Notes on the characterization of prokaryote strains for taxonomic purposes.

By Brian J. Tindall, Ramon Rosselló-Mora, H. Busse, Wolfgang Ludwig, Peter Kämpfer. International Journal of Systematic and Evolutionary Microbiology, 2010

1,367 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/bf1427a857cf1e81f2225e090986f8e064798cbc

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Citations in the corpus

Taxonomy of Pseudomonas syringae. (2010, background): “One possibility will see an insistence on the continuation of descriptions based on polyphasic classification (Vandamme et al., 1996; Gillis et al., 2005) with comprehensive phenotypic descriptions (Tindall et al., 2010).”
Benchmarking of Methods for Genomic Taxonomy (2014, background): “Previous studies, however, have also pointed to the many limitations of the 16S rRNA gene for taxonomic purposes (5–9).”
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, methodology): “…as an alternative to the tedious DDH, and it is now generally accepted that DDH is only required when 16S rRNA gene sequence similarity between two strains is over 97 % (Tindall et al., 2010), even though higher thresholds of 98.7–99.0 % have also been used (Stackebrandt & Ebers, 2006).”
The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota (2015, methodology): “(252) proposed that ANI could be used to replace DNA-DNA hybridization in characterizing prokaryotic species, and thus far, this method has been used to describe several new taxa (271–273).”
Pseudomonas aeruginosa population structure revisited under environmental focus (2010, background): “Thus, the polyphasic approach is successfully solving the problem of the bacterial species affiliation, dealing with the enormous amount of diversity (Tindall et al., 2009).”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “…applicable dataset around which descriptions of bacterial diversity can be assembled, complementing methods such as whole-genome hybridization (Tindall et al., 2010), which is not a practical approach for certain data, such as those obtained in metagenomic studies (Stackebrandt et al., 2002).”
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison (2010, methodology): “All established variations of DDH determination are technically demanding, labor-intensive and time-consuming procedures, therefore DDH determination is now performed by only a few specialized laboratories, and microbial taxonomists apply DDH only in cases where the strains to be differentiated have”
Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. (2014, methodology): “Of course, in the polyphasic approach other criteria (such as phenotypic comparison) are applied in addition to DDH (RossellóMora & Amann, 2001; Tindall et al., 2010).”
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes (2021, positive): “Comparisons with the genome sequences of type strains are mandatory when classifying novel strains (4).”
Morphological Identification of Actinobacteria (2016, background): “The key elements that should be acquired and analyzed in characterization studies of prokaryotes were outlined [18]: the phenotypic features are the foundation for description of taxa.”
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. (2012, methodology): “Among the several thousand genes within a bacterial genome, the 16S rRNA gene has served as the primary key for phylogeny-based identification when compared against well-curated 16S rRNA gene sequence databases (RossellóMora & Amann, 2001; Tindall et al., 2010).”