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Calibration and analysis of genome-based models for microbial ecology
Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibra...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608356/ https://www.ncbi.nlm.nih.gov/pubmed/26473972 http://dx.doi.org/10.7554/eLife.08208 |
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author | Louca, Stilianos Doebeli, Michael |
author_facet | Louca, Stilianos Doebeli, Michael |
author_sort | Louca, Stilianos |
collection | PubMed |
description | Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology. DOI: http://dx.doi.org/10.7554/eLife.08208.001 |
format | Online Article Text |
id | pubmed-4608356 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-46083562015-10-19 Calibration and analysis of genome-based models for microbial ecology Louca, Stilianos Doebeli, Michael eLife Computational and Systems Biology Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology. DOI: http://dx.doi.org/10.7554/eLife.08208.001 eLife Sciences Publications, Ltd 2015-10-16 /pmc/articles/PMC4608356/ /pubmed/26473972 http://dx.doi.org/10.7554/eLife.08208 Text en © 2015, Louca and Doebeli http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Computational and Systems Biology Louca, Stilianos Doebeli, Michael Calibration and analysis of genome-based models for microbial ecology |
title | Calibration and analysis of genome-based models for microbial ecology |
title_full | Calibration and analysis of genome-based models for microbial ecology |
title_fullStr | Calibration and analysis of genome-based models for microbial ecology |
title_full_unstemmed | Calibration and analysis of genome-based models for microbial ecology |
title_short | Calibration and analysis of genome-based models for microbial ecology |
title_sort | calibration and analysis of genome-based models for microbial ecology |
topic | Computational and Systems Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608356/ https://www.ncbi.nlm.nih.gov/pubmed/26473972 http://dx.doi.org/10.7554/eLife.08208 |
work_keys_str_mv | AT loucastilianos calibrationandanalysisofgenomebasedmodelsformicrobialecology AT doebelimichael calibrationandanalysisofgenomebasedmodelsformicrobialecology |