Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing
ABSTRACT The transition from a petroleum‐based manufacturing to biomanufacturing is an important step towards a sustainable bio‐economy. In particular, biotechnological processes which use one carbon (C1) compounds as feedstock represent an interesting avenue. Many bacterial species evolved naturall...
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| Format: | Article |
| Language: | English |
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Wiley
2025-07-01
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| Series: | Microbial Biotechnology |
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| Online Access: | https://doi.org/10.1111/1751-7915.70201 |
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| author | Magnus G. Jespersen Emil Funk Vangsgaard Mariana Arango Saavedra Stefano Donati Lars K. Nielsen |
| author_facet | Magnus G. Jespersen Emil Funk Vangsgaard Mariana Arango Saavedra Stefano Donati Lars K. Nielsen |
| author_sort | Magnus G. Jespersen |
| collection | DOAJ |
| description | ABSTRACT The transition from a petroleum‐based manufacturing to biomanufacturing is an important step towards a sustainable bio‐economy. In particular, biotechnological processes which use one carbon (C1) compounds as feedstock represent an interesting avenue. Many bacterial species evolved naturally to thrive on such compounds, among them Cupriavidus necator, which has been studied in the past due to its range of metabolic capabilities in utilisation and production of compounds of interest. Cupriavidus necator strain H16 is the reference laboratory strain for this species and by far the most extensively studied. In contrast, research efforts and genomic characterisation of other strains within this species have been limited and sporadic. Therefore, the genomic diversity and full metabolic potential across the broader species remain poorly understood. In this work, we collected publicly available genomes along with newly sequenced ones. From a collection of 44 genomes, we curated a final collection of 22 genomes deemed to be C. necator. We examined hallmark metabolic functions, including carbon dioxide fixation, formate assimilation and hydrogen utilisation. We identified methylation motifs and restriction modification systems. Finally, strains ATCC 25207, TA06, and 1978 are proposed as candidate strains of interest based on their genomic make‐up and observations from literature. This work provides a comprehensive genomic resource for the C. necator species, facilitating its development as a biomanufacturing platform and advancing our understanding of its metabolic diversity and potential applications. |
| format | Article |
| id | doaj-art-17f2e8451dc94c16aaeae117beb028cc |
| institution | DOAJ |
| issn | 1751-7915 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Microbial Biotechnology |
| spelling | doaj-art-17f2e8451dc94c16aaeae117beb028cc2025-08-20T03:09:00ZengWileyMicrobial Biotechnology1751-79152025-07-01187n/an/a10.1111/1751-7915.70201Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based BiomanufacturingMagnus G. Jespersen0Emil Funk Vangsgaard1Mariana Arango Saavedra2Stefano Donati3Lars K. Nielsen4The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby DenmarkThe Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby DenmarkThe Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby DenmarkThe Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby DenmarkThe Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby DenmarkABSTRACT The transition from a petroleum‐based manufacturing to biomanufacturing is an important step towards a sustainable bio‐economy. In particular, biotechnological processes which use one carbon (C1) compounds as feedstock represent an interesting avenue. Many bacterial species evolved naturally to thrive on such compounds, among them Cupriavidus necator, which has been studied in the past due to its range of metabolic capabilities in utilisation and production of compounds of interest. Cupriavidus necator strain H16 is the reference laboratory strain for this species and by far the most extensively studied. In contrast, research efforts and genomic characterisation of other strains within this species have been limited and sporadic. Therefore, the genomic diversity and full metabolic potential across the broader species remain poorly understood. In this work, we collected publicly available genomes along with newly sequenced ones. From a collection of 44 genomes, we curated a final collection of 22 genomes deemed to be C. necator. We examined hallmark metabolic functions, including carbon dioxide fixation, formate assimilation and hydrogen utilisation. We identified methylation motifs and restriction modification systems. Finally, strains ATCC 25207, TA06, and 1978 are proposed as candidate strains of interest based on their genomic make‐up and observations from literature. This work provides a comprehensive genomic resource for the C. necator species, facilitating its development as a biomanufacturing platform and advancing our understanding of its metabolic diversity and potential applications.https://doi.org/10.1111/1751-7915.70201alcaligenes eutrophuscupriavidus necatorhydrogenomonas eutropharalstonia eutrophawautersia eutropha |
| spellingShingle | Magnus G. Jespersen Emil Funk Vangsgaard Mariana Arango Saavedra Stefano Donati Lars K. Nielsen Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing Microbial Biotechnology alcaligenes eutrophus cupriavidus necator hydrogenomonas eutropha ralstonia eutropha wautersia eutropha |
| title | Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing |
| title_full | Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing |
| title_fullStr | Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing |
| title_full_unstemmed | Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing |
| title_short | Comparative Genomic Assessment of the Cupriavidus necator Species for One‐Carbon Based Biomanufacturing |
| title_sort | comparative genomic assessment of the cupriavidus necator species for one carbon based biomanufacturing |
| topic | alcaligenes eutrophus cupriavidus necator hydrogenomonas eutropha ralstonia eutropha wautersia eutropha |
| url | https://doi.org/10.1111/1751-7915.70201 |
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