Shifting the genomic gold standard for the prokaryotic species definition

By Michael Richter, Ramon Rosselló-Mora. Proceedings of the National Academy of Sciences of the United States of America, 2009

5,928 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc61d59947face8a7933ded83291631455167284

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Citations in the corpus

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”
Complete nitrification by a single microorganism (2015, methodology): “FISH probes used in this study (Extended Data Table 2) were 5’ labelled with the dyes FLUOS (5(6)-carboxyfluorescein-N-hydroxysuccinimide ester), Cy3 or Cy5 (Thermo Electron Corporation, Ulm, Germany).”
Uncultivated microbes in need of their own taxonomy (2017, background): “It is also important to note that ANI/AAI values can be accurately estimated even for draft (incomplete) genomes, based on as few as ~100 randomly distributed genes across the genome or ~ 4% of the genome (Konstantinidis et al., 2006; Richter and Rossello-Mora, 2009).”
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy (2019, methodology): “In contrast, to the linear models used to justify original ANI and JSpecies, which do not really ﬁ t the conventional DDH data, dDDH was based on a non-linear model applied to a larger empirical data set 7 .”
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).”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “Goris et al. (2007), and Richter and Rosello´-Mo´ra (2009) proposed 95–96 % average nucleotide identity (ANI) of homologous genomic regions as a gold standard for species delimitation and also as an alternative to DNA–DNA hybridization.”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, background): “This uneven landscape of bacterial diversity, however, includes some clusters that remain distinct from their close relatives and are of recent evolutionary divergence (Richter & Rosselló-Móra, 2009).”
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication (2017, methodology): “Because it relies on Mash, dRep can only be used if the genomes in the comparison set are >50% complete. dRep combines checkM for completeness-based genome filtering (Parks et al., 2015), Mash (Ondov et al., 2016) for fast grouping of similar genomes, gANI (Varghese et al., 2015) or ANIm (Richter an”
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies (2017, background): “For example, average nucleotide identity (ANI) [9] and OrthoANI [10] suggested a species boundary of 95–96%.”
Pseudomonas aeruginosa population structure revisited under environmental focus (2010, methodology): “In the current genome era propositions of new, several genome sequence based algorithms for the species affiliation emerge, which are meant to replace the laboratory work of DNA-DNA hybridization (Auch et al., 2010; Richter & Rossello-Mora, 2009).”
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights (2014, methodology): “by use of jSpecies software with the BLAST algorithm (17).”
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI (2018, positive): “[9]), average nucleotide identity (ANI) is widely used and has been proposed as the best option to determine species boundaries and confirm identification [10, 11].”
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. (2018, methodology): “Several software tools for calculating the original ANI and its improved versions were developed for taxonomic purposes [5, 8, 9, 30].”