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Genomics and bioinformatics of food bacteria

The Bacterial Genomics group was founded by Prof. R.L. Siezen in 2000 and studies the genomes of food-relevant bacteria in collaboration with the Top Institute Food and Nutrition(TIFN, previously Wageningen Center for Food Sciences; WCFS), NIZO food research (Ede), and the Kluyver Centre for Genomics of Industrial Microorganisms. Microorganisms(Delft). Microorganisms such as yeasts, fungi and bacteria are used extensively in the preparation of food. The carefully controlled use of food-grade bacteria plays an important role in starter cultures (mainly lactic acid bacteria) and in the production of specific metabolites and other ingredients. In addition, so-called `probiotic' bacteria are added to some foods in an attempt to enhance human health. In contrast, any unintentional microbial contamination of food can adversely affect food safety and shelf-life.

Numerous bacterial genomes have been fully sequenced in the past few years, and the information content of genome databases is increasing rapidly. The initial focus was on medically important pathogens, such as Haemophilus influenzae, Helicobacter pylori, E. coli, Mycobacterium tuberculosis, etc., but more recently many bacteria related to food production have been fully sequenced, or are nearing completion. Gram-positive bacteria in particular play a pivotal role in various aspects of food fermentation, ingredient production and food safety.

The main approach is to use various bioinformatical tools to analyse and compare genes, gene clusters, encoded proteins, biochemical pathways, regulatory mechanisms, and so on. The most advanced bioinformatical tools are used for functional annotation of genes, functional and structural prediction of encoded proteins, comparative genomics, and reconstruction of metabolic, regulatory and transport networks.

Genomics of lactic acid bacteria

The genomes of several lactic acid bacteria are being studied, in collaboration with NIZO food research and the Wageningen Center for Food Sciences (WCFS), who have sequenced a Lactobacillus genome. In the immediate future, research in this area will involve:

  • identification of genes and functional annotation of lactic acid bacteria genomes
  • mapping of their metabolic, regulatory and transport networks
  • comparative genomics of lactic acid bacteria (various species of Lactobacillus, Lactococcus, Bifidobacterium, Streptococcus). This should lead to insights into the conservation and variability of gene and protein sequences, gene ordering and clustering, metabolic pathways, regulatory mechanisms, and so on.
  • biodiversity and genotype-phenotype matching

Virtual cell databases and metabolic models

This research aims to reconstruct the cellular processes, metabolic potential and regulatory networks of selected gram-positive Bacteria and Archaea, by in silico analysis of all proteins encoded by their chromosome. The results are incorporated into "virtual cell" databases and metabolic models, which are then used to predict the dynamics of the networks under different environmental conditions.

Genomics of pathogenic and spoilage bacteria

The genomes of gram-positive food pathogens and spoilage bacteria are being compared, by data mining in genome databases. In the immediate future, research in this area will include:

  • comparative genomics of gram-positive food pathogens and spoilage bacteria (e.g. Listeria monocytogenes, Enterococcus faecalis, Streptococcus sp., Bacillus cereus, Clostridium difficile)
  • comparative genomics of these gram-positive bacteria with gram-negative pathogenic and food spoilage bacteria (e.g. E. coli, Salmonella, Campylobacter).