DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.

By J. Goris, Konstantinos T. Konstantinidis, J. Klappenbach, T. Coenye, Peter Vandamme, James M. Tiedje. International Journal of Systematic and Evolutionary Microbiology, 2007

4,440 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/96675e2ac895afe4117d26cdd8d41d78e60934e5

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Citations in the corpus

Pseudomonas genomes: diverse and adaptable. (2011, background): “Moreover, it was shown that Pto DC3000 and Psy B728a had low DDH, ANI and AAI values below the species thresholds and therefore may not be part of the same species (Fig.”
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights (2014, background): “with the level of DDH, and a 95 to 96% ANI value can serve as a genomic measure for prokaryotic species delineation (16, 17).”
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, methodology): “Of these, ANI has been most widely used as a possible next-generation gold standard for species delineation (Chan et al., 2012; Goris et al., 2007; Grim et al., 2013; Haley et al., 2010; Konstantinidis & Tiedje, 2005; Richter & Rosselló-Móra, 2009; Yi et al., 2012).”
The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota (2015, background): “In 2005, it was suggested that the average nucleotide identity (ANI) between two bacterial species could constitute an effective alternative to DNADNA hybridization (268, 269).”
EDGAR 2.0: an enhanced software platform for comparative gene content analyses (2016, positive): “ANI values are computed as described in (18) and as implemented in the popular JSpecies package (19).”
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014, methodology): “For novel species, a cut-off of 95% AAI (instead of 85% AAI from Figure 2) was used because this was found to better represent recently described species, which are, in general, more homogenous than older species designations included in our analysis (33).”
Scaling laws predict global microbial diversity (2016, background): “97% for species-level) and taxa assignment including a maximum evalue (probability of observing an equal or better match in a database of a given size) of 10, a 274 minimum alignment length of 50 base pairs, and minimum percent sequence similarities of 95, 97, and 99% to the closest reference sequen”
Notes on the characterization of prokaryote strains for taxonomic purposes. (2010, background): “…and Maximal Unique Matches (MUM; Deloger et al., 2009) indexes as they have been hypothesized to be able to substitute for DDH. ANI has been demonstrated to correlate with DDH, where the range of ~ 95–96 % similarity may reflect the current boundary of 70 % DDH similarity (Goris et al., 2007).”
Morphological Identification of Actinobacteria (2016, background): “microbial morphological traits, growth requirements, physiological and biochemical features [2]; (ii) numerical taxonomy analyzing huge volumes of phenotypic data to derive meaningful relationships amongst a large number of microorganisms can be carried out using computer programs [3, 4]; (iii) chem”
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries (2017, methodology): “Nevertheless, it closely reﬂects the traditional microbiological concept of DNA-DNA hybridization relatedness for deﬁning species (3), as it takes into account the ﬂuid nature of the bacterial gene pool and hence implicitly considers shared function.”
The bacterial species definition in the genomic era (2006, background): “In contrast, environments like soil, with great complexity, mixing and slow growth rates (Grey & Williams 1971), which would facilitate mixing of populations before the divergence of populations takes place, may support a continuum of diversity (the importance of selection is discussed below).”
Microbiome definition re-visited: old concepts and new challenges (2020, background): “For prokaryotes, however, such a definition based on reproduction does not exist: current species definitions are based on DNA homologies between organisms such as the “more than 70% DNA-similarity” revealed by DNA-DNA hybridization [58], or by the average nucleotide identity as recommended by Goris”