All-Food-Seq AFS: a quantifiable screen for species in biological samples by deep DNA sequencingReport as inadecuate




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BMC Genomics

, 15:639

Comparative and evolutionary genomics

Abstract

BackgroundDNA-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.

ResultsSequence 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.

ConclusionsOur 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.

KeywordsIllumina Next-generation sequencing Real-time PCR Species identification Metagenomics AbbreviationsAFSAll food sequencing

KalDKalibrator D

KLyoAKalibrator Lyoner A

GPUsGraphics processing units

NGSNext-generation sequencing.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-639 contains supplementary material, which is available to authorized users.

Fabian Ripp, Christopher Felix Krombholz contributed equally to this work.

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Author: Fabian Ripp - Christopher Felix Krombholz - Yongchao Liu - Mathias Weber - Anne Schäfer - Bertil Schmidt - Rene Köppel -

Source: https://link.springer.com/



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