All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing
Open accessAbstract
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.
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Shotgun metagenomics is the sole approach able to comprehensively survey the microbial composition of a sample and unearth its genomic potential along with the reconstruction of genomes of multiple strains.
“While cultivation has extended to high-throughput settings, 14 shotgun metagenomics is the sole approach able to comprehensively survey the microbial composition of a sample and unearth its genomic potential 12,15 along with the reconstruction of genomes of multiple strains. 16,17”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [16]
The Background (page unavailable) says sequencing total genomic DNA can, in principle, detect species without the primer biases of barcoding, and the Results and discussion describe identifying bacterial reads. The paper does not establish that shotgun metagenomics is the sole approach for comprehensively surveying microbial composition or show that it reveals genomic potential. The separate claim about reconstructing multiple strain genomes is attached to other citations in the citing sentence. (LLM, conf=0.85)
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References 54 · Cited by 66
- Authors
- Ripp, F., Krombholz, C. F., Liu, Y., Weber, M., Schäfer, A., Schmidt, B., Köppel, R., & Hankeln, T.
- Affiliations
- Johannes Gutenberg University Mainz (DE)
- Corresponding author
- Hankeln, Thomas
- Venue
- BMC Genomics
- Published
- 2014-07-31
- Volume
- 15
- Issue
- 1
- Pages
- 639-639
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC4131036
- OpenAlex
- W2001405665
- Cited by
- 66
- References
- 54
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 1 · 2023: 9 · 2022: 4 · 2021: 7 · 2020: 9 · 2019: 9 · 2018: 7 · 2017: 11 · 2016: 3 · 2015: 3
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Gutenberg Open Science (submittedVersion, cc-by-nd)
- Gutenberg Open Science (cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Identification and Quantification in Food
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- species identification, food authentication, metagenomics, read counting, food adulteration, allergen testing, pathogen detection, biosurveillance, sausage
- MeSH terms
- Animals, Calibration, Chromosome Mapping, Humans, Meat, Species Specificity, Sequence Analysis, DNA, Databases, Genetic, Biosurveillance, Metagenomics, High-Throughput Nucleotide Sequencing, Food Quality
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