Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jul 31;15(1):639.
doi: 10.1186/1471-2164-15-639.

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

Fabian Ripp, Christopher Felix Krombholz, Yongchao Liu, Mathias Weber, Anne Schäfer, Bertil Schmidt, Rene Köppel, Thomas Hankeln  1
Affiliations

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

Fabian Ripp et al. BMC Genomics. .

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Outline of the AFS pipeline.
Figure 2
Figure 2
Metagenomic analysis of unmapped reads. Results of the metagenomic analysis of sequence reads obtained from the KalD reference sausage. The global result of the BLAST/MEGAN step is shown in the box (grey frame). A more detailed classification of matches is displayed for mammals, viruses, bacteria and plants.
Figure 3
Figure 3
Determination of the optimal number of sequence reads necessary to obtain accurate quantification results for species components. The number of sequence reads used in the mapping (x-axis) was plotted against the values of mapping accuracy (y-axis), calculated as the cumulated absolute deviation in% of mapping results versus expected species proportions.
See this image and copyright information in PMC

References

    1. Das Eidgenössische Departement des Innern Verordnung über Lebensmittel tierischer Herkunft. Swiss Food Legislation. 2005;23:11.
    1. Bundesministerium der Justiz und für Verbraucherschutz Gesetz über den Verkehr von Arzneimitteln. German Drug Law. 2011;22:12.
    1. Meyer R, Candrian U, Lüthy J. Detection of pork in heated meat products by the polymerase chain reaction. J AOAC Int. 1994;77(3):617–622. - PubMed
    1. Woolfe M, Primrose S. Food forensics: using DNA technology to combat misdescription and fraud. Trends Biotechnol. 2004;22(5):222–226. - PubMed
    1. Asensio L, Gonzalez I, Garcia T, Martin R. Determination of food authenticity by enzyme-linked immunosorbent assay (ELISA) Food Control. 2008;19(1):1–8.

Publication types