Towards a Genome-Based Taxonomy for Prokaryotes

By Konstantinos T. Konstantinidis, James M. Tiedje. Journal of Bacteriology, 2005

927 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c564255fd468c9474340a2e8540d1680bac79d35

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. Konstantinos T. Konstantinidis
2. James M. Tiedje
3. Ramon Rosselló-Mora
4. Philip Hugenholtz
5. Rob Knight
6. R. Amann
7. Donovan H. Parks
8. James R. Cole

In Genetics

1. Konstantinos T. Konstantinidis
2. Ramon Rosselló-Mora
3. R. Amann
4. Philip Hugenholtz
5. Donovan H. Parks
6. Gene W. Tyson
7. A. Oren
8. James M. Tiedje

In Molecular Biology

1. Konstantinos T. Konstantinidis
2. Philip Hugenholtz
3. Ramon Rosselló-Mora
4. James M. Tiedje
5. Donovan H. Parks
6. Rob Knight
7. R. Amann
8. James R. Cole

Citations in the corpus

• CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (2015, methodology): “These two types of contamination are differentiated automatically by CheckM by using the amino acid identity (AAI) be-tween multicopy genes as a measure of phylogenetic relatedness (Konstantinidis and Tiedje 2005).”
• The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018, background): “, there are less than ten common universal gene matches in the two genomes) or is close to saturation (hAAI ≥ 90%), MiGA estimates the complete AAI (6) using aai.”
• FunGene: the functional gene pipeline and repository (2013, background): “In contrast, the corresponding overall ortholog Average Amino Acid Identity (AAI; see list of abbreviations, Table 1 ) cutoff for a species is about 5% difference (Konstantinidis and Tiedje, 2005).”
• Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review (2011, background): “Therefore, prokaryotic taxonomy is nowadays based on genomic data, which allow classification of nonculturable bacteria as well (Rosselló-Mora and Amann 2001; Konstantinidis and Tiedje 2005).”
• Pseudomonas genomes: diverse and adaptable. (2011, background): “The AAI for P. fluorescens was approximately 83% (Silby et al., 2009), which is well below the species cutoff (Konstantinidis & Tiedje, 2005).”
• Uncultivated microbes in need of their own taxonomy (2017, methodology): “Further, there is a tight correlation between AAI and percentage of the genes in genome shared; thus the two variables are not independent from each other and AAI values are good predictors of functional gene content similarity (Konstantinidis and Tiedje, 2005).”
• Resistance, resilience, and redundancy in microbial communities (2008, background): “Although it is clear that phylogenetic relationships of taxa are not perfect predictors of microbial physiology (59, 60), there are phylogenetic signals of physiological traits (e.”