NGS-based barcoding with mini-COI gene target is useful for pet food market surveys aimed at mislabelling detection

DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan

Background

Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.

Methods

To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.

Results

We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.

Development of ion torrent-based targeted next-generation sequencing panel for identification of animal species in pet foods

Manufacturers may intentionally or unintentionally incorporate ingredients not specified on the label of canned pet foods. Including any unacknowledged ingredients in a food product is considered food fraud or misbranding. Contamination of pet foods may occur in the processing of the foods, including potential cross-contamination in packaging facilities. Of the methods available to identify meat species in food products, Sanger sequencing and several next-generation sequencing methods are available, but there are limitations including the number of targets analyzed at a time and the method specificity. In this study, we developed a targeted next-generation sequencing panel to detect meat species in canned pet foods using Ion Torrent technology. The panel contains multiple primers targeting mitochondrial genes from as many as 27 animal species, of which 7 major animal species were validated. The meat species targets could be identified from samples spiked with as low as 0.01% w/w of the contaminating meat species in a vegetarian food matrix material. Targeted NGS in the current study enriches species-specific multiple target areas in the mitochondrial genome of the target material, which gives high accuracy in the sequencing results.

Benchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding

DNA-metabarcoding is becoming more widely used for routine authentication of meat-based food and feed products. Several methods validating species identification methods through amplicon sequencing have already been published. These use a variety of barcodes and analysis workflows, however, no methodical comparison of available algorithms and parameter optimization are published hitherto for meat-based products' authenticity. Additionally, many published methods use very small subsets of the available reference sequences, thereby limiting the potential of the analysis and leading to over-optimistic performance estimates. We here predict and compare the ability of published barcodes to distinguish taxa in the BLAST NT database. We then use a dataset of 79 reference samples, spanning 32 taxa, to benchmark and optimize a metabarcoding analysis workflow for 16S rDNA Illumina sequencing. Furthermore, we provide recommendations as to the parameter choices, sequencing depth, and thresholds that should be used to analyze meat metabarcoding sequencing experiments. The analysis workflow is publicly available, and includes ready-to-use tools for validation and benchmarking.

Detection of chicken DNA in commercial dog foods

BACKGROUND

These days the number of potential food allergens is very large, but chicken is one of the most common allergens in dogs. Elimination diet is one of the clinical tools for the diagnosis of allergies and allergy tests are not very reliable. The restriction diet is most commonly carried out by feeding pet foods, relying on the ingredients on the label to select an elimination diet not containing previously eaten foods. Unfortunately, mislabeling of pet food is quite common. The purpose of this study was to determine the absence or presence of chicken DNA using both qualitative and quantitative polymerase chain reaction (PCR) analysis methods in dry and wet maintenance complete pet foods for adult dogs. Results were used to verify the declared composition on the labels.

RESULTS

Eleven out of fifteen (73%) dog foods were produced as declared by the manufacturer, two of which showed the presence of chicken protein as stated on the label. The remaining nine foods contained amounts of chicken DNA below 1%, consistent with declarations that no chicken was added in the composition. Four of tested dog foods (27%) were not produced consistently with the declaration on the packaging. Two dog foods (one dry and one wet) did not contain the claimed chicken protein. In two foods the addition of chicken DNA was detected at the level of over 2% and almost 6%, respectively.

CONCLUSIONS

In this study, we focused on one of the most commonly undeclared animal species on the label-chicken protein-and performed DNA analyzes to investigate possible contamination and mislabeling. The results showed some inaccuracies. However, most of them are trace amounts below 1%, which proves compliance with the label. Our results showed that undeclared animal species can be as common as missing an animal protein declared on the label. The conducted research indicates that both dry and wet analyzed foods should not be recommended as a diagnostic tool in elimination tests, because it may result in false negative results. Over-the-counter maintenance foods for dogs should not be recommended for the diagnosis and treatment of food hypersensitivity.

MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences

Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats (‘fasta’ for sequences & ‘tsv’ for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines.

Database URL: https://github.com/bachob5/MetaCOXI

Using a next-generation sequencing approach to DNA metabarcoding for identification of adulteration and potential sources of mercury in commercial cat and dog foods

Studies have demonstrated that some commercial pet (i.e., cat and dog) food products contain high concentrations of mercury (Hg), and some products have Hg concentrations that are higher than expected based on the ingredients included in the package ingredient list. Additionally, concentrations of methylmercury, a particularly toxic form of Hg commonly associated with fish-based ingredients, are largely unstudied despite the widespread use of such ingredients in pet food products. This study aimed to quantify total Hg and methylmercury in a variety of commercial pet food products (n = 127), and use genetic tools to determine if specific ingredients contributed to high Hg concentrations in the final product. Results indicate that total Hg concentrations were above suggested maximum tolerable limits in three of the tested pet food products, and that methylmercury concentrations were at safe levels in all tested products. Next-generation amplicon sequencing using ten barcode primers was conducted to target distinct taxa and to determine if one primer set outperformed the others in amplifying the often heavily degraded DNA found in pet food products. The 16sUniF_16sUniR primer set generated a relatively higher number of reads across the broadest set of taxa, although several of the primer sets were useful in identifying common animal- and plant-based ingredients in commercial pet food products. Combined with the Hg results, it was demonstrated that pet food product ingredients are consistent among and between product lots. However, these results also revealed that adulteration is prevalent in pet food products.