COmmunity and Single Microbe Optimisation System (COSMOS)
Abstract Bioprocessing utilises microbial monocultures and communities to convert renewable resources into valuable products. While monocultures offer simplicity, communities provide metabolic diversity and cooperative biosynthesis. To systematically evaluate these systems, we developed COmmunity an...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-05-01
|
| Series: | npj Systems Biology and Applications |
| Online Access: | https://doi.org/10.1038/s41540-025-00534-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850124812843745280 |
|---|---|
| author | Lavanya Raajaraam Karthik Raman |
| author_facet | Lavanya Raajaraam Karthik Raman |
| author_sort | Lavanya Raajaraam |
| collection | DOAJ |
| description | Abstract Bioprocessing utilises microbial monocultures and communities to convert renewable resources into valuable products. While monocultures offer simplicity, communities provide metabolic diversity and cooperative biosynthesis. To systematically evaluate these systems, we developed COmmunity and Single Microbe Optimisation System (COSMOS), a dynamic computational framework that simulates and compares monocultures and co-cultures to determine optimal microbial systems tailored to a specific environment. COSMOS revealed key factors shaping biosynthetic performance, such as environmental conditions, microbial interactions, and carbon sources. Notably, it predicted the Shewanella oneidensis–Klebsiella pneumoniae co-culture as the most efficient producer of 1,3-propanediol under anaerobic conditions, aligning closely with experimental data, including optimal carbon source concentrations and inoculum ratios. Additional findings highlight the resilience of microbial communities in nutrient-limited processes and emphasise the role of computational tools in balancing productivity with operational simplicity. Overall, this study advances the rational design of microbial systems, paving the way for sustainable bioprocesses and circular bio-economies. |
| format | Article |
| id | doaj-art-2008943d304949d89ea1a569d19488bb |
| institution | OA Journals |
| issn | 2056-7189 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Systems Biology and Applications |
| spelling | doaj-art-2008943d304949d89ea1a569d19488bb2025-08-20T02:34:14ZengNature Portfolionpj Systems Biology and Applications2056-71892025-05-0111111510.1038/s41540-025-00534-wCOmmunity and Single Microbe Optimisation System (COSMOS)Lavanya Raajaraam0Karthik Raman1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) MadrasDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) MadrasAbstract Bioprocessing utilises microbial monocultures and communities to convert renewable resources into valuable products. While monocultures offer simplicity, communities provide metabolic diversity and cooperative biosynthesis. To systematically evaluate these systems, we developed COmmunity and Single Microbe Optimisation System (COSMOS), a dynamic computational framework that simulates and compares monocultures and co-cultures to determine optimal microbial systems tailored to a specific environment. COSMOS revealed key factors shaping biosynthetic performance, such as environmental conditions, microbial interactions, and carbon sources. Notably, it predicted the Shewanella oneidensis–Klebsiella pneumoniae co-culture as the most efficient producer of 1,3-propanediol under anaerobic conditions, aligning closely with experimental data, including optimal carbon source concentrations and inoculum ratios. Additional findings highlight the resilience of microbial communities in nutrient-limited processes and emphasise the role of computational tools in balancing productivity with operational simplicity. Overall, this study advances the rational design of microbial systems, paving the way for sustainable bioprocesses and circular bio-economies.https://doi.org/10.1038/s41540-025-00534-w |
| spellingShingle | Lavanya Raajaraam Karthik Raman COmmunity and Single Microbe Optimisation System (COSMOS) npj Systems Biology and Applications |
| title | COmmunity and Single Microbe Optimisation System (COSMOS) |
| title_full | COmmunity and Single Microbe Optimisation System (COSMOS) |
| title_fullStr | COmmunity and Single Microbe Optimisation System (COSMOS) |
| title_full_unstemmed | COmmunity and Single Microbe Optimisation System (COSMOS) |
| title_short | COmmunity and Single Microbe Optimisation System (COSMOS) |
| title_sort | community and single microbe optimisation system cosmos |
| url | https://doi.org/10.1038/s41540-025-00534-w |
| work_keys_str_mv | AT lavanyaraajaraam communityandsinglemicrobeoptimisationsystemcosmos AT karthikraman communityandsinglemicrobeoptimisationsystemcosmos |