Bioinformatics platform to predict probiotic functionality

European research institutes have partnered with SMEs to develop a bioinformatics platform to predict the functionality of food bacteria and probiotics based on their genome sequence. Coordinated by NIZO food research, the platform - GENOBOX - will allow the companies to determine specific functional benefits in a fast, cheap and reproducible way.

To determine the functionality and performance of a microorganism by experiments requires an elaborate, time-consuming and expensive process. The functional potential of a microorganism is largely determined by its genomic sequence that encodes enzymes and proteins, therefore many companies have sequenced their industrial strains.

The GENOBOX project aims to translate the genomic data into strain functionality such as GI survival, yield, probiotic properties, safety and production of flavour compounds. This requires a bioinformatics infrastructure and expertise to develop, manage and interpret these data.

A consortium of research institutes and SMEs from the dairy and probiotic industry decided to tackle the issue by constructing a software platform - GENOBOX. With this platform, the genomic sequence of a microorganism can be used to predict its functional properties.

GENOBOX will include a set of algorithms for annotation of genes, metabolic modelling, text mining and transcriptome analysis. It can compare the data with hundreds of genomes of microorganisms available in the public domain.

“The new pipeline, as I call it, will allow companies to select the most promising strains for, say, a new flavour, based on genomic sequence data alone, instead of doing a lot of elaborate and expensive experiments,” said Wynand Alkema, coordinator of the consortium.

“The GENOBOX platform offers new insights in the potential functionalities of probiotic strains and provides the opportunity to design effective multispecies probiotic mixtures,” added Saskia van Hemert, senior scientist at Winclove Probiotics.

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

The GENOBOX platform is expected to be up and running in approximately 18 months.