{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T06:19:54Z","timestamp":1789712394549,"version":"4.0.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012736","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T00:00:00Z","timestamp":1737072000000}}],"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T00:00:00Z","timestamp":1736208000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006132","name":"Office of Science","doi-asserted-by":"publisher","award":["DE-SC0021234"],"award-info":[{"award-number":["DE-SC0021234"]}],"id":[{"id":"10.13039\/100006132","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Secure Biosystems Design Science Focus Area","award":["DE-AC36-08GO28308"],"award-info":[{"award-number":["DE-AC36-08GO28308"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2325172"],"award-info":[{"award-number":["DMS-2325172"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The denitrifying bacterium <jats:italic>Thauera sp<\/jats:italic>. MZ1T, a common member of microbial communities in wastewater treatment facilities, can produce different compounds from a range of carbon (C) and nitrogen (N) sources under aerobic and anaerobic conditions. In these different conditions, <jats:italic>Thauera<\/jats:italic> modifies its metabolism to produce different compounds that influence the microbial community. In particular, <jats:italic>Thauera sp<\/jats:italic>. MZ1T produces different exopolysaccharides with floc-forming properties, impacting the physical disposition of wastewater consortia and the efficiency of nutrient assimilation by the microbial community. Under N-limiting conditions, <jats:italic>Thauera sp<\/jats:italic>. MZ1T decreases its growth rate and accelerates the accumulation of polyhydroxyalkanoate-related (PHA) compounds including polyhydroxybutyrate (PHB), which plays a fundamental role as C and energy storage in this \u03b2-proteobacterium. However, the metabolic mechanisms employed by <jats:italic>Thauera sp<\/jats:italic>. MZ1T to assimilate and catabolize many of the different C and N sources under aerobic and anaerobic conditions remain unknown. Systems biology approaches such as genome-scale metabolic modeling have been successfully used to unveil complex metabolic mechanisms for various microorganisms. Here, we developed a comprehensive metabolic model (M-model) for <jats:italic>Thauera sp<\/jats:italic>. MZ1T (<jats:italic>i<\/jats:italic>Thauera861), consisting of 1,744 metabolites, 2,384 reactions, and 861 genes. We validated the model experimentally using over 70 different C and N sources under both aerobic and anaerobic conditions. <jats:italic>i<\/jats:italic>Thauera861 achieved a prediction accuracy of 95% for growth on various C and N sources and close to 85% for assimilation of aromatic compounds under denitrifying conditions. The M-model was subsequently deployed to determine the effects of substrates, oxygen presence, and the C:N ratio on the production of PHB and exopolysaccharides (EPS), showing the highest polymer yields are achieved with nucleotides and amino acids under aerobic conditions. This comprehensive M-model will help reveal the metabolic processes by which this ubiquitous species influences communities in wastewater treatment systems and natural environments.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012736","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T18:49:06Z","timestamp":1736275746000},"page":"e1012736","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8819-4150","authenticated-orcid":true,"given":"Diego","family":"Tec-Campos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan D.","family":"Tibocha-Bonilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Celina","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0448-794X","authenticated-orcid":true,"given":"Anurag","family":"Passi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0248-5329","authenticated-orcid":true,"given":"Deepan","family":"Thiruppathy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristal","family":"Zu\u00f1iga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camila","family":"Posadas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0587-5039","authenticated-orcid":true,"given":"Alejandro","family":"Zepeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8062-3296","authenticated-orcid":true,"given":"Karsten","family":"Zengler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"pcbi.1012736.ref001","doi-asserted-by":"crossref","first-page":"325","DOI":"10.4056\/sigs.2696029","article-title":"Complete genome sequence of Thauera aminoaromatica strain MZ1T.","volume":"6","author":"K Jiang","year":"2012","journal-title":"Stand Genomic Sci."},{"key":"pcbi.1012736.ref002","first-page":"1","volume-title":"Thauera. 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