Advances in DNA metabarcoding for food and wildlife forensic species identification

Abstract

Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders’ needs.

Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication

“…The combination of high‐throughput sequencing (HTS) and DNA barcoding, known as DNA metabarcoding, enables simultaneous high‐throughput multi‐taxa identification by using the extracellular and/or total DNA extracted from complex samples containing DNA of different origins (Taberlet et al ., ; Staats et al ., ). DNA metabarcoding is applicable to identification of plant species diversity in a range of products and has been used to investigate the level of discrepancy between the expected and detected plant species based on the label claims of marketed herbal products (Cheng et al ., ; Coghlan et al ., ; Ivanova et al ., ; Raclariu et al ., , ).…”

“…All these studies report varying degrees of authentication success. Therefore, obtaining a representative assessment of complex herbal mixtures is influenced by many factors, including the quality and type of raw material, as well as several elements of the analysis that can however be varied to optimise the results (Staats et al, 2016). Some limitations of DNA metabarcoding are similar to those found in DNA barcoding.…”

“…The greatest advantage of DNA metabarcoding is its ability to identify each single species within complex multi-ingredient and processed mixtures simultaneously, where the application of DNA barcoding and conventional analytical methods is limited considerably. Importantly, DNA metabarcoding data is usable for qualitative evaluation only, to determine presence of taxa, and not for quantitative assessment of relative species abundance based on sequence read numbers, as many variables considerably impact the obtained sequence read results (Staats et al, 2016). Clearly, in the context of pharmacognosy and pharmacovigilance, a combination of analytical methods is unavoidable for comprehensive authentication and quality control of raw material and resulting products (Shetti et al, 2011;Mishra et al, 2016;Parveen et al, 2016;Heinrich et al, 2017;Pawar et al, 2017), and DNA-based approaches offer important novel insights.…”

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

“…Wood, Holland & Goulson 2015); environmental change can be inferred through species-level identification of ancient DNA derived, e.g. from lake sediments (Pansu et al 2015); in food and medicine, DNA barcoding can be used to improve food safety and wildlife forensics (Wong & Hanner 2008;Coghlan et al 2012;Staats et al 2016); and finally, metabarcoding can be used to monitor nature reserves and to detect endangered species (Schnell et al 2012).…”

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

“…The increasing ease and decreasing costs of obtaining DNA sequence data has accelerated advances in systematics, taxonomy, community ecology, and conservation (reviewed in Kress et al., 2015); food and wildlife forensics (reviewed in Staats et al., 2016); monitoring of agricultural pests and invasive species (Ashfaq and Hebert, 2016); and a myriad of human health applications including identification of parasites and disease vectors (Ondrejicka et al., 2014). …”