High proportions of bacteria and archaea across most biomes remain uncultured

Abstract

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.

Fig. 1

Best hit percent identities of environmental sequences to both isolate 16S rRNA gene sequences in the SILVA database (left column) and a filtered version of the RDP database (right column) from a two PCR-based studies analyzed in Martiny 2019, and b a large set of dereplicated OTU sequences free from primer bias and from diverse environments [16]. Median best hit percent identities for each dataset are marked with a red line and the percentage of sequences, which had best hits at >97% identity are marked in green