Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA.
Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
ISME J. 2019 Dec;13(12):3126-3130. doi: 10.1038/s41396-019-0484-y. Epub 2019 Aug 6.
A recent paper by Martiny argues that "high proportions" of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer "culturability" because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.
马蒂尼最近的一篇论文认为，在地球上各种不同的环境中，“很大比例”的细菌已经被培养出来。在这里，我们重新分析了该论文中的一部分数据，并认为这一结论是基于几个技术错误，最显著的是序列相似性的计算没有考虑序列间隙，以及依赖于已知偏向培养生物的 16S rRNA 基因扩增子。我们进一步认为，这篇论文还基于一个概念错误：即，序列相似性不能用来推断“可培养性”，因为不能从 16S rRNA 基因序列推断生理机能。结合其他最近的、更可靠的研究，这些证据支持了大多数细菌和古菌门仍然未被培养的结论。
