More is Different: Metabolic Modeling of Diverse Microbial Communities
ABSTRACT Microbial consortia drive essential processes, ranging from nitrogen fixation in soils to providing metabolic breakdown products to animal hosts. However, it is challenging to translate the composition of microbial consortia into their emergent functional capacities. Community-scale metabol...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-04-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01270-22 |
| _version_ | 1797838286520057856 |
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| author | Christian Diener Sean M. Gibbons |
| author_facet | Christian Diener Sean M. Gibbons |
| author_sort | Christian Diener |
| collection | DOAJ |
| description | ABSTRACT Microbial consortia drive essential processes, ranging from nitrogen fixation in soils to providing metabolic breakdown products to animal hosts. However, it is challenging to translate the composition of microbial consortia into their emergent functional capacities. Community-scale metabolic models hold the potential to simulate the outputs of complex microbial communities in a given environmental context, but there is currently no consensus for what the fitness function of an entire community should look like in the presence of ecological interactions and whether community-wide growth operates close to a maximum. Transitioning from single-taxon genome-scale metabolic models to multitaxon models implies a growth cone without a well-specified growth rate solution for individual taxa. Here, we argue that dynamic approaches naturally overcome these limitations, but they come at the cost of being computationally expensive. Furthermore, we show how two nondynamic, steady-state approaches approximate dynamic trajectories and pick ecologically relevant solutions from the community growth cone with improved computational scalability. |
| first_indexed | 2024-04-09T15:39:28Z |
| format | Article |
| id | doaj.art-14d17af00d4e4a888ae2842b9ffe8f2e |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-04-09T15:39:28Z |
| publishDate | 2023-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-14d17af00d4e4a888ae2842b9ffe8f2e2023-04-27T13:02:45ZengAmerican Society for MicrobiologymSystems2379-50772023-04-018210.1128/msystems.01270-22More is Different: Metabolic Modeling of Diverse Microbial CommunitiesChristian Diener0Sean M. Gibbons1Institute for Systems Biology, Seattle, Washington, USAInstitute for Systems Biology, Seattle, Washington, USAABSTRACT Microbial consortia drive essential processes, ranging from nitrogen fixation in soils to providing metabolic breakdown products to animal hosts. However, it is challenging to translate the composition of microbial consortia into their emergent functional capacities. Community-scale metabolic models hold the potential to simulate the outputs of complex microbial communities in a given environmental context, but there is currently no consensus for what the fitness function of an entire community should look like in the presence of ecological interactions and whether community-wide growth operates close to a maximum. Transitioning from single-taxon genome-scale metabolic models to multitaxon models implies a growth cone without a well-specified growth rate solution for individual taxa. Here, we argue that dynamic approaches naturally overcome these limitations, but they come at the cost of being computationally expensive. Furthermore, we show how two nondynamic, steady-state approaches approximate dynamic trajectories and pick ecologically relevant solutions from the community growth cone with improved computational scalability.https://journals.asm.org/doi/10.1128/msystems.01270-22flux balance analysismetabolic modelingmetabolismmicrobial communitiesmicrobial ecologysystems biology |
| spellingShingle | Christian Diener Sean M. Gibbons More is Different: Metabolic Modeling of Diverse Microbial Communities mSystems flux balance analysis metabolic modeling metabolism microbial communities microbial ecology systems biology |
| title | More is Different: Metabolic Modeling of Diverse Microbial Communities |
| title_full | More is Different: Metabolic Modeling of Diverse Microbial Communities |
| title_fullStr | More is Different: Metabolic Modeling of Diverse Microbial Communities |
| title_full_unstemmed | More is Different: Metabolic Modeling of Diverse Microbial Communities |
| title_short | More is Different: Metabolic Modeling of Diverse Microbial Communities |
| title_sort | more is different metabolic modeling of diverse microbial communities |
| topic | flux balance analysis metabolic modeling metabolism microbial communities microbial ecology systems biology |
| url | https://journals.asm.org/doi/10.1128/msystems.01270-22 |
| work_keys_str_mv | AT christiandiener moreisdifferentmetabolicmodelingofdiversemicrobialcommunities AT seanmgibbons moreisdifferentmetabolicmodelingofdiversemicrobialcommunities |