[{"doi":"10.1093/molbev/msag238","year":"2026","quality_controlled":"1","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Payne, P., Plevka, P., Bollback, J. P., &#38; Guet, C. C. (2026). Herd immunity underlies homologous recombination in stationary phase bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msag238\">https://doi.org/10.1093/molbev/msag238</a>","ieee":"P. Payne, P. Plevka, J. P. Bollback, and C. C. Guet, “Herd immunity underlies homologous recombination in stationary phase bacteria,” <i>Molecular Biology and Evolution</i>, vol. 43, no. 10. Oxford University Press, 2026.","ista":"Payne P, Plevka P, Bollback JP, Guet CC. 2026. Herd immunity underlies homologous recombination in stationary phase bacteria. Molecular Biology and Evolution. 43(10), msag238.","mla":"Payne, Pavel, et al. “Herd Immunity Underlies Homologous Recombination in Stationary Phase Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 43, no. 10, msag238, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/molbev/msag238\">10.1093/molbev/msag238</a>.","chicago":"Payne, Pavel, Pavel Plevka, Jonathan P Bollback, and Calin C Guet. “Herd Immunity Underlies Homologous Recombination in Stationary Phase Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/molbev/msag238\">https://doi.org/10.1093/molbev/msag238</a>.","short":"P. Payne, P. Plevka, J.P. Bollback, C.C. Guet, Molecular Biology and Evolution 43 (2026).","ama":"Payne P, Plevka P, Bollback JP, Guet CC. Herd immunity underlies homologous recombination in stationary phase bacteria. <i>Molecular Biology and Evolution</i>. 2026;43(10). doi:<a href=\"https://doi.org/10.1093/molbev/msag238\">10.1093/molbev/msag238</a>"},"publication_status":"epub_ahead","corr_author":"1","researchdata_availability":"no","pmid":1,"article_number":"msag238","supplementarymaterial":"yes","article_type":"original","OA_place":"publisher","oa":1,"das_tickbox":"1","publisher":"Oxford University Press","issue":"10","intvolume":"        43","OA_type":"gold","keyword":["homologous recombination","defense systems","CRISPR-Cas","herd immunity","stationary phase","bacterial evolution"],"volume":43,"date_created":"2026-10-11T22:02:04Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","DOAJ_listed":"1","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"type":"journal_article","article_processing_charge":"Yes","department":[{"_id":"CaGu"}],"status":"public","has_accepted_license":"1","month":"10","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1093/molbev/msag238","abstract":[{"lang":"eng","text":"Homologous recombination is ubiquitous across evolution, generating variation through genetic reshuffling. Although bacteria lack meiotic recombination, homologous recombination has been known to extensively shape their genomes. However, the mechanisms and ecological conditions sustaining frequent recombination in bacteria remain unclear. Using an Escherichia coli–P1 phage model system, we reveal how frequent recombination emerges from CRISPR-based herd immunity to a generalized transducing phage (DNA vector). Herd immunity maintains phage-susceptible donor bacteria, recipient immune bacteria, and transducing phage, which promotes chromosomal gene flow that exceeds spontaneous mutation by up to two orders of magnitude. Notably, recombination begins as bacterial cultures enter stationary phase, when canonical mutation supply through population growth and DNA replication is strongly reduced, and recombination can be reinitiated by brief fresh nutrient pulses. Genetic analysis showed that stationary-phase recombination requires recA, recB, and recG, connecting this process to a defined homologous recombination pathway, and suggests a plausible transcriptional regulatory link to transition to nutrient limitation. Bacterial herd immunity therefore has an unexpected evolutionary consequence: it can promote homologous recombination by turning phages into de facto pollinators. This mechanism can help explain how high rates of homologous recombination may be sustained across bacterial populations and suggests that bacterial immune systems can shape molecular evolution not only by blocking infection but also by regulating genetic exchange."}],"date_updated":"2026-10-12T10:51:54Z","day":"03","author":[{"full_name":"Payne, Pavel","last_name":"Payne","first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453"},{"first_name":"Pavel","full_name":"Plevka, Pavel","last_name":"Plevka"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"scopus_import":"1","publication":"Molecular Biology and Evolution","external_id":{"pmid":["42827080"]},"dataavailabilitystatement":"The data underlying this article are available in the article and in its online material.","_id":"23090","acknowledgement":"We thank Stuart Baird, Nick Barton, Max Joesch, Meriem El Karoui, Mato Lagator, Ivana Mašlaňová, Stepan Ovchinnikov, Roman Pantůček, Maroš Pleška, Jitka Polechová, and Bryan Wu for their feedback on the manuscript. We are grateful to the Redlinger Hut for hosting many discussions about the project away from the daily buzz. We acknowledge the core facility CELLIM supported by the Czech-BioImaging large RI project (LM2023050 funded by MEYS CR) for their support. This work was supported by H2020 European Research Council EVOLHGT No. 648440 to JPB, European Commission Programme EXCELES project LX22NPO5103 “National Institute of Virology and Bacteriology” to PPl, and a bilateral Czech-Austrian mobility grant 8J3AT003 funded by MEYS CR and OeAD AT to PPa and CCG.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/molbev/msag238"}],"oa_version":"Published Version","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"title":"Herd immunity underlies homologous recombination in stationary phase bacteria","date_published":"2026-10-03T00:00:00Z"},{"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","publisher":"Dryad","date_published":"2018-03-12T00:00:00Z","author":[{"first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453"},{"last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas","first_name":"Lukas"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"oa_version":"Published Version","oa":1,"related_material":{"record":[{"id":"423","relation":"used_in_publication","status":"public"}]},"_id":"9840","month":"03","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2025-04-15T08:17:50Z","day":"12","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"fulldoi":"https://doi.org/10.5061/dryad.42n44","citation":{"ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>."},"date_created":"2021-08-09T13:10:02Z","doi":"10.5061/dryad.42n44","year":"2018","type":"research_data_reference","article_processing_charge":"No"},{"isi":1,"project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"oa":1,"related_material":{"record":[{"relation":"research_data","id":"9840","status":"public"}]},"article_number":"e32035","file":[{"date_updated":"2020-07-14T12:46:25Z","file_name":"2018_eLife_Payne.pdf","access_level":"open_access","creator":"dernst","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","file_size":3533881,"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T10:36:07Z"}],"publisher":"eLife Sciences Publications","intvolume":"         7","quality_controlled":"1","ddc":["576"],"ec_funded":1,"year":"2018","doi":"10.7554/eLife.32035","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>"},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"423","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","oa_version":"Published Version","publication":"eLife","scopus_import":"1","author":[{"orcid":"0000-0002-2711-9453","first_name":"Pavel","full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"}],"external_id":{"isi":["000431035800001"]},"date_published":"2018-03-09T00:00:00Z","file_date_updated":"2020-07-14T12:46:25Z","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"7400","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","type":"journal_article","date_created":"2018-12-11T11:46:23Z","volume":7,"fulldoi":"https://doi.org/10.7554/eLife.32035","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"date_updated":"2025-03-31T16:00:24Z","day":"09","status":"public","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","month":"03","language":[{"iso":"eng"}]},{"day":"01","date_updated":"2026-04-08T14:16:28Z","abstract":[{"text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.","lang":"eng"}],"language":[{"iso":"eng"}],"month":"02","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","type":"dissertation","article_processing_charge":"No","date_created":"2019-04-09T15:16:45Z","file_date_updated":"2021-02-22T13:45:59Z","date_published":"2017-02-01T00:00:00Z","title":"Bacterial herd and social immunity to phages","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","_id":"6291","author":[{"orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne"}],"corr_author":"1","publication_status":"published","citation":{"apa":"Payne, P. (2017). <i>Bacterial herd and social immunity to phages</i>. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","mla":"Payne, Pavel. <i>Bacterial Herd and Social Immunity to Phages</i>. Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"degree_awarded":"PhD","year":"2017","page":"83","alternative_title":["ISTA Thesis"],"file":[{"creator":"dernst","access_level":"closed","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","file_id":"6292","date_updated":"2020-07-14T12:47:27Z","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","date_created":"2019-04-09T15:15:32Z","file_size":3025175,"relation":"main_file","content_type":"application/pdf"},{"checksum":"af531e921a7f64a9e0af4cd8783b2226","file_id":"9187","success":1,"access_level":"open_access","creator":"dernst","file_name":"2017_Payne_Thesis.pdf","date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","content_type":"application/pdf","file_size":3111536,"relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"oa":1,"OA_place":"publisher"}]