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

BMC Genomics

Thomas Hankeln²  Rene Köppel³  Bertil Schmidt¹  Anne Schäfer²  Mathias Weber²  Yongchao Liu¹  Christopher Felix Krombholz²  Fabian Ripp² 

[1] Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany;Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany;Official Food Control Authority of the Canton Zürich, Zürich, Switzerland

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

Others  :  1216357
DOI  :  10.1186/1471-2164-15-639

 received in 2013-07-23, accepted in 2014-07-24,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Ripp et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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