The bacterial species definition in the genomic era

By Konstantinos T. Konstantinidis, A. Ramette, James M. Tiedje. Philosophical Transactions of the Royal Society B: Biological Sciences, 2006

615 citations recorded by the source corpus.

Subfields: Insect Science, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4e54ba473af7856ef428681022f0d8f6ce28e107

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Citations in the corpus

Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment (2011, background): “However, being a highly conserved molecule, the 16S rRNA gene does not provide sufficient resolution at species and strain level (Konstantinidis et al. 2006).”
Notes on the characterization of prokaryote strains for taxonomic purposes. (2010, background): “Noteworthy are the Average Nucleotide Identity (ANI; Konstantinidis et al., 2006) 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 m”
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis (2011, background): “For example, the operational definition of a species, 3% dissimilarity, is often cited but controversial (6, 8, 11, 22).”
FROGS: Find, Rapidly, OTUs with Galaxy Solution (2018, background): “…rule is applied to all OTUs during clustering and the 3% level of divergence is usually considered sufficient to infer different species, even if the matter is the subject of debate (Goodrich et al., 2014; Goris et al., 2007; Hugenholtz et al., 1998; Kim et al., 2014; Konstantinidis et al., 2006).”
The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool (2010, background): “Whereas strains within typical bacterial species can diverge by up to 5% at orthologous genes [48], no pair of A.”
Shifting the genomic gold standard for the prokaryotic species definition (2009, background): “Prokaryotes are not exempt from this problem, and even the existence of discrete biological units is being questioned (2).”
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, background): “These include average nucleotide identity (ANI) (Konstantinidis et al., 2006), genome BLAST distance phylogeny (GBDP) (Henz et al.”
Multivariate analyses in microbial ecology (2007, background): “Those factors are generally hypothesized to be of a discontinuous nature, but the rationale of generally representing molecular differences as discontinuous clusters in microbial ecology and microbial genomic studies has only started to be questioned (Konstantinidis et al., 2006).”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “represent a genetic continuum (Konstantinidis et al. 2006).”
Structure of the Archaeal Community of the Rumen (2008, background): “Detailed genome analysis may help reveal which interpretation is correct, although in the end the analysis will depend largely on the definition of a prokaryotic species, especially if the genomes also form a gradation of genotypes (20).”
Microbial strain-level population structure and genetic diversity from metagenomes (2017, neutral): “We note that despite a large body of work on strain-level phenotypic characterization and genetic comparisons from microbial isolates, a clear definition of the concept of “ strain ” is still lacking (Dijkshoorn et al. 2000; Konstantinidis et al. 2006).”