Molecular technologies, such as metabarcoding, have become powerful tools for conservation purposes. Here, we present a non-invasive study analyzing the diet of one population of European pond turtle (Emys orbicularis) during its whole activity period and of four other populations during the same period, based on faecal sample, and using for the first time on this species, a long metabarcoding approach. Emys orbicularis is an emblematic freshwater species of wetlands in Europe. In several countries, this species is endangered and, in Switzerland, Emys orbicularis is ranked as critically endangered on the Swiss Red List. A national conservation program was created to reintroduce this species and raised the question if this reintroduced species could be a threat for other endangered species. We developed a new method of long metabarcoding analysis, using universal PCR primers to determine prey species occurrence in the faeces. The analysis conducted on 174 faeces collected on 142 individuals revealed 1153 preys from 270 species. Emys orbicularis consumed plants throughout the year with a more diverse diet during the reproduction period (April- June). This study therefore not only determines precisely the omnivorous and opportunistic diet of the Emys orbicularis, but also shows that this species is not a threat to its environment, as 85.5% of the consumed species were not list on the Swiss Red List. Moreover, it also demonstrated that the genetic analyses of faeces could be an efficient tool to determine trophic interaction with a high level of precision, yielding promising perspectives for food web ecology.

分子技术，例如元条形码，已经成为保护目的的强大工具。在这里，我们提出了一种非侵入性的研究，分析欧洲池龟（之一人口的饮食Emys眼轮匝在其整个活动期间和同一时期其他四个群体的基础上，粪便样品），并使用第一次这个物种，很长的元条形码方法。Emys orbicularis是欧洲湿地的象征性淡水物种。在一些国家，该物种濒临灭绝，在瑞士，轮虫（Emys orbicularis）在瑞士红色名录中被列为极度濒危。制定了一项国家保护计划以重新引入该物种，并提出了一个问题，即该重新引入的物种是否可能对其他濒危物种构成威胁。我们开发了一种新的长元条形码分析方法，使用通用PCR引物来确定粪便中的猎物种类。对从142个个体收集的174粪便进行的分析揭示了来自270个物种的1153个猎物。在繁殖期（4月至6月），整株虫全年都以不同的饮食来食用植物。因此，这项研究不仅精确地确定了轮虫的杂食性和机会性饮食，但也表明该物种对环境没有威胁，因为85.5％的食用物种未列入瑞士红色名录。此外，它还表明，粪便的遗传学分析可能是确定营养相互作用的高效工具，具有很高的精确度，为食物网生态学提供了广阔的前景。