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

Key Points

  • As the number of environmental small subunit (SSU) ribosomal RNA gene sequences has greatly surpassed the number of cultured microorganisms, reconciliation of the established taxonomy and classification of the uncultured microorganisms are crucial.

  • Rational taxonomic boundaries have been proposed for the high taxa (that is, genus and above) of the Bacteria and the Archaea on the basis of 16S rRNA gene sequence identities. These are : 94.5% for genus, 86.5% for family, 82.0% for order, 78.5% for class and 75.0% for phylum.

  • The application of these thresholds to the clustering of the SILVA database confirms that the current number of formally described taxa at any rank (for example, 30 phyla) is negligible compared with the total number of detected taxa (for example, 1,300 phyla).

  • In addition, the study of the annual rate of taxa discovery enables a new extrapolation of the total number of species (4 × 105) and high taxa on Earth (for example, 1 × 105 genera), which indicates that most common terrestrial and aquatic habitats will be exhaustively described within the next 5 years.

  • Taxon recovery tests that were carried out using partial 16S rRNA gene sequences show that short reads are not suitable for accurate richness estimations and accurate classifications of high taxa.

  • On the basis of the general taxonomic thresholds and phylogenetic considerations, we suggest a new biodiversity unit known as the candidate taxonomic unit (CTU), which is compatible with the hierarchy that was established in the Bacteriological Code. The ability to specify a taxonomic rank for particular clades is a major advance in understanding tree topologies and goes beyond the classic phylogenetic delineation.

  • The usefulness of CTUs has been intensively tested in the reclassification of the phylum Spirochaetes and the classification of 15 candidate divisions and environmental clades that are presented in this Analysis article, which also provide new insights into the coherence of classes, phyla and superphyla.

  • By providing explicit and well-documented guidelines, it is hoped that this work will facilitate the implementation of the many changes in the current taxonomy that are necessary to develop a common taxonomic classification of high taxa of bacteria and archaea on the basis of SSU rRNA gene sequences.

Abstract

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 circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.

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Figure 1: Variable regions of the 16S ribosomal RNA.
Figure 2: Predicting taxa richness using partial 16S ribosomal RNA sequences.
Figure 3: Classification of phylum Spirochaetes into candidate taxonomic units.
Figure 4: Phylogenetic reconstruction of the SAR11 group within the Proteobacteria based on 16S ribosomal RNA gene sequences.

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Acknowledgements

This work has been co-funded by the Max Planck Society and the European Union (EU) project SYMBIOMICS (grant number 264774). R.R.M. acknowledges the scientific support given by the Spanish Ministry of Economy with the projects CE-CSD2007-0005 and CGL2012-39627-C03-03, which are both also supported with European Regional Development Fund (FEDER) funds, and the preparatory phase of Microbial Resource Research Infrastructure (MIRRI) funded by the EU (grant number 312251). W.B.W. acknowledges support of the Dimensions in Biodiversity program at the US National Science Foundation (NSF). P.Y. acknowledges support of the EU's Seventh Framework Program funds BioVeL, grant no. 283359.

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Correspondence to Pablo Yarza or Ramon Rosselló-Móra.

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Supplementary information

Supplementary information S1 (table)

Intra-taxon sequence identity measures used to calculate the taxonomic thresholds. (XLS 114 kb)

Supplementary information S2 (Box)

Additional tables and figures. (PDF 776 kb)

Supplementary information S3 (figure)

Phylogenetic reconstruction of 15 candidate divisions and environmental clades (PDF 11624 kb)

Supplementary information S4 (table)

Sequence associated meta-data including CTU classification. Fields: acc,start,stop,tax_CTU,tax_xref_embl (XLS 1080 kb)

Glossary

Diversity

A term used to describe the effective number of taxa (that is, the richness) of a particular rank and their respective abundances (that is, the evenness).

SSU

(Small subunit). The small subunit of the ribosome, which is 16S ribosomal RNA for the Bacteria and the Archaea and 18S rRNA for the Eukarya.

Bacterial and archaeal species

A monophyletic group of organisms with a high degree of coherence in their genetic and phenotypic traits, which differentiate it from its close relatives.

High taxonomic ranks

The taxonomic categories of genus and above.

OTUs

(Operational taxonomic units). Groups of sequences that are meaningfully separated from other sequences by hierarchical clustering techniques (independent of phylogenetic inferences) and using strict sequence identity thresholds.

CTU

(Candidate taxonomic unit). A biological entity that is delineated by a monophyletic set of sequences with a sequence identity that stays within, or very close to, the taxonomic threshold that is proposed for a given rank.

OPU

(Operational phylogenetic unit). A group of sequences that appear as a monophyletic clade that is meaningfully separated from the remaining sequences in a genealogical reconstruction.

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Yarza, P., Yilmaz, P., Pruesse, E. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12, 635–645 (2014). https://doi.org/10.1038/nrmicro3330

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