{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:58:42Z","timestamp":1790621922539,"version":"4.1.0"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-2435227"],"award-info":[{"award-number":["NSF-2435227"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-2242763"],"award-info":[{"award-number":["NSF-2242763"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"United States Department of Agriculture (USDA) - National Institute of Food and Agriculture (NIFA).","award":["2025-38502-45540"],"award-info":[{"award-number":["2025-38502-45540"]}],"id":[{"id":"https:\/\/ror.org\/05qx3fv49","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"\n Microbial cocultures exhibit complex population dynamics that are difficult to interpret because internal physiological states are only partially observable. In particular, active and dormant cell states can influence system-level behavior but are rarely resolved from standard fermentation measurements. In this study, we present a hybrid modeling framework that combines structured population-state reconstruction with sparse identification of nonlinear dynamics (SINDy) to analyze a\n Clostridium acetobutylicum<\/jats:italic>\n -\n Clostridium ljungdahlii<\/jats:italic>\n coculture under perfusion mode. The framework estimates active\n \n \n \n \n \n \n C<\/mml:mi>\n \n a<\/mml:mi>\n c<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n and\n \n \n \n \n \n \n C<\/mml:mi>\n \n l<\/mml:mi>\n j<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n biomass-equivalent trajectories from observable biomass and activity measurements, reconstructs dormant populations as model-constrained latent states, and uses these states to identify extracellular metabolite dynamics. After accounting for first-principles perfusion transport, SINDy identified sparse biological reaction terms associated with organic acid turnover, solvent formation, and acetone-to-isopropanol conversion. The resulting model captured active-biomass and metabolite trajectories and suggested that the coculture dynamics are consistent with acid-associated state transitions and sequential metabolic exchange. This framework provides a transparent strategy for interpreting partially observed microbial cocultures while explicitly treating dormant biomass as a latent reconstructed state.\n <\/jats:p>","DOI":"10.1371\/journal.pcbi.1014759","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T17:56:47Z","timestamp":1790618207000},"page":"e1014759","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["From observable fermentation data to hidden cell states: A modeling study of a mixotrophic Clostridium coculture under perfusion mode"],"prefix":"10.1371","volume":"22","author":[{"given":"Juhyeon","family":"Kim","sequence":"first","affiliation":[{"name":"Texas A&M University","place":["College Station, Texas, United States of America"],"department":["Artie McFerrin Department of Chemical Engineering"]},{"name":"Texas A&M University","place":["College Station, Texas, United States of America"],"department":["Texas A&M Energy Institute"]},{"name":"The Ohio State University","place":["Columbus, Ohio, United States of America"],"department":["William G. Lowrie Department of Chemical and Biomolecular Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9920-094X","authenticated-orcid":true,"given":"Hangjun","family":"Cho","sequence":"additional","affiliation":[{"name":"The Ohio State University","place":["Columbus, Ohio, United States of America"],"department":["William G. Lowrie Department of Chemical and Biomolecular Engineering"]},{"name":"Kongju National University","place":["Kongju, Republic of Korea"],"department":["Department of Mathematics Education"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin Hong","family":"Mok","sequence":"additional","affiliation":[{"name":"Dongguk University\u2013Seoul","place":["Goyang-si, Gyeonggi-do, Republic of Korea"],"department":["Department of Food Science and Biotechnology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyeongmin","family":"Seo","sequence":"additional","affiliation":[{"name":"The University of Iowa","place":["Iowa City, Iowa, United States of America"],"department":["Department of Chemical and Biochemical Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7903-5681","authenticated-orcid":true,"given":"Joseph Sang-Il","family":"Kwon","sequence":"additional","affiliation":[{"name":"The Ohio State University","place":["Columbus, Ohio, United States of America"],"department":["William G. 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