{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T18:15:40Z","timestamp":1780596940314,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014339","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000}}],"reference-count":73,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["RGY0064\/2022"],"award-info":[{"award-number":["RGY0064\/2022"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["1281\/20"],"award-info":[{"award-number":["1281\/20"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014385","name":"Kreitman School of Advanced Graduate Studies, Ben-Gurion University of the Negev","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014385","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Plasmids drive evolution by transferring traits across microbial hosts. Transmission depends on both host\u2013plasmid (infection) and plasmid\u2013plasmid (compatibility) interactions, yet how the structure of these networks shapes transmission remains poorly understood. We hypothesized that these two ecological networks interact in non-additive ways to influence community outcomes. To test this, we developed a stochastic agent-based model that embeds both network structures and simulates coupled host\u2013plasmid dynamics. We systematically varied the structure of each network, both individually and in combination, to isolate the effect of structure on host-plasmid dynamics. A modular (interactions organized into clusters) and hub (interactions concentrated on the highly connected) plasmid-plasmid compatibility network promoted transient host coexistence, while a modular host-plasmid infection network promoted plasmid diversity and stable host coexistence. Importantly, structured networks interacted non-additively, and their impact was most apparent when plasmid carriage imposed a moderate fitness cost on hosts. For example, combining a modular infection network with a hub compatibility network reversed the expected plasmid prevalence patterns, demonstrating that the structure of one network can counteract the effects of the other. We further re-parameterized our model to recapitulate empirical host-plasmid community dynamics, showing that infection network structure can strongly shape plasmid prevalence even in the presence of substantial biological heterogeneity. Our results highlight the necessity of jointly considering host\u2013plasmid infection and plasmid\u2013plasmid compatibility networks to understand host\u2013plasmid community dynamics and their eco-evolutionary potential. More broadly, this work provides an initial mechanistic framework for generating testable hypotheses and underscores that systems involving multiple hosts and infectious agents require explicit consideration of how different ecological networks interact to shape community dynamics.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1014339","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T17:46:37Z","timestamp":1779817597000},"page":"e1014339","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["The interplay between ecological networks drives host-plasmid community dynamics"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9091-6423","authenticated-orcid":true,"given":"Ying-Jie","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9033-9646","authenticated-orcid":true,"given":"Kaitlin A.","family":"Schaal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Nauta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Armun","family":"Liaghat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5158-8594","authenticated-orcid":true,"given":"Manlio","family":"De Domenico","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James P. J.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0430-5568","authenticated-orcid":true,"given":"Shai","family":"Pilosof","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"issue":"1","key":"pcbi.1014339.ref001","article-title":"Plasmid detection, characterization, and ecology","volume":"3","author":"S Kornelia","year":"2015","journal-title":"Microbiology Spectrum"},{"issue":"12","key":"pcbi.1014339.ref002","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1016\/j.tim.2018.06.007","article-title":"Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context","volume":"26","author":"A San Millan","year":"2018","journal-title":"Trends Microbiol"},{"issue":"6","key":"pcbi.1014339.ref003","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41579-020-00497-1","article-title":"Beyond horizontal gene transfer: the role of plasmids in bacterial evolution","volume":"19","author":"J Rodr\u00edguez-Beltr\u00e1n","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"pcbi.1014339.ref004","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.MTBP-0016-2017","article-title":"Fitness Costs of Plasmids: a Limit to Plasmid Transmission","volume":"5","author":"A San Millan","year":"2017","journal-title":"Microbiol Spectr"},{"issue":"10","key":"pcbi.1014339.ref005","article-title":"Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation","volume":"19","author":"JPJ Hall","year":"2021","journal-title":"PLoS Biol"},{"issue":"10","key":"pcbi.1014339.ref006","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.tim.2016.06.011","article-title":"The Ecology and Evolution of Microbial Competition","volume":"24","author":"M Ghoul","year":"2016","journal-title":"Trends Microbiol"},{"issue":"11","key":"pcbi.1014339.ref007","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3001847","article-title":"Horizontal gene transfer and ecological interactions jointly control microbiome stability","volume":"20","author":"KZ Coyte","year":"2022","journal-title":"PLoS Biol"},{"issue":"1842","key":"pcbi.1014339.ref008","doi-asserted-by":"crossref","first-page":"20200478","DOI":"10.1098\/rstb.2020.0478","article-title":"Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics","volume":"377","author":"C Igler","year":"2022","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"7","key":"pcbi.1014339.ref009","doi-asserted-by":"crossref","first-page":"001362","DOI":"10.1099\/mic.0.001362","article-title":"A mathematician\u2019s guide to plasmids: an introduction to plasmid biology for modellers","volume":"169","author":"I Dewan","year":"2023","journal-title":"Microbiology (Reading)"},{"issue":"29","key":"pcbi.1014339.ref010","doi-asserted-by":"crossref","first-page":"8260","DOI":"10.1073\/pnas.1600974113","article-title":"Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities","volume":"113","author":"JPJ Hall","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9","key":"pcbi.1014339.ref011","doi-asserted-by":"crossref","first-page":"001086","DOI":"10.1099\/mic.0.001086","article-title":"The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities","volume":"167","author":"A Kottara","year":"2021","journal-title":"Microbiology (Reading)"},{"issue":"12","key":"pcbi.1014339.ref012","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/s41559-020-01312-z","article-title":"The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification","volume":"4","author":"S Pilosof","year":"2020","journal-title":"Nat Ecol Evol"},{"issue":"1","key":"pcbi.1014339.ref013","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/s12866-020-01825-4","article-title":"Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis","volume":"20","author":"JB Alderliesten","year":"2020","journal-title":"BMC Microbiol"},{"issue":"21","key":"pcbi.1014339.ref014","doi-asserted-by":"crossref","DOI":"10.1016\/j.molcel.2022.09.008","article-title":"The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA","volume":"82","author":"A Deep","year":"2022","journal-title":"Mol Cell"},{"issue":"7905","key":"pcbi.1014339.ref015","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41586-022-04546-y","article-title":"Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae","volume":"604","author":"M Jask\u00f3lska","year":"2022","journal-title":"Nature"},{"issue":"4","key":"pcbi.1014339.ref016","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1128\/mr.51.4.381-395.1987","article-title":"Plasmid incompatibility","volume":"51","author":"RP Novick","year":"1987","journal-title":"Microbiol Rev"},{"issue":"3","key":"pcbi.1014339.ref017","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/ismej.2013.182","article-title":"Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations","volume":"8","author":"A San Millan","year":"2014","journal-title":"ISME J"},{"key":"pcbi.1014339.ref018","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.plasmid.2019.01.003","article-title":"Interactions between plasmids and other mobile genetic elements affect their transmission and persistence","volume":"102","author":"F Dionisio","year":"2019","journal-title":"Plasmid"},{"issue":"23","key":"pcbi.1014339.ref019","doi-asserted-by":"crossref","first-page":"12643","DOI":"10.1073\/pnas.220077897","article-title":"Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids","volume":"97","author":"TF Cooper","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pcbi.1014339.ref020","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.ESP-0028-2021","article-title":"A Brief History of Plasmids","volume":"10","author":"DR Helinski","year":"2022","journal-title":"EcoSal Plus"},{"issue":"4","key":"pcbi.1014339.ref021","doi-asserted-by":"crossref","first-page":"2000","DOI":"10.1093\/nar\/gkz1197","article-title":"Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids","volume":"48","author":"R Pinilla-Redondo","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1014339.ref022","article-title":"Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?","volume":"20","author":"EPC Rocha","year":"2022","journal-title":"PLoS Biol"},{"issue":"7","key":"pcbi.1014339.ref023","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/j.tim.2023.01.007","article-title":"Conceptualizing microbe-plasmid communities as complex adaptive systems","volume":"31","author":"S Pilosof","year":"2023","journal-title":"Trends Microbiol"},{"issue":"1","key":"pcbi.1014339.ref024","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1038\/s41467-024-45154-w","article-title":"Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species","volume":"15","author":"S Zhu","year":"2024","journal-title":"Nat Commun"},{"issue":"1","key":"pcbi.1014339.ref025","doi-asserted-by":"crossref","first-page":"5589","DOI":"10.1038\/s41467-020-19368-7","article-title":"The persistence potential of transferable plasmids","volume":"11","author":"T Wang","year":"2020","journal-title":"Nat Commun"},{"issue":"1","key":"pcbi.1014339.ref026","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41467-024-44827-w","article-title":"Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes","volume":"15","author":"A Risely","year":"2024","journal-title":"Nat Commun"},{"issue":"7241","key":"pcbi.1014339.ref027","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1038\/nature07950","article-title":"The architecture of mutualistic networks minimizes competition and increases biodiversity","volume":"458","author":"U Bastolla","year":"2009","journal-title":"Nature"},{"issue":"5993","key":"pcbi.1014339.ref028","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1126\/science.1188321","article-title":"Stability of ecological communities and the architecture of mutualistic and trophic networks","volume":"329","author":"E Th\u00e9bault","year":"2010","journal-title":"Science"},{"issue":"4","key":"pcbi.1014339.ref029","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41559-017-0101","article-title":"The multilayer nature of ecological networks","volume":"1","author":"S Pilosof","year":"2017","journal-title":"Nat Ecol Evol"},{"issue":"6","key":"pcbi.1014339.ref030","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000336","article-title":"Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum","volume":"17","author":"S Pilosof","year":"2019","journal-title":"PLoS Biol"},{"issue":"217","key":"pcbi.1014339.ref031","doi-asserted-by":"crossref","first-page":"20240195","DOI":"10.1098\/rsif.2024.0195","article-title":"Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution","volume":"21","author":"A Liaghat","year":"2024","journal-title":"J R Soc Interface"},{"issue":"6261","key":"pcbi.1014339.ref032","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1126\/science.aad2602","article-title":"The ecology of the microbiome: Networks, competition, and stability","volume":"350","author":"KZ Coyte","year":"2015","journal-title":"Science"},{"key":"pcbi.1014339.ref033","doi-asserted-by":"crossref","first-page":"1173748","DOI":"10.3389\/fmicb.2023.1173748","article-title":"Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota","volume":"14","author":"L Li","year":"2023","journal-title":"Front Microbiol"},{"issue":"22","key":"pcbi.1014339.ref034","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2118361119","article-title":"Fitness effects of plasmids shape the structure of bacteria-plasmid interaction networks","volume":"119","author":"A Newbury","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"28","key":"pcbi.1014339.ref035","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1101595108","article-title":"Statistical structure of host-phage interactions","volume":"108","author":"CO Flores","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1014339.ref036","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.tim.2012.11.003","article-title":"Phage-bacteria infection networks","volume":"21","author":"JS Weitz","year":"2013","journal-title":"Trends Microbiol"},{"key":"pcbi.1014339.ref037","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1146\/annurev-marine-010213-135108","article-title":"Antagonistic coevolution of marine planktonic viruses and their hosts","volume":"6","author":"JBH Martiny","year":"2014","journal-title":"Ann Rev Mar Sci"},{"issue":"6","key":"pcbi.1014339.ref038","doi-asserted-by":"crossref","first-page":"20130033","DOI":"10.1098\/rsfs.2013.0033","article-title":"Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks","volume":"3","author":"SJ Beckett","year":"2013","journal-title":"Interface Focus"},{"issue":"5","key":"pcbi.1014339.ref039","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1111\/evo.13731","article-title":"Coevolutionary dynamics shape the structure of bacteria-phage infection networks","volume":"73","author":"MA Fortuna","year":"2019","journal-title":"Evolution"},{"issue":"5","key":"pcbi.1014339.ref040","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/j.mib.2011.07.027","article-title":"Trends and barriers to lateral gene transfer in prokaryotes","volume":"14","author":"O Popa","year":"2011","journal-title":"Curr Opin Microbiol"},{"issue":"2","key":"pcbi.1014339.ref041","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/ismej.2016.116","article-title":"Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction","volume":"11","author":"O Popa","year":"2017","journal-title":"ISME J"},{"issue":"3","key":"pcbi.1014339.ref042","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1128\/MMBR.00020-10","article-title":"Mobility of plasmids","volume":"74","author":"C Smillie","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"issue":"9","key":"pcbi.1014339.ref043","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003844","article-title":"Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids","volume":"9","author":"W Jiang","year":"2013","journal-title":"PLoS Genet"},{"issue":"102449","key":"pcbi.1014339.ref044","article-title":"The winding journey of conjugative plasmids toward a novel host cell","volume":"78","author":"N Fraikin","year":"2024","journal-title":"Curr Opin Microbiol"},{"issue":"12","key":"pcbi.1014339.ref045","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1038\/ismej.2010.72","article-title":"Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein","volume":"4","author":"M Sota","year":"2010","journal-title":"ISME J"},{"key":"pcbi.1014339.ref046","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.3389\/fmicb.2020.02033","article-title":"Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations","volume":"11","author":"JA Gama","year":"2020","journal-title":"Front Microbiol"},{"key":"pcbi.1014339.ref047","article-title":"Plasmids link antibiotic resistance genes and phage defense systems in E. coli","author":"W \u015alesak","year":"2025","journal-title":"bioRxiv"},{"issue":"2","key":"pcbi.1014339.ref048","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01735-16","article-title":"A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance","volume":"61","author":"A Santos-Lopez","year":"2017","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"pcbi.1014339.ref049","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.jtbi.2008.01.023","article-title":"Relaxing the zero-sum assumption in neutral biodiversity theory","volume":"252","author":"B Haegeman","year":"2008","journal-title":"J Theor Biol"},{"issue":"8","key":"pcbi.1014339.ref050","article-title":"Transient invaders can induce shifts between alternative stable states of microbial communities","volume":"6","author":"DR Amor","year":"2020","journal-title":"Sci Adv"},{"issue":"12","key":"pcbi.1014339.ref051","doi-asserted-by":"crossref","first-page":"5008","DOI":"10.1111\/1462-2920.12901","article-title":"Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects","volume":"17","author":"JPJ Hall","year":"2015","journal-title":"Environ Microbiol"},{"key":"pcbi.1014339.ref052","article-title":"The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities","author":"d Valle AA","year":"2020","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1014339.ref053","doi-asserted-by":"crossref","first-page":"2653","DOI":"10.1038\/s41467-021-22849-y","article-title":"Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities","volume":"12","author":"A Alonso-Del Valle","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1014339.ref054","article-title":"Species interactions determine plasmid persistence in a 3-member bacterial community","author":"KA Schaal","year":"2025","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1014339.ref055","article-title":"Detection of rare plasmid hosts using a targeted Hi-C approach","volume":"5","author":"S Casta\u00f1eda-Barba","year":"2025","journal-title":"ISME Commun"},{"issue":"5","key":"pcbi.1014339.ref056","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1093\/jac\/dkz028","article-title":"Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15","volume":"74","author":"MMC Lam","year":"2019","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"pcbi.1014339.ref057","doi-asserted-by":"crossref","DOI":"10.1093\/ismejo\/wrad032","article-title":"Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens","volume":"18","author":"X Wang","year":"2024","journal-title":"ISME J"},{"issue":"1","key":"pcbi.1014339.ref058","doi-asserted-by":"crossref","DOI":"10.1093\/femsec\/fix172","article-title":"Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species","volume":"94","author":"A Kottara","year":"2018","journal-title":"FEMS Microbiol Ecol"},{"issue":"7","key":"pcbi.1014339.ref059","doi-asserted-by":"crossref","first-page":"001369","DOI":"10.1099\/mic.0.001369","article-title":"The distribution of fitness effects of plasmid pOXA-48 in clinical enterobacteria","volume":"169","author":"A Fern\u00e1ndez-Calvet","year":"2023","journal-title":"Microbiology (Reading)"},{"key":"pcbi.1014339.ref060","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.plasmid.2018.09.009","article-title":"Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance","volume":"99","author":"JA Gama","year":"2018","journal-title":"Plasmid"},{"issue":"4","key":"pcbi.1014339.ref061","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1093\/molbev\/msv339","article-title":"Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance","volume":"33","author":"W Loftie-Eaton","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pcbi.1014339.ref062","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/s41467-021-27583-z","article-title":"Resolving the structure of phage-bacteria interactions in the context of natural diversity","volume":"13","author":"KM Kauffman","year":"2022","journal-title":"Nat Commun"},{"issue":"51","key":"pcbi.1014339.ref063","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2314135120","article-title":"Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria","volume":"120","author":"A Alonso-Del Valle","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"pcbi.1014339.ref064","doi-asserted-by":"crossref","DOI":"10.1002\/ecs2.3184","article-title":"Does functional redundancy affect ecological stability and resilience? A review and meta\u2010analysis","volume":"11","author":"CR Biggs","year":"2020","journal-title":"Ecosphere"},{"issue":"8","key":"pcbi.1014339.ref065","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1093\/biosci\/biab010","article-title":"The Importance of Eco-evolutionary Potential in the Anthropocene","volume":"71","author":"ZT Wood","year":"2021","journal-title":"BioScience"},{"issue":"1","key":"pcbi.1014339.ref066","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1038\/s42003-024-06616-5","article-title":"Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity","volume":"7","author":"F Puente-S\u00e1nchez","year":"2024","journal-title":"Commun Biol"},{"issue":"3","key":"pcbi.1014339.ref067","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1111\/jeb.14158","article-title":"Evolutionary coexistence in a fluctuating environment by specialization on resource level","volume":"36","author":"MT Wortel","year":"2023","journal-title":"J Evol Biol"},{"issue":"4","key":"pcbi.1014339.ref068","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/ismej.2014.191","article-title":"Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community","volume":"9","author":"U Kl\u00fcmper","year":"2015","journal-title":"ISME J"},{"issue":"11","key":"pcbi.1014339.ref069","article-title":"Hi-C-resolved metagenomics reveals host range variation among mobile genetic elements within the European honey bee","volume":"16","author":"CRP Robinson","year":"2025","journal-title":"mBio"},{"key":"pcbi.1014339.ref070","doi-asserted-by":"crossref","unstructured":"Paulsson J. Plasmids as stochastic model systems. In: SPIE Proceedings, 2003. 125. https:\/\/doi.org\/10.1117\/12.500143","DOI":"10.1117\/12.500143"},{"issue":"23","key":"pcbi.1014339.ref071","doi-asserted-by":"crossref","first-page":"2760","DOI":"10.1016\/j.ecolmodel.2010.08.019","article-title":"The ODD protocol: A review and first update","volume":"221","author":"V Grimm","year":"2010","journal-title":"Ecol Modell"},{"issue":"3","key":"pcbi.1014339.ref072","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00586-15","article-title":"Bacteriophages limit the existence conditions for conjugative plasmids","volume":"6","author":"E Harrison","year":"2015","journal-title":"mBio"},{"key":"pcbi.1014339.ref073","doi-asserted-by":"crossref","first-page":"673260","DOI":"10.3389\/fmicb.2021.673260","article-title":"Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota","volume":"12","author":"K Neil","year":"2021","journal-title":"Front Microbiol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1014339","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014339","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T17:42:38Z","timestamp":1780594958000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014339"}},"subtitle":[],"editor":[{"given":"Jacopo","family":"Grilli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,5,26]]},"references-count":73,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1014339","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,26]]}}}