{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:48:19Z","timestamp":1782280099037,"version":"3.54.5"},"posted":{"date-parts":[[2025,4,1]]},"group-title":"Microbiology","reference-count":56,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["U19AI158076"],"award-info":[{"award-number":["U19AI158076"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["F31AI179118"],"award-info":[{"award-number":["F31AI179118"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,11]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>\n                  Many bacteria carry phage genome(s) in their chromosome, which intertwines the fitness of the bacterium and the phage. Most\n                  <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                  strains carry filamentous phages called Pf that establish chronic infections and do not require host lysis to spread. However, spontaneous mutations in the Pf repressor gene (\n                  <jats:italic>pf5r<\/jats:italic>\n                  ) can allow extreme phage production that slows bacterial growth and increases cell death, violating an apparent d\u00e9tente between bacterium and phage. We observed this paradoxical outcome in an evolution experiment with\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  in media simulating nutrients from the cystic fibrosis airway. Bacteria containing\n                  <jats:italic>pf5r<\/jats:italic>\n                  mutant phage grow to a lower density but directly outcompete their ancestor and convert them into\n                  <jats:italic>pf5r<\/jats:italic>\n                  mutants via phage superinfection. Reduced fitness therefore spreads throughout the bacterial population, driven by weaponized Pf. Yet high intracellular phage replication facilitates another evolutionary conflict: \u201ccheater miniphages\u201d lacking capsid genes and the superinfection exclusion gene (\n                  <jats:italic>pfsE<\/jats:italic>\n                  ) invade populations of full-length phages within cells. Although bacteria containing both full-length phages and miniphages are most immune to superinfection by limiting the Pf receptor, this hybrid vigor is extremely unstable, as a classic Tragedy of the Commons scenario ensues that causes complete prophage loss. The entire cycle \u2013 from phage hyperactivation to miniphage invasion to prophage loss \u2013 can occur within 24h, showcasing rapid coevolution between bacteria and their filamentous phages. This study demonstrates that\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  , and potentially many other bacterial species that carry filamentous prophages, risk being exploited by these phages in a runaway process that reduces fitness of both host and virus.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Abstract Figure<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"646652v4_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.1101\/2025.04.01.646652","type":"posted-content","created":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T18:40:12Z","timestamp":1743532812000},"source":"Crossref","is-referenced-by-count":2,"title":["Filamentous cheater phages drive bacterial and phage populations to lower fitness"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9118-6706","authenticated-orcid":false,"given":"Nanami","family":"Kubota","sequence":"first","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle R.","family":"Scribner","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7726-0765","authenticated-orcid":false,"given":"Vaughn S.","family":"Cooper","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA"},{"name":"Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041202014519000_2025.04.01.646652v4.1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00402-23"},{"key":"2026041202014519000_2025.04.01.646652v4.2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010925"},{"key":"2026041202014519000_2025.04.01.646652v4.3","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00648-16"},{"key":"2026041202014519000_2025.04.01.646652v4.4","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01036-23"},{"key":"2026041202014519000_2025.04.01.646652v4.5","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1146"},{"key":"2026041202014519000_2025.04.01.646652v4.6","doi-asserted-by":"publisher","DOI":"10.1111\/evo.14153"},{"key":"2026041202014519000_2025.04.01.646652v4.7","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02441-21"},{"key":"2026041202014519000_2025.04.01.646652v4.8","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1128\/br.33.2.172-209.1969","article-title":"Filamentous Bacterial Viruses","volume":"33","year":"1969","journal-title":"Bacteriological reviews"},{"key":"2026041202014519000_2025.04.01.646652v4.9","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(74)90150-0"},{"key":"2026041202014519000_2025.04.01.646652v4.10","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aau9748"},{"key":"2026041202014519000_2025.04.01.646652v4.11","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00244"},{"key":"2026041202014519000_2025.04.01.646652v4.12","unstructured":"Cystic Fibrosis Foundation Patient Registry 2022 Annual Data Report (2023). 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