Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Louca, Stilianos, Doebeli, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2015
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
_version_ 1782395660458262528
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