immun."},{"key":"2438_CR13","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1111\/1462-2920.12123","volume":"15","author":"V Bondarev","year":"2013","unstructured":"Bondarev, V. et al. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ. Microbiol. 15, 2095\u20132113 (2013).","journal-title":"Environ. Microbiol."},{"key":"2438_CR14","doi-asserted-by":"publisher","first-page":"2745","DOI":"10.1099\/ijs.0.026336-0","volume":"61","author":"C Moretti","year":"2011","unstructured":"Moretti, C. et al. Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Int. J. Syst. Evol. Microbiol. 61, 2745\u20132752 (2011).","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"2438_CR15","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.76182","volume":"12","author":"K Schmidt","year":"2023","unstructured":"Schmidt, K. et al. Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara. eLife 12, e76182 (2023).","journal-title":"eLife"},{"key":"2438_CR16","doi-asserted-by":"publisher","DOI":"10.1126\/science.aax2685","volume":"365","author":"M Xue","year":"2019","unstructured":"Xue, M. et al. Structure elucidation of colibactin and its DNA cross-links. Science 365, eaax2685 (2019).","journal-title":"Science"},{"key":"2438_CR17","doi-asserted-by":"publisher","first-page":"11537","DOI":"10.1073\/pnas.1001261107","volume":"107","author":"G Cuevas-Ramos","year":"2010","unstructured":"Cuevas-Ramos, G. et al. Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proc. Natl Acad. Sci. USA 107, 11537\u201311542 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR18","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/s41586-020-2080-8","volume":"580","author":"C Pleguezuelos-Manzano","year":"2020","unstructured":"Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269\u2013273 (2020).","journal-title":"Nature"},{"key":"2438_CR19","doi-asserted-by":"publisher","first-page":"6986","DOI":"10.1128\/AAC.00130-16","volume":"60","author":"T Fa\u00efs","year":"2016","unstructured":"Fa\u00efs, T. et al. Antibiotic activity of Escherichia coli against multiresistant Staphylococcus aureus. Antimicrob. Agents Chemother. 60, 6986\u20136988 (2016).","journal-title":"Antimicrob. Agents Chemother."},{"key":"2438_CR20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2121180119","volume":"119","author":"J Chen","year":"2022","unstructured":"Chen, J. et al. A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling. Proc. Natl Acad. Sci. USA 119, e2121180119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR21","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41586-022-04444-3","volume":"603","author":"JE Silpe","year":"2022","unstructured":"Silpe, J. E., Wong, J. W. H., Owen, S. V., Baym, M. & Balskus, E. P. The bacterial toxin colibactin triggers prophage induction. Nature 603, 315\u2013320 (2022).","journal-title":"Nature"},{"key":"2438_CR22","doi-asserted-by":"publisher","first-page":"e1010766","DOI":"10.1371\/journal.ppat.1010766","volume":"18","author":"JJ Wong","year":"2022","unstructured":"Wong, J. J. et al. Escherichia coli BarA-UvrY regulates the pks island and kills Staphylococci via the genotoxin colibactin during interspecies competition. PLoS Pathog. 18, e1010766 (2022).","journal-title":"PLoS Pathog."},{"key":"2438_CR23","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01875-24","volume":"16","author":"E Lowry","year":"2024","unstructured":"Lowry, E. & Mitchell, A. Colibactin-induced damage in bacteria is cell contact independent. mBio 16, e0187524 (2024).","journal-title":"mBio"},{"key":"2438_CR24","doi-asserted-by":"publisher","first-page":"e00589-20","DOI":"10.1128\/msphere.00589-20","volume":"5","author":"S Tronnet","year":"2020","unstructured":"Tronnet, S. et al. The genotoxin colibactin shapes gut microbiota in mice. mSphere 5, e00589-20 (2020).","journal-title":"mSphere"},{"key":"2438_CR25","doi-asserted-by":"publisher","first-page":"3704","DOI":"10.1128\/IAI.00716-15","volume":"83","author":"AJ McCarthy","year":"2015","unstructured":"McCarthy, A. J. et al. The genotoxin colibactin is a determinant of virulence in Escherichia coli K1 experimental neonatal systemic infection. Infect. Immun. 83, 3704\u20133711 (2015).","journal-title":"Infect. Immun."},{"key":"2438_CR26","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/s41684-018-0173-x","volume":"47","author":"H Zheng","year":"2018","unstructured":"Zheng, H., Steele, M. I., Leonard, S. P., Motta, E. V. S. & Moran, N. A. Honey bees as models for gut microbiota research. Lab. Anim. 47, 317\u2013325 (2018).","journal-title":"Lab. Anim."},{"key":"2438_CR27","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00103-21","volume":"9","author":"JE Powell","year":"2021","unstructured":"Powell, J. E., Carver, Z., Leonard, S. P. & Moran, N. A. Field-realistic tylosin exposure impacts honey bee microbiota and pathogen susceptibility, which is ameliorated by native gut probiotics. Microbiol. Spectr. 9, e0010321 (2021).","journal-title":"Microbiol. Spectr."},{"key":"2438_CR28","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2222437","volume":"15","author":"N Bossuet","year":"2023","unstructured":"Bossuet, N. et al. Oxygen concentration modulates colibactin production. Gut Microbes 15, 2222437 (2023).","journal-title":"Gut Microbes"},{"key":"2438_CR29","doi-asserted-by":"publisher","first-page":"3359","DOI":"10.1021\/ja312154m","volume":"135","author":"CA Brotherton","year":"2013","unstructured":"Brotherton, C. A. & Balskus, E. P. A prodrug resistance mechanism is involved in colibactin biosynthesis and cytotoxicity. J. Am. Chem. Soc. 135, 3359\u20133362 (2013).","journal-title":"J. Am. Chem. Soc."},{"key":"2438_CR30","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1111\/mmi.13272","volume":"99","author":"N Bossuet-Greif","year":"2016","unstructured":"Bossuet-Greif, N. et al. Escherichia coli ClbS is a colibactin resistance protein. Mol. Microbiol. 99, 897\u2013908 (2016).","journal-title":"Mol. Microbiol."},{"key":"2438_CR31","doi-asserted-by":"publisher","first-page":"e0286070","DOI":"10.1371\/journal.pone.0286070","volume":"18","author":"JE Powell","year":"2023","unstructured":"Powell, J. E. et al. The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes. PLoS ONE 18, e0286070 (2023).","journal-title":"PLoS ONE"},{"key":"2438_CR32","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1126\/science.aaf3951","volume":"353","author":"AH Moeller","year":"2016","unstructured":"Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380\u2013382 (2016).","journal-title":"Science"},{"key":"2438_CR33","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1146\/annurev-micro-092412-155715","volume":"69","author":"A Brune","year":"2015","unstructured":"Brune, A. & Dietrich, C. The gut microbiota of termites: digesting the diversity in the light of ecology and evolution. Annu. Rev. Microbiol. 69, 145\u2013166 (2015).","journal-title":"Annu. Rev. Microbiol."},{"key":"2438_CR34","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1600513","volume":"3","author":"WK Kwong","year":"2017","unstructured":"Kwong, W. K. et al. Dynamic microbiome evolution in social bees. Sci. Adv. 3, e1600513 (2017).","journal-title":"Sci. Adv."},{"key":"2438_CR35","doi-asserted-by":"publisher","first-page":"17719","DOI":"10.1021\/jacs.7b09971","volume":"139","author":"P Tripathi","year":"2017","unstructured":"Tripathi, P. et al. ClbS is a cyclopropane hydrolase that confers colibactin resistance. J. Am. Chem. Soc. 139, 17719\u201317722 (2017).","journal-title":"J. Am. Chem. Soc."},{"key":"2438_CR36","doi-asserted-by":"publisher","first-page":"3286","DOI":"10.1021\/acschembio.8b00714","volume":"13","author":"EE Shine","year":"2018","unstructured":"Shine, E. E. et al. Model colibactins exhibit human cell genotoxicity in the absence of host bacteria. ACS Chem. Biol. 13, 3286\u20133293 (2018).","journal-title":"ACS Chem. Biol."},{"key":"2438_CR37","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/s41564-025-02177-3","volume":"11","author":"S Yang","year":"2026","unstructured":"Yang, S. et al. Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut. Nat. Microbiol. 11, 53\u201366 (2026).","journal-title":"Nat. Microbiol."},{"key":"2438_CR38","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00063-21","volume":"6","author":"MI Steele","year":"2021","unstructured":"Steele, M. I. & Moran, N. A. Evolution of interbacterial antagonism in bee gut microbiota reflects host and symbiont diversification. mSystems 6, e00063-21 (2021).","journal-title":"mSystems"},{"key":"2438_CR39","doi-asserted-by":"publisher","first-page":"6895","DOI":"10.1021\/acs.orglett.1c02461","volume":"23","author":"CS Kim","year":"2021","unstructured":"Kim, C. S., Turocy, T., Moon, G., Shine, E. E. & Crawford, J. M. Escherichia coli-derived \u03b3-lactams and structurally related metabolites are produced at the intersection of colibactin and fatty acid biosynthesis. Org. Lett. 23, 6895\u20136899 (2021).","journal-title":"Org. Lett."},{"key":"2438_CR40","doi-asserted-by":"publisher","first-page":"e1003437","DOI":"10.1371\/journal.ppat.1003437","volume":"9","author":"P Martin","year":"2013","unstructured":"Martin, P. et al. Interplay between siderophores and colibactin genotoxin biosynthetic pathways in Escherichia coli. PLoS Pathog. 9, e1003437 (2013).","journal-title":"PLoS Pathog."},{"key":"2438_CR41","doi-asserted-by":"publisher","first-page":"4775","DOI":"10.1073\/pnas.1701819114","volume":"114","author":"H Zheng","year":"2017","unstructured":"Zheng, H., Powell, J. E., Steele, M. I., Dietrich, C. & Moran, N. A. Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proc. Natl Acad. Sci. USA 114, 4775\u20134780 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR42","doi-asserted-by":"publisher","first-page":"501","DOI":"10.4161\/gmic.21737","volume":"3","author":"M Olier","year":"2012","unstructured":"Olier, M. et al. Genotoxicity of Escherichia coli Nissle 1917 strain cannot be dissociated from its probiotic activity. Gut Microbes 3, 501\u2013509 (2012).","journal-title":"Gut Microbes"},{"key":"2438_CR43","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1101\/gr.279517.124","volume":"34","author":"E Lowry","year":"2024","unstructured":"Lowry, E., Wang, Y., Dagan, T. & Mitchell, A. Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage. Genome Res. 34, 1154\u20131164 (2024).","journal-title":"Genome Res."},{"key":"2438_CR44","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01392-24","volume":"15","author":"PJ Lariviere","year":"2024","unstructured":"Lariviere, P. J. et al. One-step genome engineering in bee gut bacterial symbionts. mBio 15, e0139224 (2024).","journal-title":"mBio"},{"key":"2438_CR45","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1021\/acssynbio.7b00399","volume":"7","author":"SP Leonard","year":"2018","unstructured":"Leonard, S. P. et al. Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. ACS Synth. Biol. 7, 1279\u20131290 (2018).","journal-title":"ACS Synth. Biol."},{"key":"2438_CR46","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2219634120","volume":"120","author":"L Guo","year":"2023","unstructured":"Guo, L., Tang, J., Tang, M., Luo, S. & Zhou, X. Reactive oxygen species are regulated by immune deficiency and Toll pathways in determining the host specificity of honeybee gut bacteria. Proc. Natl Acad. Sci. USA 120, e2219634120 (2023).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2438_CR47","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/jisesa\/ieae107","volume":"24","author":"JD Evans","year":"2024","unstructured":"Evans, J. D. et al. Bee cups 2.0: P-cups as single-use cages for honey bee (Hymenoptera: Apidae) experiments. J. Insect. Sci. 24, 3 (2024).","journal-title":"J. Insect. Sci."},{"key":"2438_CR48","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852\u2013857 (2019).","journal-title":"Nat. Biotechnol."},{"key":"2438_CR49","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10\u201312 (2011).","journal-title":"EMBnet J."},{"key":"2438_CR50","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00191-16","volume":"2","author":"A Amir","year":"2017","unstructured":"Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2, e00191-16 (2017).","journal-title":"mSystems"},{"key":"2438_CR51","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590\u2013D596 (2013).","journal-title":"Nucleic Acids Res."},{"key":"2438_CR52","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0470-z","volume":"6","author":"NA Bokulich","year":"2018","unstructured":"Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin. Microbiome 6, 90 (2018).","journal-title":"Microbiome"},{"key":"2438_CR53","doi-asserted-by":"publisher","first-page":"2830","DOI":"10.1128\/AEM.07810-11","volume":"78","author":"VG Martinson","year":"2012","unstructured":"Martinson, V. G., Moy, J. & Moran, N. A. Establishment of characteristic gut bacteria during development of the honeybee worker. Appl. Environ. Microbiol. 78, 2830\u20132840 (2012).","journal-title":"Appl. Environ. Microbiol."},{"key":"2438_CR54","doi-asserted-by":"publisher","first-page":"7378","DOI":"10.1128\/AEM.01861-14","volume":"80","author":"JE Powell","year":"2014","unstructured":"Powell, J. E., Martinson, V. G., Urban-Mead, K. & Moran, N. A. Routes of acquisition of the gut microbiota of the honey bee Apis mellifera. Appl. Environ. Microbiol. 80, 7378\u20137387 (2014).","journal-title":"Appl. Environ. Microbiol."},{"key":"2438_CR55","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1007\/978-1-4939-0554-6_12","volume":"1151","author":"DE Deatherage","year":"2014","unstructured":"Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165\u2013188 (2014).","journal-title":"Methods Mol. Biol."},{"key":"2438_CR56","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","volume":"37","author":"CLM Gilchrist","year":"2021","unstructured":"Gilchrist, C. L. M. & Chooi, Y. H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473\u20132475 (2021).","journal-title":"Bioinformatics"},{"key":"2438_CR57","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"2438_CR58","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsdottir","year":"2013","unstructured":"Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14, 178\u2013192 (2013).","journal-title":"Brief Bioinform."},{"key":"2438_CR59","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","volume":"33","author":"Z Xie","year":"2017","unstructured":"Xie, Z. & Tang, H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 33, 3340\u20133347 (2017).","journal-title":"Bioinformatics"},{"key":"2438_CR60","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).","journal-title":"Genome Res."},{"key":"2438_CR61","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).","journal-title":"BMC Bioinform."},{"key":"2438_CR62","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"2438_CR63","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"2438_CR64","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"2438_CR65","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78\u2013W82 (2024).","journal-title":"Nucleic Acids Res."},{"key":"2438_CR66","doi-asserted-by":"publisher","unstructured":"Guo, J., Vik, D., Pratama, A. A., Roux, S. & Sullivan, M. Viral sequence identification SOP with VirSorter2. protocols.io https:\/\/doi.org\/10.17504\/protocols.io.bwm5pc86 (2021).","DOI":"10.17504\/protocols.io.bwm5pc86"},{"key":"2438_CR67","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00990-y","volume":"9","author":"J Guo","year":"2021","unstructured":"Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).","journal-title":"Microbiome"},{"key":"2438_CR68","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","volume":"39","author":"S Nayfach","year":"2021","unstructured":"Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578\u2013585 (2021).","journal-title":"Nat. Biotechnol."},{"key":"2438_CR69","doi-asserted-by":"publisher","first-page":"8883","DOI":"10.1093\/nar\/gkaa621","volume":"48","author":"M Shaffer","year":"2020","unstructured":"Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883\u20138900 (2020).","journal-title":"Nucleic Acids Res."},{"key":"2438_CR70","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac776","volume":"39","author":"G Bouras","year":"2023","unstructured":"Bouras, G. et al. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics 39, btac776 (2023).","journal-title":"Bioinformatics"},{"key":"2438_CR71","unstructured":"Fox, J. & Weisberg, S. An R Companion to Applied Regression 3rd edn (Sage Publications, 2019); https:\/\/cran.r-project.org\/web\/packages\/car\/"},{"key":"2438_CR72","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).","journal-title":"J. Open Source Softw."},{"key":"2438_CR73","unstructured":"Eklund, A. & Trimble, J. beeswarm: the bee swarm plot, an alternative to stripchart. R package version 0.4.0 https:\/\/cran.r-project.org\/web\/packages\/beeswarm\/ (2021)."},{"key":"2438_CR74","unstructured":"Tiedemann, F. gghalves: compose half-half plots using your favourite geoms. R package version 0.1.4 https:\/\/cran.r-project.org\/web\/packages\/gghalves\/ (2025)."},{"key":"2438_CR75","unstructured":"Kassambara, A., Kosinski, M. & Biecek, P. survminer: drawing survival curves using \u2018ggplot2\u2019. R package version 0.5.2 https:\/\/cran.r-project.org\/web\/packages\/survminer\/ (2024)."},{"key":"2438_CR76","unstructured":"Therneau, T. A package for survival analysis in R. R package version 3.8-6 https:\/\/cran.r-project.org\/web\/packages\/survival\/ (2024)."},{"key":"2438_CR77","unstructured":"Therneau, T. coxme: mixed effects cox models. R package version 2.2-22 https:\/\/cran.r-project.org\/web\/packages\/coxme\/ (2024)."},{"key":"2438_CR78","unstructured":"Lenth, R. emmeans: estimated marginal means, aka least-squares means. R package version 2.0.3 https:\/\/cran.r-project.org\/web\/packages\/emmeans\/ (2024)."},{"key":"2438_CR79","unstructured":"Ogle, D. H., Doll, J. C., Wheeler, A. P. & Dinno, A. FSA: simple fisheries stock assessment methods. R package version 0.10.1 https:\/\/cran.r-project.org\/web\/packages\/FSA\/ (2025)."},{"key":"2438_CR80","doi-asserted-by":"publisher","unstructured":"Aguilar Ramos, M. A. LC\u2013MS dataset for \u2018Colibactin produced by a honeybee gut symbiont mediates pathogen defense.\u2019. Zenodo https:\/\/doi.org\/10.5281\/zenodo.20682763 (2026).","DOI":"10.5281\/zenodo.20682763"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02438-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02438-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02438-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T15:05:10Z","timestamp":1787929510000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-026-02438-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,24]]},"references-count":80,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["2438"],"URL":"https:\/\/doi.org\/10.1038\/s41564-026-02438-9","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,24]]},"assertion":[{"value":"2 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 August 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"}}]}}