Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq)

  • Sören Lukas Hellmann
  • Fabian Ripp
  • Sven-Ernö Bikar
  • Bertil Schmidt
  • Rene Köppel
  • Thomas HankelnEmail author
Original Paper


Complex food matrices bear the risk of intentional or accidental admixture of non-declared species. Moreover, declared components can be present in false proportions, since expensive taxa might be exchanged for cheaper ones. We have previously reported that PCR-free metagenomic sequencing of total DNA extracted from sausage samples combined with bioinformatic analysis (termed All-Food-Seq, AFS) can be a valuable screening tool to identify the taxon composition of food ingredients. Here, we illustrate this principle by analysing regional Doner kebap samples, which revealed unexpected and unlabelled poultry and plant components in three of five cases. In addition, we systematically apply AFS to a broad set of reference meat material of known composition (i.e. reference sausages) to evaluate quantification accuracy and potential limitations. We include a detailed analysis of the effect of different food matrices and the possibility of false-positive sequence read assignment to closely related species, and we compare AFS quantification results to quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). AFS emerges as a potent PCR-free screening tool, which can detect multiple target species of different kingdoms of life within a single assay. Mathematical calibration accounting for pronounced matrix effects can significantly improve AFS quantification accuracy. In comparison, AFS performs better than classical qPCR, and is on par with ddPCR.


Food metagenomics Species identification Doner Kebap Read mapping Next-generation-sequencing 



TH and SLH gratefully acknowledge funding by the Federal Office for Agriculture and Food (project ID: 2816503814), Johannes Gutenberg University Center for Computational Sciences (CSM) and the Ministry of Justice and for Consumer Safety Rhineland-Palatinate.

Compliance with ethics standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

This article does not contain any studies with human and animal subjects.

Supplementary material

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Supplementary material 1 (DOCX 29 kb)
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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome AnalysisJohannes Gutenberg University MainzMainzGermany
  2. 2.MVZ Labor VolkmannKarlsruheGermany
  3. 3.StarSEQ GmbHMainzGermany
  4. 4.Institute of InformaticsJohannes Gutenberg University MainzMainzGermany
  5. 5.Official Food Control Authority of the Canton ZurichZurichSwitzerland

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