Combining experimental data and in silico analysis to model the metabolic network of Lactobacillus plantarum

The complete genome of Lactobacillus plantarum WCFS1 has recently been sequenced within the Wageningen Centre for Food Sciences. Lactobacillus plantarum is a versatile lactic acid bacterium that is important in many food and feed fermentation processes. Putative biological functions could be assigned to 2,120 (70%) of the 3,052 predicted protein-encoding genes. After prediction of gene function, the focus is now on the development and improvement of methods and tools to go from genome sequence to gene annotation, to pathway reconstruction and to prediction of phenotype through metabolic models. Important aspects are how and where to incorporate and use experimental (genomics) data, and how and to what extent parts of the process can be automated. We have Set up different bioinformatics tools, including web-interfaced databases and simulation software. This paper described some of these tools, and how they are used and combined with experimental data to come to a model of the metabolic network of Lactobacillus plantarum. The use and type of questions that can be addressed with these type of models will be discussed.