Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that were analyzed and interpreted and clearly stating the strategy used for metagenomic profiling.

准确的微生物鉴定和丰度估计对于宏基因组学分析至关重要。已经开发了各种用于宏基因组数据分类和分类学概况估计的方法，广泛称为宏基因组分析器。尽管如此，宏基因组分析器的基准测试仍然具有挑战性，因为一些工具旨在报告相对序列丰度，而其他工具则报告相对分类学丰度。在这里，我们展示了在对宏基因组分析器进行基准测试时，如何通过忽略相对丰度类型之间的区别来得出误导性结论。此外，我们展示了令人信服的证据，表明互换序列丰度和分类学丰度将影响每个样本的汇总统计数据和跨样本比较。