Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

  title={Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences},
  author={Pablo Yarza and Pelin Yilmaz and Elmar Pruesse and Frank Oliver Gl{\"o}ckner and Wolfgang Ludwig and Karl Heinz Schleifer and William B. Whitman and Jean P. Euz{\'e}by and Rudolf I. Amann and Ramon Rossell{\'o}-M{\'o}ra},
  journal={Nature Reviews Microbiology},
Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the… 
A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index
Genetic coherence is an emergent property of genera in Bacteria and Archaea that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species in this study.
A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation
Results show that a distinct difference between distant relatives and close relatives at the genome level (i.e., genomic coherence) is an emergent property of genera in Bacteria and Archaea.
Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
An improved framework is assessed by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks, where the two SILVA frameworks performed best at assigning sequences to genus-level taxa.
The 16S rRNA gene in the study of marine microbial communities El gen ARNr 16S en el estudio de comunidades microbianas marinas
Complete 16S rRNA sequences are needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities, forcing a review of concepts and methods for the taxonomic classification of these organisms.
Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
Draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics, and the majority of taxa were found to be monophyletic.
Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques
A review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era is presented.


Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria
It is shown that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis, regularly contain numerous self-splicing introns of variable length, which do not inhibit the formation of functional ribosomes.
New Perspective on Uncultured Bacterial Phylogenetic Division OP11
The phylogeny of the bacterial candidate division OP11 is resolved and two new candidate bacterial divisions are identified, OP11-derived 1 (OD1) and Sulphur River 1 (SR1).
Bacterial phylogeny based on 16S and 23S rRNA sequence analysis.
Phylogenetic trees based on almost equivalent data sets of bacterial 23S and 16S rRNAs are in good agreement and their overall topologies are supported by alternative phylogenetic markers such as elongation factors and ATPase subunits.
Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.
A classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypec characteristics on which the delineation of taxa has been based in the past is presented.
Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.
It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process, however, serious effort will be needed to harmonize them and to prevent inaccurate material.
Molecular phylogeny of microorganisms
This book is an ideal introduction to molecular phylogeny for all microbiologists and is an essential review of current concepts for experts in the field.
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.
  • T. Cavalier-smith
  • Biology
    International journal of systematic and evolutionary microbiology
  • 2002
The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began.