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All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing

Fabian Ripp1, Christopher Felix Krombholz1, Yongchao Liu2, Mathias Weber1, Anne Schäfer1, Bertil Schmidt2, Rene Köppel3 and Thomas Hankeln1*

Author Affiliations

1 Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany

2 Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany

3 Official Food Control Authority of the Canton Zürich, Zürich, Switzerland

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BMC Genomics 2014, 15:639  doi:10.1186/1471-2164-15-639

Published: 31 July 2014



DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components.


Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (chicken, turkey) species are able to quantify material correctly at the 1% discrimination level via a read counting approach. An additional metagenomic step facilitates identification of traces from animal, plant and microbial DNA including unexpected species, which is prospectively important for the detection of allergens and pathogens.


Our data suggest that deep sequencing of total genomic DNA from samples of heterogeneous taxon composition promises to be a valuable screening tool for reference species identification and quantification in biosurveillance applications like food testing, potentially alleviating some of the problems in taxon representation and quantification associated with targeted PCR-based approaches.

Illumina; Next-generation sequencing; Real-time PCR; Species identification; Metagenomics