How much do rRNA gene surveys underestimate extant bacterial diversity?

How much do rRNA gene surveys underestimate extant bacterial diversity? Appl Environ Microbiol. 2018 Jan 05;: Authors: Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT Abstract The most common practice in studying and cataloguing prokaryotic diversity involves the grouping of sequences into Operational Taxonomic Units (or OTUs) at the 97% 16S rRNA gene sequence identity level, often using partial gene sequences such as PCR-generated amplicons. Due to the high sequence conservation of rRNA genes, organisms belonging to closely related yet distinct species may be grouped under the same OTU. However, it remains unclear how much diversity has been underestimated by this practice. To address this question, we compared OTUs of genomes defined at the 97% or 98.5% 16S rRNA gene identity level against OTUs of the same genomes defined at the 95% whole-genome average nucleotide identity (ANI), which is a much more accurate proxy for species. Our results show that OTUs resulting from 98.5% 16S rRNA gene identity are more accurate than 97% when compared to 95% ANI (90.5% vs. 89.9% accuracy) but indistinguishable from any other threshold in the 98.29-98.78% range. Even with the more stringent thresholds, however, the 16S rRNA gene-based approach commonly underestimates the number of OTUs by ∼12%, on average, compared to the ANI-based approach (∼14% underestimation when using the 97% identity threshold). More import...
Source: Applied and Environmental Microbiology - Category: Microbiology Authors: Tags: Appl Environ Microbiol Source Type: research