Genomic insights that advance the species definition for prokaryotes.

By Konstantinos T. Konstantinidis, James M. Tiedje. Proceedings of the National Academy of Sciences of the United States of America, 2005

2,018 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0c47a85517ab0de1e49b07f26a4215d3449044c5

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Citations in the corpus

Gene transfer into the fungi (2011, background): “For example, large-scale comparisons have demonstrated that up to 40 % of BLASTp best matches do not represent the nearest neighbour in subsequent phylogenetic analyses (Koski and Golding, 2001).”
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2010, background): “Perhaps because 16S rRNA phylogenies tend to correspond well to trends in overall gene content (8), the ability to relate trends at the species level to host or environmental parameters has proven immensely powerful (9).”
RESCRIPt: Reproducible sequence taxonomy reference database management (2020, methodology): “Furthermore, NCBI-Taxonomy continually runs taxonomic consistency checks on assembled genomes with average nucleotide identity (ANI)[100].”
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences (2013, background): “The accuracy of such approaches has not been characterized, but the correlation between gene content and phylogeny 8, 9, 16 (excepting special cases such as laterally transferred elements and intracellular endosymbionts with reduced genomes) suggests that it may be possible to approximately predict…”
Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification (2015, background): “Some authors postulate that all prokaryotes are species-less or fuzzy (e.g. Hanage et al. 2005; Konstantinidis and Tiedje 2005; Hanage 2013), because they lack ecologically or genetically coherent groups.”
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).”
The evolution of the genome (2005, background): “Strains of the same species can vary by up to 30% in gene content, raising questions as to whether they should even be regarded as the same species (Konstantinidis & Tiedje 2005).”
Microbial species delineation using whole genome sequences (2015, methodology): “The algo-rithm implemented to determine the AF and gANI between two genomes is a modification of the original method proposed by Konstantinidis and Tiedje (4).”
Chemical transformation of xenobiotics by the human gut microbiota (2017, background): “Metabolic functions rarely correlate directly withmicrobial phylogeny, and considerable strain-level variation exists even within the same species (108), which limits the information gained from assessing the composition of the gut microbiota alone.”
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018, methodology): “Nevertheless, it closely reflects the traditional microbiological concept of DNADNA hybridization (DDH) relatedness for genomically circumscribing species (2,3), as it takes into account the fluid nature of the bacterial gene pool and hence, implicitly considers shared function.”
Shifting the genomic gold standard for the prokaryotic species definition (2009, methodology): “The first attempt to evaluate the meaning of ANI was based on pairwise genome comparison of all shared orthologous protein coding genes (11).”
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].”
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database (2019, methodology): “This is generally accomplished by manually inspecting the placement of genomes in 16S rRNA or concatenated protein phylogenies along with 16S rRNA percent identity or average nucleotide identity (ANI; Konstantinidis and Tiedje, 2005) statistics to support assignments to specific taxonomic ranks.”