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This project will contribute to the identification of the molecular mechanism of action of probiotic microorganisms, based on the identification of the synthesis pathways of molecular patterns relevant to their functional action. A double approach is proposed: computational and experimental. Thus, a series of metabolic models will be developed at a genomic scale (GEM) from the annotated sequences of bifidobacteria genomes.
Description

Title: Genomic-scale metabolic models and bacterial reverse ecology: application to bacteria of economic interest

Research groups: Biotechnology and Synthetic Biology and Systems Metabolic Engineering

This project will contribute to the identification of the molecular mechanism of action of probiotic microorganisms, based on the identification of the synthesis pathways of molecular patterns relevant to their functional action. A double approach is proposed: computational and experimental. Thus, a series of metabolic models will be developed at a genomic scale (GEM) from the annotated sequences of bifidobacteria genomes. This will allow us to obtain the functional metabolic reconstructions and to analyze, among other aspects, growth capacities, carbon source utilization or essential factor requirements. Likewise, the production of metabolites of interest can be simulated and analyzed. This knowledge will serve as a basis for the characterization of the mechanisms of probiotic action. In this way, it will be possible to obtain loss of function mutants in the microorganisms of interest, through the selective deletion of candidate genes based on the comparative analysis of their genomes and associated metabolic models. Finally, by means of reverse ecology analysis, physiological intervention strategies will be evaluated. The general strategy of reverse ecology is also applicable to microorganisms that present very slow growth kinetics, since it allows us to optimize, first in silico and then in vitro, the culture conditions. As a proof of concept, we propose the design of a minimum culture medium for the growth of the phytopathogen Xylella fastidosa.

Ref.PIE202020E120

Consejo Superior de Investigaciones Científicas (CSIC)

Non-UV principal researchers

Juli Peretó

Non-UV participating researchers

Patricia Álvarez, Alba Arévalo, Paola Corbín, José Luis García López, Daniel Ramón, Marta Tortajada.

Start date
2020 May
End date
2021 December
Funding agencies:

Consell Superior d'Investigacions Científiques (CSIC).