Abstract In this study, we tested the Ion Torrent next generation semiconductor based sequencing technology for meat species identification in several highly processed and complex meat products and meat derived broths (a doner kebab, a beef/pork pate, a meat based filling of tortellini, one instantaneous granular preparation of broth stock made by meat and two ready to use meat broths from different producers). The detection protocol included the sequencing of targeted mitochondrial DNA (mtDNA) regions amplified with universal primer pairs and a bioinformatic pipeline designed to interpret sequencing results. Six libraries were sequenced producing a total of 1,363,351 filtered reads. Data mining detected expected and unexpected meat species in the analysed products. Pork was identified in the kebab and Bubalus bubalis DNA was identified in the beef/pork pate. For products for which the precise meat species ingredient information was not available, it was possible to obtain it. Human contamination based on human detected reads could be useful to evaluate the hygienic level of highly processed products. Mitochondrial haplotypes (mitotypes) were identified for several mtDNA-species combinations providing another level of information useful for the authentication of meat derived products. This work defined a methodological framework to establish assays using this sequencing platform for routine species identification in complex and highly processed food.

中文翻译：

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下一代基于半导体的测序在物种鉴定和物种内线粒体分析中的应用，可用于肉制品的鉴定

摘要 在本研究中，我们测试了基于 Ion Torrent 下一代半导体的测序技术在几种高度加工和复杂的肉制品和肉源肉汤（烤肉串、牛肉/猪肉酱、肉馅饺子馅、一种由肉制成的即时颗粒状肉汤和两种来自不同生产商的即用型肉汤）。检测方案包括对使用通用引物对扩增的靶向线粒体 DNA (mtDNA) 区域进行测序，以及用于解释测序结果的生物信息学管道。对六个文库进行测序，产生总共 1,363,351 个过滤读数。数据挖掘在分析的产品中检测到预期和意外的肉类种类。在烤肉串中鉴定出猪肉，在牛肉/猪肉酱中鉴定出 Bubalus bubalis DNA。对于无法获得准确的肉种成分信息的产品，可以获得它。基于人类检测读数的人类污染可能有助于评估高度加工产品的卫生水平。确定了几种 mtDNA 物种组合的线粒体单倍型（mitotypes），为肉制品的鉴定提供了另一层次的信息。这项工作定义了一个方法学框架，以使用该测序平台建立分析，用于复杂和高度加工食品中的常规物种鉴定。基于人类检测读数的人类污染可能有助于评估高度加工产品的卫生水平。确定了几种 mtDNA 物种组合的线粒体单倍型（mitotypes），为肉制品的鉴定提供了另一层次的信息。这项工作定义了一个方法学框架，以使用该测序平台建立分析，用于复杂和高度加工食品中的常规物种鉴定。基于人类检测读数的人类污染可能有助于评估高度加工产品的卫生水平。确定了几种 mtDNA 物种组合的线粒体单倍型（mitotypes），为肉制品的鉴定提供了另一层次的信息。这项工作定义了一个方法学框架，以使用该测序平台建立分析，用于复杂和高度加工食品中的常规物种鉴定。