Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation

(2013) Christopher J Grim et al.   BMC GENOMICS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms

(2012) Yemin Lan et al.   PLoS One

Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence

(2011) Hana Yi et al.   FEMS MICROBIOLOGY LETTERS

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

(2011) O.-S. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries

(2011) Jae-Hak Lee et al.   JOURNAL OF MICROBIOLOGY

Classifier chains for multi-label classification

(2011) Jesse Read et al.   MACHINE LEARNING

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

(2010) A. Y. Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae

(2010) Bradd J Haley et al.   BMC MICROBIOLOGY

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium

(2008) Heng-Lin Cui et al.   EXTREMOPHILES

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

(2008) M. Deloger et al.   JOURNAL OF BACTERIOLOGY