New bioinformatics platform set to predict bacterial functionalities based on genes alone

NIZO's Wynand Alkema: “The new pipe line, as I call it, will allow companies to select the most promising strains for – say – a new flavor..."

A new bioinformatics platform created by a consortium of European SMEs and research institutes could help industry predict the functionality of food bacteria and probiotics based on their genome.

The GENOBOX platform will allow industry to determine specific functional benefits of bacterial species in a fast, cheap, and reproducible way, according to NIZO Food Research - who coordinate the consortium behind the platform.

“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," explained Wynand Alkema of NIZO.

Saskia van Hemert, senior scientist at Winclove Probiotics added that the platform will also offer valuable new insights in to the potential functionalities in specific probiotic strains, "and provides the opportunity to design effective multispecies probiotic mixtures.”

Bacterial functionality

Alkema and her colleagues noted that determining the functionality and performance of a bacterial strain using standard experimentation can be an elaborate, time consuming, and expensive process.

However, because the functional potential of such micro-organisms are largely determined by its genomic sequence that encodes enzymes and proteins, it is theoretically possible to reveal functionalities from sequencing the genes alone.

Many companies have already sequenced their industrial strains, and now the GENOBOX project is targeting novel ways to translate this genomic data into strain functionality  traits such as GI-survival, yield, probiotic properties, safety, or production of flavour compounds.

By using a specialist bioinformatics infrastructure and expertise to develop, manage and interpret these data the GENOBOX consortium aims to predict the functional properties of bacterial strains based solely on their genomic sequencing and will compare the data with hundreds of genomes of micro-organisms available in the public domain.

Alkema suggested that she expects the GENOBOX platform to be up and running in one and a half years time.

The consortium is made up of six partners from the dairy and probiotics industry: Bioprox, LB Bulgaricum, NIZO food research, Radboud university medical center, Sacco and Winclove Probiotics.

Work carried out in the consortium is financed partly by the EU under the EU-FP7 program.

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