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

Canning Processes Reduce the DNA-Based Traceability of Commercial Tropical Tunas

Canned tuna is one of the most widely traded seafood products internationally and is of growing demand. There is an increasing concern over the vulnerability of canned tuna supply chains to species mislabelling and fraud. Extensive processing conditions in canning operations can lead to the degradation and fragmentation of DNA, complicating product traceability. We here employed a forensically validated DNA barcoding tool (cytochrome b partial sequences) to assess the effects of canning processes on DNA degradation and the identification of four tropical tuna species (yellowfin, bigeye, skipjack and longtail tuna) collected on a global scale, along their commercial chains. Each species was studied under five different canning processes i.e., freezing, defrosting, cooking, and canning in oil and brine, in order to investigate how these affect DNA-based species identification and traceability. The highest percentage of nucleotide substitutions were observed after brine-canning operations and were greatest for yellowfin and skipjack tuna. Overall, we found that DNA degradation significantly increased along the tuna canning process for most specimens. Consequently, most of the specimens canned in oil or brine were misidentified due to the high rate of nucleotide substitution in diagnostic sequences

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)

11openInternationalInternational coauthor/editorMonitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.openLeontidou, Kleopatra; Vokou, Despoina; Sandionigi, Anna; Bruno, Antonia; Lazarina, Maria; De Groeve, Johannes; Li, Mingai; Varotto, Claudio; Girardi, Matteo; Casiraghi, Maurizio; Cristofori, AntonellaLeontidou, K.; Vokou, D.; Sandionigi, A.; Bruno, A.; Lazarina, M.; De Groeve, J.; Li, M.; Varotto, C.; Girardi, M.; Casiraghi, M.; Cristofori, A

Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy)

While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its “biological simplicity.” During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community

Analisi paleogenetiche condotte sui reperti umani nella necropoli romana del Frizzone (Lucca)

In generale, si pensa che la diversità genomica entro e fra popolazioni moderne sia frutto dei cambiamenti demografici e delle pressioni evolutive che hanno interessato i loro antenati preistorici e proto-storici (Ammerman e Cavalli Sforza, 1984; von Haeseler, A. et al., 1995; Ri- chards, M.B. et al., 2000; Torroni, A. et al., 2001; Underhill, P.A. et al., 2001). L’ipotesi principale è che i processi che hanno determinato la variabilità genetica complessiva di una nazione intera, come l’Italia, debbano essere avvenuti quando la densità di popolazione era bassa, cioé in tempi molto remoti (Piazza, A. et al., 1988). Finora però, non è stato possibile verificare pienamente questa assunzione, proprio perché non esistono molti dati sulle popolazioni antiche e quelli che esistono sono in parte contrastanti. Dati recenti sulla popolazione Etrusca (Verenesi, C. et al., 2004) fanno pensare che ci sia una discontinuità genetica tra questa e le attuali popolazioni che abitano la medesima area; inoltre da uno dei pochi studi su larga scala disponibili sul DNA antico è stato dimostrato come un drastico cambiamento nel pool genico mitocondriale possa richiedere anche solo pochi secoli (Wang, L. et al., 2000). Alla luce di quanto esposto appare perciò necessario raccogliere dati su altre popolazioni antiche, e paragonare gli individui moderni ed antichi in varie località e in tempi differenti al fine eseguire uno studio genetico diacronico e sincronico. Per questo motivo nasce il progetto “Eredità genetica dell’Italia Antica” in cui questa tesi è inserita. Dai 13 campioni iniziali analizzati in questo studio provenienti dalla necropoli del Frizzone (II sec. a.C., I sec. d.C.) sono state ricostruite 8 sequenze complete, attraverso tecniche di antropologia molecolare /paleogenetica, della lunghezza di 360 bp della regione HVR-I (16024-16383), la regione di controllo (D-Loop) del DNA mitocondriale (mtDNA). Il confronto di queste sequenze mitocondriali attraverso il tempo e lo spazio dovrebbe permettere di ricostruire uno scenario più realistico di quelli che erano i rapporti fra i lucchesi antichi, fra essi e le altre popolazioni italiche antiche e le popolazioni che vivono ora nelle stesse aree. Lo scopo ultimo di questo progetto è introdurre una dimensione temporale nello studio della variabilità genetica, che ci permetta di comprendere con quanta rapidità le linee mitocondriali vengano rimpiazzate attraverso il tempo, e quindi che livelli di continuità genealogica esistano fra popolazioni che hanno occupato la stessa regione geografica in diversi intervalli di tempo

Viruslab: A tool for customized sars-cov-2 data analysis

Since the beginning of 2020, the COVID-19 pandemic has posed unprecedented challenges to viral data analysis and connected host disease diagnostic methods. We propose VirusLab, a flexible system for analysing SARS-CoV-2 viral sequences and relating them to metadata or clinical information about the host. VirusLab capitalizes on two existing resources: ViruSurf, a database of public SARS-CoV-2 sequences supporting metadata-driven search, and VirusViz, a tool for visual analysis of search results. VirusLab is designed for taking advantage of these resources within a server-side architecture that: (i) covers pipelines based on approaches already in use (ARTIC, Galaxy) but entirely cutomizable upon user request; (ii) predigests analysis of raw sequencing data from different platforms (Oxford Nanopore and Illumina); (iii) gives access to public archives datasets; (iv) supplies user-friendly reporting – making it a tool that can also be integrated into a business environment. VirusLab can be installed and hosted within the premises of any organization where information about SARS-CoV-2 sequences can be safely integrated with information about hosts (e.g., clinical metadata). A system such as VirusLab is not currently available in the landscape of similar providers: our results show that VirusLab is a powerful tool to generate tabular/graphical and machine readable reports that can be integrated in more complex pipelines. We foresee that the proposed system can support many research-oriented and therapeutic scenarios within hospitals or the tracing of viral sequences and their mutational processes within organizations for viral surveillance

VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants

Variant visualization plays an important role in supporting the viral evolution analysis, extremely valuable during the COVID-19 pandemic. VirusViz is a web-based application for comparing variants of selected viral populations and their sub-populations; it is primarily focused on SARS-CoV-2 variants, although the tool also supports other viral species (SARS-CoV, MERS-CoV, Dengue, Ebola). As input, VirusViz imports results of queries extracting variants and metadata from the large database ViruSurf, which integrates information about most SARS-CoV-2 sequences publicly deposited worldwide. Moreover, VirusViz accepts sequences of new viral populations as multi-FASTA files plus corresponding metadata in CSV format; a bioinformatic pipeline builds a suitable input for VirusViz by extracting the nucleotide and amino acid variants. Pages of VirusViz provide metadata summarization, variant descriptions, and variant visualization with rich options for zooming, highlighting variants or regions of interest, and switching from nucleotides to amino acids; sequences can be grouped, groups can be comparatively analyzed. For SARS-CoV-2, we manually collect mutations with known or predicted levels of severity/virulence, as indicated in linked research articles; such critical mutations are reported when observed in sequences. The system includes light-weight project management for downloading, resuming, and merging data analysis sessions. VirusViz is freely available at http://gmql.eu/virusviz/

It’s a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality

Microbial communities interact with us and affect our health in ways that are only beginning to be understood. Microorganisms have been detected in every ecosystem on Earth, as well as in any built environment that has been investigated. Drinking water sources, drinking water treatment plants and distribution systems provide peculiar microbial ecological niches, dismantling the belief of the “biological simplicity” of drinking water. Nevertheless, drinking water microbiomes are understudied compared to other microbiomes. Recent DNA sequencing and meta-omics advancements allow a deeper understanding of drinking water microbiota. Thus, moving beyond the limits of day-to-day testing for specific pathogenic microbes, new approaches aim at predicting microbiome changes driven by disturbances at the macro-scale and overtime. This will foster an effective and proactive management of water sources, improving the drinking water supply system and the monitoring activities to lower public health risk. Here, we want to give a new angle on drinking water microbiome research. Starting from a selection of 231 scientific publications on this topic, we emphasize the value of biodiversity in drinking water ecosystems and how it can be related with industrialization. We then discuss how microbiome research can support sustainable drinking water management, encouraging collaborations across sectors and involving the society through responsible research and innovation

DNA barcoding in mammals: What's new and where next?

DNA barcoding is a universal molecular identification system of living beings for which efficacy and universality have been largely demonstrated in the last decade in many contexts. It is common to link DNA barcoding to phylogenetic reconstruction, and there is indeed an overlap, but identification and phylogenetic positioning/classification are two different processes. In mammals, a better phylogenetic reconstruction, able to dig in fine details the relationships among biological entities, is really welcomed, but do we need DNA barcoding too? In our opinion, the answer is positive, but not only for the identification power, nor for the supposed ability of DNA barcoding to discover new species. We do need DNA barcoding because it is a modern tool, able to create an integrated system, in which it is possible to link the many aspects of the biology of living beings starting from their identification. With 7000 species estimated and a growing interest in knowledge, exploitation and conservation, mammals are one of the best animal groups to achieve this goal