{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL2411260001?filename=iSJ444.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/MODEL2411260001?filename=iSJ444_memote_report.html","https://www.ebi.ac.uk/biomodels/model/download/MODEL2411260001?filename=iSJ444_fluxer_map.png","https://www.ebi.ac.uk/biomodels/model/download/MODEL2411260001?filename=iSJ444_FROG_analysis.omex"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["William Scott"],"curationStatus":["Non-curated"],"modellingApproach":["constraint-based model"],"levelVersion":["L3V1"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL2411260001"],"publication_pubmed":["40046987"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Scott2024   Genome scale metabolic model of Clostridium luticellarii"],"publication_year":["2025"],"submissionId":["MODEL2411260001"],"publication_authors":["William T Scott, Siemen Rockx, Quinten Mariën, Alberte Regueira, Pieter Candry, Ramon Ganigué, Jasper J Koehorst, Peter J Schaap"],"first_author":["William T Scott"],"publication":["40046987,\n                            Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of <i>Clostridia</i> species, such as <i>Clostridium kluyveri</i>, <i>Clostridium autoethanogenum</i>, and <i>Clostridium ljungdahlii</i>. <i>Clostridium luticellarii</i>, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create <i>iSJ444</i>, a constraint-based metabolic model of <i>C. luticellarii</i> using <i>iHN637</i> of a close relative <i>C. ljungdahlii</i> as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that <i>C. luticellarii</i> maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that <i>C. luticellarii</i> might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of <i>C. luticellarii</i> as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of <i>C. luticellarii</i> to enhance syngas fermentation platforms.. null, 27.\n                            UNLOCK, Wageningen University & Research, Stippeneng 2, Wageningen, 6703 HB, the Netherlands."],"submitter_mail":["william.scott@wur.nl"],"submitter_affiliation":["Wageningen University & Research"],"pubmed_abstract":["Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of <i>Clostridia</i> species, such as <i>Clostridium kluyveri</i>, <i>Clostridium autoethanogenum</i>, and <i>Clostridium ljungdahlii</i>. <i>Clostridium luticellarii</i>, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create <i>iSJ444</i>, a constraint-based metabolic model of <i>C. luticellarii</i> using <i>iHN637</i> of a close relative <i>C. ljungdahlii</i> as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that <i>C. luticellarii</i> maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that <i>C. luticellarii</i> might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of <i>C. luticellarii</i> as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of <i>C. luticellarii</i> to enhance syngas fermentation platforms."],"pubmed_title":["Implementation of a &lt;i&gt;Clostridium luticellarii&lt;/i&gt; genome-scale model for upgrading syngas fermentations."],"pubmed_authors":["Scott William T WT, Rockx Siemen S, Mariën Quinten Q, Regueira Alberte A, Candry Pieter P, Ganigué Ramon R, Koehorst Jasper J JJ, Schaap Peter J PJ"],"additional_accession":[]},"is_claimable":false,"name":"Scott2024 - Genome-scale metabolic model of Clostridium luticellarii","description":"No 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