PDF(Pubmed)
Abstract：
BACKGROUND: Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol.
METHODS: We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process.
RESULTS: We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups.
CONCLUSIONS: Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
METHODS: We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process.
RESULTS: We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups.
CONCLUSIONS: Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
摘要：
背景：胃肠道蠕虫是一类非常普遍的肠道寄生虫，可在其宿主中引起重大健康问题，包括严重的疾病或死亡。使用显微镜鉴定蠕虫寄生虫的传统方法耗时且分类分辨率差，需要熟练的观察者。在过去的几十年中，DNA元编码已成为评估各种样本类型中社区组成的强大替代方法。虽然已经对在其他研究领域中使用的元编码方法进行了审查，最近才开始广泛使用代谢编码来治疗寄生虫.因此，有必要合成寄生虫元编码方法，并强调在制定协议时要考虑的因素。
方法：我们回顾了已发表的利用DNA代谢编码鉴定脊椎动物宿主中胃肠蠕虫寄生虫的文献。我们从2014年至2023年发表的62篇同行评审论文中提取了信息，并创建了元编码过程的逐步指南。
结果：我们发现，在我们的综述中，研究在技术和方法上有所不同，例如使用的样品类型，靶向遗传标记区域和使用的生物信息学数据库。元编码的主要限制是寄生虫丰度数据可能无法从序列读数可靠地获得，metabarcoding数据可能不能代表宿主中存在的物种，并且使用这种方法所需的成本和生物信息学专业知识可能会使某些群体望而却步。
结论：总体而言，与传统方法相比，使用代谢编码来评估胃肠道寄生虫群落是更可取的，产生更高的分类分辨率，由于其在任何地理位置的实用性，更高的吞吐量和增加的多功能性，有各种各样的样本类型，以及几乎任何脊椎动物宿主物种。此外,对于宿主和寄生虫的进化有令人兴奋的新发现。
方法：我们回顾了已发表的利用DNA代谢编码鉴定脊椎动物宿主中胃肠蠕虫寄生虫的文献。我们从2014年至2023年发表的62篇同行评审论文中提取了信息，并创建了元编码过程的逐步指南。
结果：我们发现，在我们的综述中，研究在技术和方法上有所不同，例如使用的样品类型，靶向遗传标记区域和使用的生物信息学数据库。元编码的主要限制是寄生虫丰度数据可能无法从序列读数可靠地获得，metabarcoding数据可能不能代表宿主中存在的物种，并且使用这种方法所需的成本和生物信息学专业知识可能会使某些群体望而却步。
结论：总体而言，与传统方法相比，使用代谢编码来评估胃肠道寄生虫群落是更可取的，产生更高的分类分辨率，由于其在任何地理位置的实用性，更高的吞吐量和增加的多功能性，有各种各样的样本类型，以及几乎任何脊椎动物宿主物种。此外,对于宿主和寄生虫的进化有令人兴奋的新发现。
