Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy.
CREA-Council for Agricultural Research and Analysis of Agricultural Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza, Lodi, Italy.
PLoS One. 2023 Jul 25;18(7):e0289108. doi: 10.1371/journal.pone.0289108. eCollection 2023.
The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.
本研究旨在评估 rbcl 作为条码标记的 DNA 代谢组学在鉴定和分类从用于生产 Grana Padano（GP）奶酪的生奶中分离出的微量植物 DNA 的能力。GP 是意大利最受欢迎的 PDO（受保护的原产地名称）之一，其生产符合 GP PDO 规范规则，该规则定义了可以用于饲养奶牛的饲料。从位于 Grana Padano 生产区的 14 家奶牛场共采集了 42 个 GP 散装奶样。为了进行分类学分类，生成了一个具有 NCBI 上 2020 年 9 月至 2021 年 3 月意大利植物区系可用的 rbcL 序列的本地数据库。共产生了 8,399,591 条reads，平均每个样品产生 204,868 条reads（范围为 37,002-408,724），分别在科、属和种水平上产生了 16、31 和 28 个优势 OTUs。对奶样中植物物种的分类分析鉴定出了 7 科、14 属和 14 种，使用 alpha 和 beta 多样性方法进行的统计分析没有突出显示出调查样本之间的差异。然而，奶样的植物变异性很高，在多个分类水平上没有差异可能是由于 GP 规则要求的饲料配给标准化所致。结果表明，DNA 代谢组学是探索牛奶等复杂基质中植物 DNA 痕迹的有价值资源。
