{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:00:45Z","timestamp":1792026045963,"version":"4.4.0"},"reference-count":103,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,2,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      For many years, antibiotics reliably protected mankind against bacterial\n                        infections, including the respiratory tract colonizer\n                      <jats:italic toggle=\"yes\">Corynebacterium tuberculostearicum<\/jats:italic>\n                      . However, the spread\n                        of antimicrobial resistance necessitates the search for new treatment\n                        options, where the microbiota may play a crucial role. One way to\n                        investigate the complex nature of bacteria and their interactions with human\n                        hosts or microbiota is through genome-scale metabolic models (GEMs).\n                        Constructing GEMs is labor-intensive and time-consuming. We introduce the\n                        Python package Mass and Charge Curation (MCC), which implements a new\n                        automated algorithm to facilitate mass and charge balancing\u2014one of\n                        the most time-consuming reconstruction steps. This package manipulates\n                        reconstructions by consolidating data from multiple resources and updating\n                        the\n                      <jats:monospace>notes<\/jats:monospace>\n                      field with relevant changes. It also\n                        visually compares draft and curated models, ensuring high-quality metabolic\n                        reconstructions. Using MCC, we developed a metabolic reconstruction of\n                      <jats:italic toggle=\"yes\">C. tuberculostearicum<\/jats:italic>\n                      strain DSM 44922. The model was\n                        improved based on standardization policies, resulting in a functional,\n                        well-annotated, high-quality product. We also simulated the\n                        organism\u2019s growth in synthetic nasal medium 3 (SNM3). The\n                        high-quality model\n                      <jats:italic toggle=\"yes\">i<\/jats:italic>\n                      CTUB2024RM consistently resembles\n                        growth behavior under realistic conditions in an artificial human nasal\n                        environment, enhancing the understanding of\n                      <jats:italic toggle=\"yes\">C.\n                            tuberculostearicum<\/jats:italic>\n                      and its potential impact on health and\n                        disease. The curation process of this model led to the development of the\n                        MCC package, which facilitates the mass and charge balancing of arbitrary\n                        flux balance constraints models in the SBML format.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>\n                        <jats:bold>IMPORTANCE<\/jats:bold>\n                      <\/jats:title>\n                      <jats:p>\n                        The rise of antibiotic resistance has made it essential to explore\n                            alternative treatments for bacterial infections, particularly those\n                            caused by respiratory tract colonizers like\n                        <jats:italic toggle=\"yes\">Corynebacterium\n                                tuberculostearicum<\/jats:italic>\n                        . Understanding the metabolic behavior of\n                            these bacteria and their interactions with the human host or microbiota\n                            is crucial. Genome-scale metabolic models (GEMs) are powerful tools for\n                            investigating these interactions, but they are time-consuming to build.\n                            Our new Python package, Mass and Charge Curation, automates a crucial\n                            step in the GEM reconstruction process\u2014mass and charge\n                            balancing\u2014making it more efficient and reliable. By applying this\n                            tool, we developed a high-quality, functional metabolic model for\n                        <jats:italic toggle=\"yes\">C. tuberculostearicum<\/jats:italic>\n                        (\n                        <jats:italic toggle=\"yes\">i<\/jats:italic>\n                        CTUB2024RM), which provides deeper insights into the\n                            organism\u2019s growth in a simulated human nasal environment. This\n                            work offers a foundation for future research into microbial communities\n                            and their role in human health.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03200-24","type":"journal-article","created":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T13:00:21Z","timestamp":1767186021000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["MCC: automated mass and charge curation at the genome scale applied                    to\n                    <i>C. tuberculostearicum<\/i>"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2479-6851","authenticated-orcid":true,"given":"Reihaneh","family":"Mostolizadeh","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/033eqas34","id-type":"ROR","asserted-by":"publisher"}],"name":"Bioinformatics and Systems Biology, Justus Liebig University Giessen","place":["Giessen, Germany"]},{"id":[{"id":"https:\/\/ror.org\/05r7n9c40","id-type":"ROR","asserted-by":"publisher"}],"name":"Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology","place":["Marburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3409-4626","authenticated-orcid":false,"given":"Finn","family":"Mier","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03a1kwz48","id-type":"ROR","asserted-by":"publisher"}],"name":"Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karl University of T\u00fcbingen","place":["T\u00fcbingen, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-5553","authenticated-orcid":true,"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05gqaka33","id-type":"ROR","asserted-by":"publisher"}],"name":"Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg","place":["Halle (Saale), Germany"]},{"id":[{"id":"https:\/\/ror.org\/03a1kwz48","id-type":"ROR","asserted-by":"publisher"}],"name":"Quantitative Biology Center (QBiC), Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of T\u00fcbingen","place":["T\u00fcbingen, Germany"]},{"id":[{"id":"https:\/\/ror.org\/028s4q594","id-type":"ROR","asserted-by":"publisher"}],"name":"German Center for Infection Research (DZIF)","place":["T\u00fcbingen, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0194-5998(03)01397-4"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00134"},{"key":"e_1_3_4_4_2","first-page":"1","article-title":"Summary health statistics for U.S. adults:\n                        national health interview survey, 2004","author":"Lethbridge-\u00c7ejku M","year":"2006","unstructured":"Lethbridge-\u00c7ejku M, Rose D, Vickerie J. 2006. 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