Re-evaluating prokaryotic species

By Dirk Gevers, Frederick M. Cohan, Jeffrey G. Lawrence, B. Spratt, T. Coenye, E. Feil, E. Stackebrandt, Y. Van de Peer, Peter Vandamme, F. Thompson and 1 more. Nature Reviews Microbiology, 2005

1,010 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5c9940fe4eb525b2b030d227bfbb8af2dd80749a

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Citations in the corpus

A diversity profile of the human skin microbiota. (2008, background): “A species-level OTU has historically been defined as containing 16S rDNA sequences that are 97% identical (Gevers et al. 2005).”
Micromonospora: An important microbe for biomedicine and potentially for biocontrol and biofuels (2010, background): “MLST utilizes allelic mismatch of a small number of housekeeping genes for recognizing distinct strains within named species, whereas MLSA uses sequences from multiple protein genes to characterize a more diverse group of microbes.”
Spatial scaling of microbial biodiversity. (2006, background): “often without reference to evolution and ecology [ 60 ].”
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, background): “However, due to the labour-intensive and error-prone nature of DDH experiments, there has been a continuous demand for an alternative genotype-based standard (Gevers et al., 2005; Stackebrandt et al., 2002).”
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. (2007, background): “Its main disadvantage, however, is that because of the comparative nature of the technique no incremental databases can be built, in contrast to sequence information, for example (Gevers et al., 2005; Stackebrandt, 2003).”
The versatile ε-proteobacteria: key players in sulphidic habitats (2006, background): “Phylogenetic and ecophysiological diversity Ideally, taxonomic classification should be performed through a polyphasic approach using more than one molecular marker and phenotypic information derived from cultured representative”
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2014, background): “…taxonomic assignments in reference databases limits diversity descriptions because microbiologists have not defined a unified species concept (Gevers et al. , 2005; Doolittle and Zhaxybayeva, 2009) and molecular databases generally lack discrete name assignments for the astonishing number of…”
The bacterial species definition in the genomic era (2006, background): “The latter is also evident from the fact that only about 4500 bacterial species have been described to date (after removing the 1200 synonyms; Garrity et al. 2004 ), which contrasts to well over 1 million eukaryotic species, and yet bacteria have been exploring evolutionary adaptations much longer ”
Three reasons to re-evaluate fungal diversity 'on Earth and in the ocean' (2011, background): “…are often not the unit of research focus and therefore under-developed as a concept, and also tend to be more genetically inclusive than in many eukaryote groups (e.g. Doolittle, 2008; Gevers et al., 2005; Koeppel et al., 2008; Konstantinidis and Tiedje, 2005; Staley, 2006; Vandamme et al., 1996).”
Microbiology and the species problem (2010, background): “As a number of microbial systematists point out, microbiologists disagree on whether prokaryotes fall into ‘‘recognizable discrete centers of variation’’ and what those centers might even be (Doolittle and Papke 2006: 116.5; also Gevers et al. 2005; Stackebrandt 2006).”
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies (2006, neutral): “Most researchers currently adopt an OTU definition based on 16S rRNA gene sequence identity, usually considering organisms displaying 97 to 98% identity in this gene to be part of the same OTU ( 16 ).”
Taxonomy of Pseudomonas syringae. (2010, result): “Such an approach would be contrary to all previous taxonomic intention (Wayne et al., 1987; Murray et al., 1990; Stackebrandt et al., 2002; Gevers et al., 2005; Tindall et al., 2010) and, whatever its merit, it is unlikely to be adopted in the foreseeable future.”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “…typing (MLST) (Maiden et al., 1998), which indexes sequence variation at housekeeping loci, have provided a means of reliably identifying the relationships among related organisms, and have been suggested as a basis for a novel approach to microbial species identification (Gevers et al., 2005).”