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DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
- J. Goris, K. Konstantinidis, J. Klappenbach, T. Coenye, P. Vandamme, J. Tiedje
- BiologyInternational Journal of Systematic and…
It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available and reveal extensive gene diversity within the current concept of "species".
Genomic insights that advance the species definition for prokaryotes.
The average nucleotide identity of the shared genes between two strains was found to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition.
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
- Chirag Jain, L. M. Rodriguez-R, A. Phillippy, K. Konstantinidis, S. Aluru
- BiologyNature Communications
- 16 November 2018
FastANI is developed, a method to compute ANI using alignment-free approximate sequence mapping, and it is shown 95% ANI is an accurate threshold for demarcating prokaryotic species by analyzing about 90,000 proKaryotic genomes.
Towards a Genome-Based Taxonomy for Prokaryotes
The AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes, and could contribute significantly to a genome-based taxonomy for all microbial organisms.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Microbial species delineation using whole genome sequences
This work demonstrates that the combination of gANI and the alignment fraction between two genomes accurately reflects their genomic relatedness, and proposes this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, to be used to address previous inconsistencies in species classification.
Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils
- R. Sanford, Darlene D. Wagner, F. Löffler
- Environmental ScienceProceedings of the National Academy of Sciences
- 12 November 2012
It is demonstrated that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers, and that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N2O consumption.
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
The enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, is described and a graphical user interface and several case studies are presented.
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
- S. Hallam, K. Konstantinidis, E. Delong
- BiologyProceedings of the National Academy of Sciences
- 28 November 2006
The C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.
The bacterial species definition in the genomic era
- K. Konstantinidis, A. Ramette, J. Tiedje
- BiologyPhilosophical Transactions of the Royal Society B…
- 29 November 2006
The analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available and the idea of biologically meaningful clusters of diversity may not be universally applicable in the microbial world.