AUTHOR=Volpiano Camila Gazolla , Sant’Anna Fernando Hayashi , Ambrosini Adriana , de São José Jackson Freitas Brilhante , Beneduzi Anelise , Whitman William B. , de Souza Emanuel Maltempi , Lisboa Bruno Brito , Vargas Luciano Kayser , Passaglia Luciane Maria Pereira 

TITLE=Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.614957

DOI=10.3389/fmicb.2021.614957

ISSN=1664-302X

ABSTRACT=<p>Taxonomic decisions within the order <italic>Rhizobiales</italic> have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of <italic>Rhizobiales</italic> order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between <italic>Aminobacter lissarensis</italic> and <italic>Aminobacter carboxidus</italic>, <italic>Aurantimonas manganoxydans</italic> and <italic>Aurantimonas coralicida</italic>, “<italic>Bartonella mastomydis</italic>,” and <italic>Bartonella elizabethae</italic>, <italic>Chelativorans oligotrophicus</italic>, and <italic>Chelativorans multitrophicus</italic>, <italic>Rhizobium azibense</italic>, and <italic>Rhizobium gallicum</italic>, <italic>Rhizobium fabae</italic>, and <italic>Rhizobium pisi</italic>, and <italic>Rhodoplanes piscinae</italic> and <italic>Rhodoplanes serenus</italic>; (ii) <italic>Chelatobacter heintzii</italic> is not a synonym of <italic>Aminobacter aminovorans</italic>; (iii) “<italic>Bartonella vinsonii</italic>” subsp. <italic>arupensis</italic> and “<italic>B. vinsonii</italic>” subsp. <italic>berkhoffii</italic> represent members of different species; (iv) the genome accessions GCF_003024615.1 (“<italic>Mesorhizobium loti</italic> LMG 6125<sup>T</sup>”), GCF_003024595.1 (“<italic>Mesorhizobium plurifarium</italic> LMG 11892<sup>T</sup>”), GCF_003096615.1 (“<italic>Methylobacterium organophilum</italic> DSM 760<sup>T</sup>”), and GCF_000373025.1 (“<italic>R. gallicum</italic> R-602 sp<sup>T</sup>”) are not from the genuine type strains used for the respective species descriptions; and v) “<italic>Xanthobacter autotrophicus</italic>” Py2 and “<italic>Aminobacter aminovorans</italic>” KCTC 2477<sup>T</sup> represent cases of misuse of the term “type strain”. <italic>Aminobacter heintzii</italic> comb. nov. and the reclassification of <italic>Aminobacter ciceronei</italic> as <italic>A. heintzii</italic> is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.</p>