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. 2013 Mar 1:2:67.
doi: 10.12688/f1000research.2-67.v1. eCollection 2013.

Streptococcal taxonomy based on genome sequence analyses

Cristiane C Thompson #  1 , Vanessa E Emmel #  1 , Erica L Fonseca  1 , Michel A Marin  1 , Ana Carolina P Vicente  1
Affiliations

Streptococcal taxonomy based on genome sequence analyses

Cristiane C Thompson et al. F1000Res. .

Abstract

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance, S. pneumoniae, S. mitis, and S. oralis. A Streptococcus species can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

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Conflict of interest statement

Competing interests: No relevant competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Neighbor-joining tree based on 16S rRNA gene sequences and MLSA concatenated sequences of Streptococcus.
The numbers at the nodes indicate the values of bootstrap statistics after 2000 replications, and values below 50% are not shown. Bars, 0.005% and 0.02% estimated sequence divergence.
See this image and copyright information in PMC

References

    1. Gevers D, Cohan FM, Lawrence JG, et al. : Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol. 2005;3(9):733–9 10.1038/nrmicro1236 - DOI - PubMed
    1. Cohan FM, Koeppel AF: The origins of ecological diversity in prokaryotes. Curr Biol. 2008;18(21):R1024–34 10.1016/j.cub.2008.09.014 - DOI - PubMed
    1. Alam S, Brailsford SR, Whiley RA, et al. : PCR-Based methods for genotyping viridans group streptococci. J Clin Microbiol. 1999;37(9):2772–6 - PMC - PubMed
    1. Stackebrandt E, Goebel BM: Taxonomic Note: A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994;44(4):846–849 10.1099/00207713-44-4-846 - DOI
    1. Wayne LG, Brenner DJ, Colwell RR, et al. : Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987;37(4):463–464 10.1099/00207713-37-4-463 - DOI