原创力文档a computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities计算探索细菌代谢多样性鉴定代谢相互作用和growth-efficient应变社区.pdfVIP
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a computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities计算探索细菌代谢多样性鉴定代谢相互作用和growth-efficient应变社区
Tzamali et al. BMC Systems Biology 2011, 5:167
/1752-0509/5/167
RESEARCH ARTICLE Open Access
A computational exploration of bacterial metabolic
diversity identifying metabolic interactions and
growth-efficient strain communities
1,2* 3 1,2 4,5*
Eleftheria Tzamali , Panayiota Poirazi , Ioannis G Tollis and Martin Reczko
Abstract
Background: Metabolic interactions involve the exchange of metabolic products among microbial species. Most
microbes live in communities and usually rely on metabolic interactions to increase their supply for nutrients and
better exploit a given environment. Constraint-based models have successfully analyzed cellular metabolism and
described genotype-phenotype relations. However, there are only a few studies of genome-scale multi-species
interactions. Based on genome-scale approaches, we present a graph-theoretic approach together with a
metabolic model in order to explore the metabolic variability among bacterial strains and identify and describe
metabolically interacting strain communities in a batch culture consisting of two or more strains. We demonstrate
the applicability of our approach to the bacterium E. coli across different single-carbon-source conditions.
Results: A different diversity graph is constructed for each growth condition. The graph-theoretic properties of the
constructed graphs reflect the inherent high metabolic redundancy of the cell to single-gene knockouts, reveal
mutant-hubs of unique metabolic capabilities regarding by-production, demonstrate consistent metabolic
behaviors across conditions and show an evolutionary difficulty towards the establishment of polymorphism, while
suggesting that communities consisting of strains specifically adapted to a given condition are
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