Foodborne pathogen detection at strain level & surveillance

BaseClear is an active partner within the Microbiome Applications for Sustainable food systems through Technologies and EnteRprise (MASTER) project*, an European Horizon 2020 project with 30 partners under 5 work packages. Using metagenome datasets and a custom built Pathogen database, BaseClear is developing a bioinformatics pipeline that enables the detection and surveillance of low abundant foodborne pathogens at strain level in a range of food matrices – a powerful tool to assess the food quality along the supply chain. Functional analysis such as pathogenicity, virulence and toxicity are among features that the pipelines is also aiming to evaluate as part of this project.

About the MASTER project

The MASTER project is a Horizon 2020 Innovation Action being coordinated by Dr Paul Cotter at Teagasc. The EU funding for the MASTER project is nearly €11 Million. This ambitious research project will be achieved over four years through the involvement of 31 leading European and international academic and industry teams. The overall aim of the MASTER project is to take a global approach to the development of concrete microbiome products, foods/feeds, services, or processes with high commercial potential. This will benefit society through improving the quantity, quality and safety of food, across multiple food chains, to include marine, plant, soil, rumen, meat, brewing, fruit and vegetable waste, and fermented foods. This will be achieved through mining microbiome data relating to the food chain, developing big data management tools to identify inter-relations between microbiomes across food chains, and generating close to market products and applications which promote sustainability, circularity and contribute to waste management and climate change mitigation.

Work package 5

The project that BaseClear is working on is part of work package 5 (WP5). The other collaboration partners of WP5 include Wageningen UR, Teagasc, University College Cork, 4D Pharma, Universidad de Leon, Oxford Nanopore Technologies, FFOQSI, Novolyze, Qiagen and Danone. WP5 aims at investigating the role of microbes in food systems and to improve quality, security and sustainability.

For this project BaseClear brings NGS and bioinformatics expertise that is required for the development of software tool and targeted reference databases for standardized analysis of microbiome samples, with the application to detect low abundant species and strains in a given sample type. This pipeline is also a first step in assessing pathogens in animal health industry and sustainable environment.

Potential applications of this tool include;

  • detection of pathogens in chicken caecum, fish digesta or rumen fluid
  • contaminant detection in the production facility
  • determination of the quality of cheese
  • assessing the grafting and colonisation of (oral) probiotics in the gut
  • and many more

Contact us for more information at

* MASTER is an Innovation Action funded by the European Commission under the Horizon 2020 Programme under grant number 818368.


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