Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling
Abstract Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lact...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-12-01
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| Series: | npj Systems Biology and Applications |
| Online Access: | https://doi.org/10.1038/s41540-021-00207-4 |
| _version_ | 1818701444500422656 |
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| author | Marie Schöpping Paula Gaspar Ana Rute Neves Carl Johan Franzén Ahmad A. Zeidan |
| author_facet | Marie Schöpping Paula Gaspar Ana Rute Neves Carl Johan Franzén Ahmad A. Zeidan |
| author_sort | Marie Schöpping |
| collection | DOAJ |
| description | Abstract Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes. |
| first_indexed | 2024-12-17T15:20:56Z |
| format | Article |
| id | doaj.art-ac2fb7f572e14a6ea4afb5d172e624ff |
| institution | Directory Open Access Journal |
| issn | 2056-7189 |
| language | English |
| last_indexed | 2024-12-17T15:20:56Z |
| publishDate | 2021-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Systems Biology and Applications |
| spelling | doaj.art-ac2fb7f572e14a6ea4afb5d172e624ff2022-12-21T21:43:25ZengNature Portfolionpj Systems Biology and Applications2056-71892021-12-017111510.1038/s41540-021-00207-4Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modelingMarie Schöpping0Paula Gaspar1Ana Rute Neves2Carl Johan Franzén3Ahmad A. Zeidan4Systems Biology, DiscoverySystems Biology, DiscoverySystems Biology, DiscoveryDivision of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of TechnologySystems Biology, DiscoveryAbstract Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.https://doi.org/10.1038/s41540-021-00207-4 |
| spellingShingle | Marie Schöpping Paula Gaspar Ana Rute Neves Carl Johan Franzén Ahmad A. Zeidan Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling npj Systems Biology and Applications |
| title | Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling |
| title_full | Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling |
| title_fullStr | Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling |
| title_full_unstemmed | Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling |
| title_short | Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling |
| title_sort | identifying the essential nutritional requirements of the probiotic bacteria bifidobacterium animalis and bifidobacterium longum through genome scale modeling |
| url | https://doi.org/10.1038/s41540-021-00207-4 |
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