MCF2Chem: A manually curated knowledge base of biosynthetic compound production
Abstract Background Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced vi...
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | Biotechnology for Biofuels and Bioproducts |
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| Online Access: | https://doi.org/10.1186/s13068-023-02419-8 |
| _version_ | 1827770708656128000 |
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| author | Pengli Cai Sheng Liu Dachuan Zhang Qian-Nan Hu |
| author_facet | Pengli Cai Sheng Liu Dachuan Zhang Qian-Nan Hu |
| author_sort | Pengli Cai |
| collection | DOAJ |
| description | Abstract Background Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. Results In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that “fatty acids”, “terpenoids”, and “shikimates and phenylpropanoids” accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. Conclusions MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists. |
| first_indexed | 2024-03-11T12:43:24Z |
| format | Article |
| id | doaj.art-18e17873a9d54683811b09b86ca6d9b7 |
| institution | Directory Open Access Journal |
| issn | 2731-3654 |
| language | English |
| last_indexed | 2024-03-11T12:43:24Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels and Bioproducts |
| spelling | doaj.art-18e17873a9d54683811b09b86ca6d9b72023-11-05T12:10:12ZengBMCBiotechnology for Biofuels and Bioproducts2731-36542023-11-0116111210.1186/s13068-023-02419-8MCF2Chem: A manually curated knowledge base of biosynthetic compound productionPengli Cai0Sheng Liu1Dachuan Zhang2Qian-Nan Hu3CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesEcological Systems Design, Institute of Environmental Engineering, ETH ZurichCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesAbstract Background Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. Results In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that “fatty acids”, “terpenoids”, and “shikimates and phenylpropanoids” accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. Conclusions MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists.https://doi.org/10.1186/s13068-023-02419-8Synthetic biologyMicrobial cell factoryBiochemical productProduction databaseRecommendation system |
| spellingShingle | Pengli Cai Sheng Liu Dachuan Zhang Qian-Nan Hu MCF2Chem: A manually curated knowledge base of biosynthetic compound production Biotechnology for Biofuels and Bioproducts Synthetic biology Microbial cell factory Biochemical product Production database Recommendation system |
| title | MCF2Chem: A manually curated knowledge base of biosynthetic compound production |
| title_full | MCF2Chem: A manually curated knowledge base of biosynthetic compound production |
| title_fullStr | MCF2Chem: A manually curated knowledge base of biosynthetic compound production |
| title_full_unstemmed | MCF2Chem: A manually curated knowledge base of biosynthetic compound production |
| title_short | MCF2Chem: A manually curated knowledge base of biosynthetic compound production |
| title_sort | mcf2chem a manually curated knowledge base of biosynthetic compound production |
| topic | Synthetic biology Microbial cell factory Biochemical product Production database Recommendation system |
| url | https://doi.org/10.1186/s13068-023-02419-8 |
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