Consortium to predict functionality of food bacteria and probiotics based on genome sequence

A consortium of European SMEs and research institutes have joined forces to develop GENOBOX, a new bioinformatics platform for predicting the functionality of food bacteria and probiotics based on their genome sequence. The platform will allow these companies to determine specific functional benefits in a fast, cheap and reproducible way. The consortium is coordinated by NIZO food research.

Determining the functionality and performance of a micro-organism by experiments is an elaborate, time consuming and expensive process. The functional potential of a micro-organism is largely determined by its genomic sequence that encodes enzymes and proteins. Therefore many companies have sequenced their industrial strains. The target of this project is to translate the genomic data into strain functionality  e.g. GI-survival, yield, probiotic properties, safety, or production of flavour compounds. This requires a bioinformatics infrastructure and expertise to develop, manage and interpret these data.

The Genobox consortium

A consortium of research institutes and SMEs from the dairy and probiotic industry  decided to tackle the issue by constructing a software platform called GENOBOX. With this platform the genomic sequence of a micro-organism can be used to predict its functional properties. GENOBOX will therefore include a set of algorithms for annotation of genes, metabolic modeling, text mining, and transcriptome analysis. It can compare the data with hundreds of genomes of micro-organisms available in the public domain.

The Genobox consortium ( consists of six partners: Bioprox, LB Bulgaricum, NIZO food research, Radboud university medical center, Sacco and Winclove Probiotics. The work carried out in the consortium is financed partly by the EU under the EU-FP7 program.

Wynand Alkema, coordinator of the consortium, is very enthusiastic about GENOBOX. “ The new pipe line, as I call it, will allow companies to select the most promising strains for – say – a new flavor, based on genomic sequence data alone, instead of doing a lot of elaborate and expensive experiments’. Saskia van Hemert, senior scientist at Winclove Probiotics: “The GENOBOX platform offers new insights in the potential functionalities of probiotic strains and provides the opportunity to design effective multispecies probiotic mixtures.” Carmen Lapadatescu of Bioprox underlines that this project also leads to improved information for the final consumers. Alkema expects the GENOBOX platform to be up and running in 1½ years.