{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T22:54:57Z","timestamp":1792623297303,"version":"4.5.0"},"reference-count":51,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:00:00Z","timestamp":1738281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:00:00Z","timestamp":1738281600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"crossref","award":["DARCH19G0"],"award-info":[{"award-number":["DARCH19G0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"crossref","award":["DARCH22P0"],"award-info":[{"award-number":["DARCH22P0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"crossref","award":["GANNON22H0"],"award-info":[{"award-number":["GANNON22H0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2025,1,31]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Bacterial aggregates are observed in both natural and artificial environments. In the context of disease, aggregates have been isolated from chronic and acute infections.\n              <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n              (\n              <jats:italic>Pa<\/jats:italic>\n              ) aggregates contribute significantly to chronic infections, particularly in the lungs of people with cystic fibrosis (CF). Unlike the large biofilm structures observed\n              <jats:italic>in vitro<\/jats:italic>\n              ,\n              <jats:italic>Pa<\/jats:italic>\n              in CF sputum forms smaller aggregates (~10\u20131,000 cells), and the mechanisms behind their formation remain underexplored. This study aims to identify genes essential and unique\n              <jats:italic>to<\/jats:italic>\n              Pa aggregate formation in a synthetic CF sputum media (SCFM2). We cultured\n              <jats:italic>Pa<\/jats:italic>\n              strain PAO1 in SCFM2 and LB, both with and without mucin, and used RNA sequencing (RNA-seq) to identify differentially expressed genes. The presence of mucin revealed 13 significantly differentially expressed (DE) genes, predominantly downregulated, with 40% encoding hypothetical proteins unique to aggregates. Using high-resolution microscopy, we assessed the ability of mutants to form aggregates. Notably, no mutant exhibited a completely planktonic phenotype. Instead, we identified multiple spatial phenotypes described as \u201cnormal,\u201d \u201centropic,\u201d or \u201cimpaired.\u201d Entropic mutants displayed tightly packed, raft-like structures, while impaired mutants had loosely packed cells. Predictive modeling linked the prioritized genes to metabolic shifts, iron acquisition, surface modification, and quorum sensing. Co-culture experiments with wild-type PAO1 revealed further spatial heterogeneity and the ability to \u201crescue\u201d some mutant phenotypes, suggesting cooperative interactions during growth. This study enhances our understanding of\n              <jats:italic>Pa<\/jats:italic>\n              aggregate biology, specifically the genes and pathways unique to aggregation in CF-like environments. Importantly, it provides insights for developing therapeutic strategies targeting aggregate-specific pathways.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              This study identifies genes essential for the formation of\n              <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n              (Pa) aggregates in cystic fibrosis (CF) sputum, filling a critical gap in understanding their specific biology. Using a synthetic CF sputum model (SCFM2) and RNA sequencing, 13 key genes were identified, whose disruption led to distinct spatial phenotypes observed through high-resolution microscopy. The addition of wild-type cells either rescued the mutant phenotype or increased spatial heterogeneity, suggesting cooperative interactions are involved in aggregate formation. This research advances our knowledge of\n              <jats:italic>Pa<\/jats:italic>\n              aggregate biology, particularly the unique genes and pathways involved in CF-like environments, offering valuable insights for developing targeted therapeutic strategies against aggregate-specific pathways.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/jb.00429-24","type":"journal-article","created":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T19:12:40Z","timestamp":1733944360000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Exploring aggregation genes in a\n            <i>P. aeruginosa<\/i>\n            chronic infection model"],"prefix":"10.1128","volume":"207","author":[{"given":"Alexa D.","family":"Gannon","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida","place":["Tampa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenet","family":"Matlack","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida","place":["Tampa, USA"]},{"name":"Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute","place":["Tampa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2800-2844","authenticated-orcid":true,"given":"Sophie E.","family":"Darch","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida","place":["Tampa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00240-17"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuac018"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00024-23"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2021-217576"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.20685"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2015.09.002"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.108782"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1719317115"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1919099117"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1400586111"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00202-10"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2011.07620.x"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep39621"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00736-17"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep41178"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.15811"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.280.5361.295"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2010.07320.x"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1806005115"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00860-21"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines11010028"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2009.06934.x"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.61885"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.11.008"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200800618"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2004.02.004"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2018.00033"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1111\/febs.15789"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00203-010-0665-6"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.11.3731-3738.2005"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-27341-1"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00753-08"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2006.01025.x"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1002\/jobm.201300091"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004518"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.15.5267-5277.2005"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-018-0067-0"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00480-17"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-021-00225-4"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.59.2.473-478.1993"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0056850"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M115.708149"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2221542120"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2036282100"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2010.01916.x"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.3791\/62420"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1227"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky427"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03819-2"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1000"}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jb.00429-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jb.00429-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T14:00:42Z","timestamp":1738332042000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/jb.00429-24"}},"subtitle":[],"editor":[{"given":"George","family":"O'Toole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,1,31]]},"references-count":51,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,31]]}},"alternative-id":["10.1128\/jb.00429-24"],"URL":"https:\/\/doi.org\/10.1128\/jb.00429-24","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,31]]},"assertion":[{"value":"2024-10-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-10-28","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-11","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00429-24"}}