The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.

宏基因组技术的进步为分析环境基质（如水和废水）中的人类寄生虫提供了新的工具。然而，宏基因组技术在环境基质中对原生动物寄生虫进行分析的应用在文献中并不常见。导致宏基因组学应用较少的关键因素是复杂性和大型真核基因组、与细菌相比环境样本中小寄生虫种群的普遍性、从 (oo) 囊肿中提取 DNA 的困难以及寄生虫参考数据库有限。这需要进一步研究以开发专门针对环境中原生动物寄生虫的优化方法。本研究回顾了当前的工作流程、方法并为技术标准化提供了建议。DNA 提取、测序方法和分析方法。该研究增强了对从高度复杂的样本中分析原生动物寄生虫群落的标准化协议的理解和应用，并进一步在没有任何偏见的情况下在数据集之间进行了足智多谋的比较。