ArticleBMC genomics2014
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Single nucleotide polymorphism information estimates breed and variety composition ratio in food.Current research in food science · 2026Article
- Article
- DNA-based detection of pork content in food.Heliyon · 2023Review
- Benchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding.Foods (Basel, Switzerland) · 2023Article
- Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species.BMC genomics · 2022Article
- Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review.Foods (Basel, Switzerland) · 2021Review
- Monitoring the microbiome for food safety and quality using deep shotgun sequencing.NPJ science of food · 2021Article
- Current issues for mammalian species identification in forensic science: a review.International journal of legal medicine · 2021Review
- Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database.Scientific reports · 2020Article
- A big data approach to metagenomics for all-food-sequencing.BMC bioinformatics · 2020Article
- Big Data in metagenomics: Apache Spark vs MPI.PloS one · 2020Article
- Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin.Frontiers in plant science · 2020Article
- Review
- Food authentication from shotgun sequencing reads with an application on high protein powders.NPJ science of food · 2019Article
- Method for the Identification of Taxon-SpecificFrontiers in plant science · 2018Article
- The potential of aerosol eDNA sampling for the characterisation of commercial seed lots.PloS one · 2018Article
- A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification.Journal of analytical methods in chemistry · 2018Article
- A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.