title: Streptococcal taxonomy based on genome sequence analyses.
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.
authors.affiliation: Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) Avenida Brasil 4365, Manguinhos, Rio de Janeiro, P. O. Box 926, Zip Code 21040-360, Brazil.
authors.forename: Cristiane C
authors.initials: CC
authors.lastname: Thompson
authors.affiliation: Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) Avenida Brasil 4365, Manguinhos, Rio de Janeiro, P. O. Box 926, Zip Code 21040-360, Brazil.
authors.forename: Vanessa E
authors.initials: VE
authors.lastname: Emmel
authors.affiliation: Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) Avenida Brasil 4365, Manguinhos, Rio de Janeiro, P. O. Box 926, Zip Code 21040-360, Brazil.
authors.forename: Erica L
authors.initials: EL
authors.lastname: Fonseca
authors.affiliation: Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) Avenida Brasil 4365, Manguinhos, Rio de Janeiro, P. O. Box 926, Zip Code 21040-360, Brazil.
authors.forename: Michel A
authors.initials: MA
authors.lastname: Marin
authors.affiliation: Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) Avenida Brasil 4365, Manguinhos, Rio de Janeiro, P. O. Box 926, Zip Code 21040-360, Brazil.
authors.forename: Ana Carolina P
authors.initials: ACP
authors.lastname: Vicente