DNA Barcoding for Minor Crops and Food Traceability

This outlook paper addresses the problem of the traceability of minor crops. These kinds of cultivations consist in a large number of plants locally distributed with a modest production in terms of cultivated acreage and quantity of final product. Because of globalization, the diffusion of minor crops is increasing due to their benefit for human health or their use as food supplements. Such a phenomenon implies a major risk for species substitution or uncontrolled admixture of manufactured plant products with severe consequences for the health of consumers. The need for a reliable identification system is therefore essential to evaluate the quality and provenance of minor agricultural products. DNA-based techniques can help in achieving this mission. In particular, the DNA barcoding approach has gained a role of primary importance thanks to its universality and versatility. Here, we present the advantages in the use of DNA barcoding for the characterization and traceability of minor crops based on our previous or ongoing studies at the ZooPlantLab (Milan, Italy). We also discuss how DNA barcoding may potentially be transferred from the laboratory to the food supply chain, from field to table

Erratum to: Orally administered multispecies probiotic formulations to prevent uro-genital infections: a randomized placebo-controlled pilot study

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DNA barcoding to trace Medicinal and Aromatic Plants from the field to the food supplement

The global market of food supplements is growing, along with consumers demand for high-quality herbal products. Nevertheless, substitution fraud, and adulteration cases remain a common safety problem of global concern. In the last years, the DNA barcoding approach has been proposed as a valid identification method and it is now commonly used in the authentication of herbal and food products. The objective of this study was to evaluate whether DNA barcoding can be applied to trace the plant species from the starting raw material to the finished commercial products. We selected a panel of 28 phytoextracts obtained through three different extraction methods (i.e., maceration, percolation and sonication) with different solvents (i.e., ethanol, deionized water and glycerol). Furthermore, we chose six plant species for which we collected and analysed all the intermediates of the industrial production. We sequenced and analyzed the sequence variability at DNA barcoding (psbA-trnH, ITS) and minibarcoding (rbcL 1-B) marker regions. Phytoextracts obtained through hydroalcoholic treatment, with the lower percentage of ethanol (<40%), and aqueous processing, at the lowest temperature, had major rate of sequencing and identification success. This study proves that DNA barcoding is a useful tool for Medicinal and Aromatic Plants (MAPs) traceability, which would provide consumers with safe and high-quality herbal products

Check Your Shopping Cart: DNA Barcoding and Mini-Barcoding for Food Authentication

The molecular approach of DNA barcoding for the characterization and traceability of food products has come into common use in many European countries. However, it is important to address and solve technical and scientific issues such as the efficiency of the barcode sequences and DNA extraction methods to be able to analyze all the products that the food sector offers. The goal of this study is to collect the most defrauded and common food products and identify better workflows for species identification. A total of 212 specimens were collected in collaboration with 38 companies belonging to 5 different fields: seafood, botanicals, agrifood, spices, and probiotics. For all the typologies of specimens, the most suitable workflow was defined, and three species-specific primer pairs for fish were also designed. Results showed that 21.2% of the analyzed products were defrauded. A total of 88.2% of specimens were correctly identified by DNA barcoding analysis. Botanicals (28.8%) have the highest number of non-conformances, followed by spices (28.5%), agrifood (23.5%), seafood (11.4%), and probiotics (7.7%). DNA barcoding and mini-barcoding are confirmed as fast and reliable methods for ensuring quality and safety in the food field

Chemical, molecular, and proteomic analyses of moss bag biomonitoring in a petrochemical area of Sardinia (Italy)

In this study, Hypnum cupressiforme moss bags were used to examine the atmospheric deposition of trace elements in the oil refinery region of Sardinia (Italy) compared with surrounding natural zones. The concentrations of 13 elements [arsenic (As), calcium (Ca), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), sodium (Na), nickel (Ni), lead (Pb), vanadium (V), and zinc (Zn)] were determined using inductively coupled plasma optical emission spectrometry. A significant accumulation of pollutants was detected using active biomonitoring with moss bags compared with a control site. The most relevant contaminants for all of the tested sites were Cr, Cu, Ni, and Zn. Moreover, the accumulation of Cr and Zn in the refinery industrial areas, IA1 and IA2, was more than five times greater than that detected at the control site. Levels of Cd, Mg, and Pb were also higher at all of the monitored sites compared with the control site. Both genomic and proteomic methods were used to study the response of H. cupressiforme to air pollution. No DNA damage or mutations were detected using the amplified fragment length polymorphisms (AFLP) method. At the protein level, 15 gel spots exhibited differential expression profiles between the moss samples collected at the IA1 site and the control site. Furthermore, among the 14 spots that showed a decrease in protein expression, nine were associated with ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and proteins of the light-harvesting complexes of photosystem (PS) II, three were associated with protein synthesis, and three were stress-related proteins. Thus, some of these proteins may represent good moss biosensors which could be used as pre-alert markers of environmental pollution

Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling

Data from: Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing PhyloH as a novel phylogenetic diversity analysis tool

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

<div><p>Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. <i>Lysinibacillus</i>, <i>Bacillus</i>, and <i>Sporosarcina</i>), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if <i>Saccharomyces cerevisiae</i> represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits’ microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.</p></div