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Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.

It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates.
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EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.

A database containing 16S rRNA gene sequences of all prokaryotic type strains was generated and a web-based tool, named EzTaxon, was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods.
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Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.

The overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla was investigated, finding an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI.
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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

An integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences, with accompanying bioinformatics tools.
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OrthoANI: An improved algorithm and software for calculating average nucleotide identity.

A new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities, providing a more robust and faster means of calculating average nucleotide identity for taxonomic purposes.
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A large-scale evaluation of algorithms to calculate average nucleotide identity

ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy, and when genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and Orthoaniu were shorter than that of ANIb by 53- and 22-fold, respectively.
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Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes.

The minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes are described.
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Evidence for several waves of global transmission in the seventh cholera pandemic

It is shown here that the seventh pandemic has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s, and several transcontinental transmission events are identified.
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Computer assisted classification and identification of actinomycetes

Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern.

Strain HA-9T contained meso-diaminopimelic acid, no diagnostic sugars, hexa- or octa-hydrogenated menaquinones with 10 isoprene units, straight-chain saturated or monounsaturated, and type III phospholipids, which consistently assign the isolate to the genus Nocardiopsis.
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