A fundamental question in studying microbial diversity is whether there is a species boundary and if the boundary can be delineated by a universal genetic discontinuity. To address this question, Jain et al. computed the pairwise average nucleotide identity (ANI) of 91,761 microbial (bacterial and archaeal) genomes (the 90K genome dataset) and found that the ANI values from the 8 billion comparisons follow a strong bimodal distribution. The authors concluded that a clear genetic discontinuum and species boundary were evident from the unprecedented large-scale ANI analysis. As a result, the researchers advocated that an ANI of 95% can be used to accurately demarcate all currently named microbial species. While the FastANI program described in the paper is useful, we argue that the paper's conclusion of a universal genetic boundary is questionable and resulted from the substantial biased sampling in genome sequencing. We also caution against being overly confident in using 95% ANI for microbial species delineation as the high benchmarks reported in the paper were inflated by using highly redundant genomes.

中文翻译：

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没有证据表明微生物物种之间存在普遍的遗传边界

研究微生物多样性的一个基本问题是是否存在物种边界，以及是否可以通过普遍的遗传不连续性划定边界。为了解决这个问题，Jain等人。通过计算91,761个微生物（细菌和古细菌）基因组（90K基因组数据集）的成对平均核苷酸同一性（ANI），发现来自80亿次比较的ANI值遵循强双峰分布。作者得出的结论是，从空前的大规模ANI分析中，明显的遗传间断和物种边界是显而易见的。结果，研究人员主张可以使用95％的ANI来准确划分所有当前命名的微生物物种。尽管本文中介绍的FastANI程序很有用，但我们认为该论文的“ 通用遗传边界的结论是有问题的，这是由于基因组测序中的大量有偏见的采样导致的。我们还告诫不要对使用95％ANI进行微生物物种鉴定过分自信，因为使用高度冗余的基因组夸大了本文报道的高基准。