Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.

中文翻译：

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整个生物群落 DNA 的 COI 元条形码的成熟：迈向生物信息学协调

从整个生物群落样本中提取的 DNA 的元条形码（wholeorgan community DNA, wocDNA）正越来越多地应用于陆地、海洋和淡水后生动物群落，为新的分子生态学研究提供快速、准确和高分辨率的数据。该领域的发展伴随着相当大的发展，其建立在微生物元条形码方法的基础上，为整个生物后生动物群落开发适当和有效的采样和实验室协议。然而，很少有人关注确保生物信息学方法在 wocDNA 元条形码中得到全面调整和应用。在这项研究中，我们检查了 600 多篇论文，并确定了 111 项对 wocDNA 进行 COI 元条形码的研究。然后，我们系统地回顾了这些论文采用的生物信息学方法，以确定最先进的技术。我们的研究结果表明，越来越多地使用 wocDNA COI 元条形码对后生动物多样性的使用的特点是明显缺乏生物信息学的协调，并且时间趋势在这种情况下几乎没有变化。回顾的文献显示（i）跨管道、任务和使用的工具的高度异质性，（ii）生物信息学程序对 COI 片段的性质的适应有限或没有适应，以及（iii）任务、软件和参数的报告不足令人担忧。基于这些发现，我们提出了一组我们认为元条形码社区应该考虑的建议，以确保生物信息学方法是适当的、全面的和可比的。