An ANI gap within bacterial species that advances the definitions of intra-species units
Luis M. Rodriguez-R,
Roth E. Conrad,
Tomeu Viver,
Dorian J. Feistel,
Blake G. Lindner,
Stephanus N. Venter,
Luis H. Orellana,
Rudolf Amann,
Ramon Rossello-Mora,
Konstantinos T. Konstantinidis
Affiliations
Luis M. Rodriguez-R
Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
Roth E. Conrad
School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Tomeu Viver
Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
Dorian J. Feistel
School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Blake G. Lindner
School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Stephanus N. Venter
Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
Luis H. Orellana
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
Rudolf Amann
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
Ramon Rossello-Mora
Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
Konstantinos T. Konstantinidis
School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
ABSTRACTLarge-scale surveys of prokaryotic communities (metagenomes), as well as isolate genomes, have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI 99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity.IMPORTANCEBacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
