Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.

By Mincheol Kim, Hyun-Seok Oh, Sang-Cheol Park, Jongsik Chun. International Journal of Systematic and Evolutionary Microbiology, 2014

3,009 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6bbda1e254f15a47108e09f34be9f39d1dfbe143

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Citations in the corpus

Insights from 20 years of bacterial genome sequencing (2015, methodology): “For ANI, 95 – 96 % sequence identity is generally used for the species delineation (Kim et al. 2014).”
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation (2017, neutral): “Seven bins assigned to the order Bacteroidales share high ANI with each other (81-91% ANI), but at values suggesting inter-rather than intraspecies relationships 32 (Supplementary Table 6; Supplementary Methods).”
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018, neutral): “Accordingly, ANI has been recognized internationally for its potential to replace DDH as the standard measure of relatedness, as it is easier to estimate and represents portable and reproducible data (4,5).”
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies (2017, background): “However, even though a bioinformatic comparison of 16S rRNA genes provides an objective and reliable way of identifying a given strain, it has a critical limitation in its use at the species level; even almost identical 16S rRNA gene sequences may not guarantee that two strains belong to the same sp”
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. (2018, methodology): “In this two-step approach, the list of species that is required to compare to the strain in question using genome sequences is obtained using a 16S-based search [11]; only species showing 98.7% or higher 16S similarity are selected for calculating OGRIs [7, 13, 14].”
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. (2020, background): “Although proposals have been made to apply a methodfree species concept that is based on cohesive evolutionary forces [6], an ANI value of 95 % (94–96 %) has been almost consistently used in recent years to describe new bacterial species [7, 8] and was suggested to reflect the biological significanc”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “Most recently, Kim et al. (2014) combined previously mentioned approaches and proposed 98.65 % similarity in 16S rRNA as a threshold for species delimitation.”
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI (2018, positive): “[11, 17]), and our observations of current taxa for which we can develop both concordant and discordant ANI values, we chose 96% as our ANI cutoff.”