Notes on the characterization of prokaryote strains for taxonomic purposes.

doi:10.1099/IJS.0.016949-0

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Notes on the characterization of prokaryote strains for taxonomic purposes.

Journal Article•DOI•

Notes on the characterization of prokaryote strains for taxonomic purposes.

Brian J. Tindall¹, Ramon Rosselló-Móra², Hans-Jürgen Busse³, Wolfgang Ludwig⁴, Peter Kämpfer⁵ - Show less +1 more•Institutions (5)

Deutsche Sammlung von Mikroorganismen und Zellkulturen¹, Spanish National Research Council², University of Veterinary Medicine Vienna³, Technische Universität München⁴, University of Giessen⁵

01 Jan 2010-International Journal of Systematic and Evolutionary Microbiology (Microbiology Society)-Vol. 60, Iss: 1, pp 249-266

TL;DR: The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.

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Abstract: Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.

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Journal Article•DOI•

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

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Ok-Sun Kim¹, Yong-Joon Cho¹, Kihyun Lee¹, Seok Hwan Yoon¹, Mincheol Kim¹, Hyunsoo Na¹, Sang-Cheol Park¹, Yoon-Seong Jeon¹, Jae-Hak Lee¹, Hana Yi¹, Sungho Won², Jongsik Chun¹ - Show less +8 more•Institutions (2)

Seoul National University¹, Chung-Ang University²

01 Mar 2012-International Journal of Systematic and Evolutionary Microbiology

TL;DR: 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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Abstract: Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. 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. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

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4,974 citations

Cites methods from "Notes on the characterization of pr..."

...Among the several thousand genes within a bacterial genome, the 16S rRNA gene has served as the primary key for phylogeny-based identification when compared against well-curated 16S rRNA gene sequence databases (RossellóMora & Amann, 2001; Tindall et al., 2010)....
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...The 16S rRNA gene sequences of these reference phylotypes were manually selected from a pool of 16S rRNA gene sequences available in GenBank and 97 % gene sequence similarity was considered as a species boundary (Stackebrandt & Goebel, 1994; Tindall et al., 2010)....
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...Among the several thousand genes within a bacterial genome, the 16S rRNA gene has served as the primary key for phylogeny-based identification when compared against well-curated 16S rRNA gene sequence databases (RossellóMora & Amann, 2001; Tindall et al., 2010)....
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...The cut-off similarity value that was employed for defining phylotypes was 97 %, which is the most widely accepted value for defining prokaryotic species (Tindall et al., 2010)....
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Journal Article•DOI•

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

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Mincheol Kim¹, Hyunseok Oh¹, Sang-Cheol Park¹, Jongsik Chun¹•Institutions (1)

Seoul National University¹

01 Feb 2014-International Journal of Systematic and Evolutionary Microbiology

TL;DR: 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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Abstract: Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA–DNA hybridization (DDH) technique. An ANI threshold range (95–96 %) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95–96 % ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65 % 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2–99.0 %) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.

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2,227 citations

Cites background or methods from "Notes on the characterization of pr..."

...…as an alternative to the tedious DDH, and it is now generally accepted that DDH is only required when 16S rRNA gene sequence similarity between two strains is over 97 % (Tindall et al., 2010), even though higher thresholds of 98.7–99.0 % have also been used (Stackebrandt & Ebers, 2006)....
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...This threshold of 16S rRNA gene sequence similarity has been widely used in bacterial classification as an alternative to the tedious DDH, and it is now generally accepted that DDH is only required when 16S rRNA gene sequence similarity between two strains is over 97 % (Tindall et al., 2010), even though higher thresholds of 98....
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...Over the last 50 years, DDH has been the ‘gold standard’ for bacterial species demarcation as it provides a clear and objective numerical threshold for a species boundary, for which 70 % DDH was suggested and is widely used (Tindall et al., 2010; Wayne et al., 1987)....
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Journal Article•DOI•

OrthoANI: An improved algorithm and software for calculating average nucleotide identity.

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Imchang Lee¹, Yeong Ouk Kim¹, Sang-Cheol Park¹, Jongsik Chun¹•Institutions (1)

Seoul National University¹

01 Feb 2016-International Journal of Systematic and Evolutionary Microbiology

TL;DR: 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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Abstract: Species demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA-DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, 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. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.

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1,838 citations

Cites background from "Notes on the characterization of pr..."

...It has been known that reciprocal DDH values between two strains are often not the same, therefore not symmetrical, when DDH methods use labelled DNA (Johnson & Whitman, 2007, Tindall et al., 2010)....
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Journal Article•DOI•

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

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Pablo Yarza¹, Pelin Yilmaz², Elmar Pruesse², Frank Oliver Glöckner³, Wolfgang Ludwig⁴, Karl-Heinz Schleifer⁴, William B. Whitman⁵, Jean Euzeby⁶, Rudolf Amann², Ramon Rosselló-Móra¹ - Show less +6 more•Institutions (6)

University of the Balearic Islands¹, Max Planck Society², Jacobs University Bremen³, Technische Universität München⁴, University of Georgia⁵, École nationale vétérinaire de Toulouse⁶

01 Sep 2014-Nature Reviews Microbiology

TL;DR: This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea.

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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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1,755 citations

Journal Article•DOI•

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

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Alexander F. Auch¹, Mathias von Jan², Hans-Peter Klenk², Markus Göker²•Institutions (2)

University of Tübingen¹, DSM²

28 Feb 2010-Standards in Genomic Sciences

TL;DR: This work investigates state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH and finds that some distance formulas are very robust against missing fractions of genomic information.

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Abstract: The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.

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1,256 citations

Cites background or methods from "Notes on the characterization of pr..."

...All established variations of DDH determination are technically demanding, labor-intensive and time-consuming procedures, therefore DDH determination is now performed by only a few specialized laboratories, and microbial taxonomists apply DDH only in cases where the strains to be differentiated have previously been shown to be closely related in terms of their 16S rRNA gene sequences [3,4]....
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...Therefore it would be very interesting to see if the same methods could also be used to estimate species boundaries, much like the 16S rRNA gene sequences are used for both inferring phylogenies and calculating pairwise dissimilarities between strains, in order to assess whether they need to be subjected to DDH for drawing conclusions about their species status [4]....
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...DDH values ≤70% are considered as an indication that the tested organism belongs to a different species than the type strain(s) used as reference(s) [2,4]....
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References

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Journal Article•DOI•

DNA sequencing with chain-terminating inhibitors

[...]

Frederick Sanger, S Nicklen, Alan Coulson

01 Dec 1977-Proceedings of the National Academy of Sciences of the United States of America

TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.

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Abstract: A new method for determining nucleotide sequences in DNA is described. It is similar to the “plus and minus” method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2′,3′-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage ϕX174 and is more rapid and more accurate than either the plus or the minus method.

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62,728 citations

"Notes on the characterization of pr..." refers methods in this paper

..., 1977), reverse transcriptase-sequencing (Sanger et al., 1977; Lane et al., 1988) and finally PCR-based gene sequencing (Saiki et al....
[...]
...…54.70.40.11 On: Thu, 08 Nov 2018 14:39:35 of the analysis of the 16S rRNA gene by cataloguing (Fox et al., 1977), reverse transcriptase-sequencing (Sanger et al., 1977; Lane et al., 1988) and finally PCR-based gene sequencing (Saiki et al., 1988) has provided a useful working hypothesis on which…...
[...]

Journal Article•DOI•

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase

[...]

Randall Keichi Saiki¹, David H. Gelfand¹, Susanne Stoffel¹, Stephen J. Scharf¹, Russell Higuchi¹, Glenn Thomas Horn¹, Kary B. Mullis¹, Henry A. Erlich¹ - Show less +4 more•Institutions (1)

Cetus Corporation¹

29 Jan 1988-Science

TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.

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Abstract: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.

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17,663 citations

"Notes on the characterization of pr..." refers background in this paper

...…by cataloguing (Fox et al., 1977), reverse transcriptase-sequencing (Sanger et al., 1977; Lane et al., 1988) and finally PCR-based gene sequencing (Saiki et al., 1988) has provided a useful working hypothesis on which other elements may be compared when investigating the taxonomy and evolution of…...
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..., 1988) and finally PCR-based gene sequencing (Saiki et al., 1988) has provided a useful working hypothesis on which other elements may be compared when investigating the taxonomy and evolution of prokaryotes....
[...]

Book•

Bergey's Manual of Systematic Bacteriology

[...]

in chief George M. Garrity

01 May 1989

TL;DR: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion.

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Abstract: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion. With v.4 the set is complete. The volumes cover, roughly, v.1, the Gram-negatives except those in v.3 ($87.95); v.2, the Gram-positives less actinomycetes ($71.95); v.

...read moreread less

16,172 citations

Journal Article•DOI•

Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics

[...]

Lawrence G. Wayne, Don J. Brenner, R. R. Colwell, Patrick A. D. Grimont, O. Kandler, Micah I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, Erko Stackebrandt, M. P. Starr, H. G. Truper - Show less +8 more

01 Oct 1987-International Journal of Systematic and Evolutionary Microbiology

6,807 citations

"Notes on the characterization of pr..." refers background or methods in this paper

...…Thu, 08 Nov 2018 14:39:35 A DDH value equal to or higher than 70 % has been recommended as a suitable threshold for the definition of members of a species (Brenner, 1973; Johnson, 1973; 1984; Wayne et al., 1987), but this value should not be used as a strict species boundary (Ursing et al., 1995)....
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...This view is adopted here and expands on principles outlined by two ad hoc committees of the ICSB (Wayne et al., 1987; Murray et al., 1990)....
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Journal Article•DOI•

Methods for characterization of Streptomyces species

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E. B. Shirling, D. Gottlieb

01 Jul 1966-International Journal of Systematic and Evolutionary Microbiology

TL;DR: The methods used by collaborators in the ISP for emendation of descriptions of type and neotype strains of the genus Streptomyces (Actinomycetales) are presented.

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Abstract: The methods used by collaborators in the International Streptomyces Project (ISP) for emendation of descriptions of type and neotype strains of the genus Streptomyces (Actinomycetales) are presented.

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5,184 citations