biostudies-literatureUnknown12Volpiano CGTaxonomic decisions within the order <i>Rhizobiales</i> 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 <i>Rhizobiales</i> 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 <i>Aminobacter lissarensis</i> and <i>Aminobacter carboxidus</i>, <i>Aurantimonas manganoxydans</i> and <i>Aurantimonas coralicida</i>, "<i>Bartonella mastomydis</i>," and <i>Bartonella elizabethae</i>, <i>Chelativorans oligotrophicus</i>, and <i>Chelativorans multitrophicus</i>, <i>Rhizobium azibense</i>, and <i>Rhizobium gallicum</i>, <i>Rhizobium fabae</i>, and <i>Rhizobium pisi</i>, and <i>Rhodoplanes piscinae</i> and <i>Rhodoplanes serenus</i>; (ii) <i>Chelatobacter heintzii</i> is not a synonym of <i>Aminobacter aminovorans</i>; (iii) "<i>Bartonella vinsonii</i>" subsp. <i>arupensis</i> and "<i>B. vinsonii</i>" subsp. <i>berkhoffii</i> represent members of different species; (iv) the genome accessions GCF_003024615.1 ("<i>Mesorhizobium loti</i> LMG 6,125^T"), GCF_003024595.1 ("<i>Mesorhizobium plurifarium</i> LMG 11,892^T"), GCF_003096615.1 ("<i>Methylobacterium organophilum</i> DSM 760^T"), and GCF_000373025.1 ("<i>R. gallicum</i> R-602 sp^T") are not from the genuine type strains used for the respective species descriptions; and v) "<i>Xanthobacter autotrophicus</i>" Py2 and "<i>Aminobacter aminovorans</i>" KCTC 2,477^T represent cases of misuse of the term "type strain". <i>Aminobacter heintzii</i> comb. nov. and the reclassification of <i>Aminobacter ciceronei</i> as <i>A. heintzii</i> 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.Frontiers in microbiology614957https://www.ebi.ac.uk/biostudies/studies/S-EPMC8026895biostudies-literatureGenomic Metrics Applied to <i>Rhizobiales</i> (<i>Hyphomicrobiales</i>): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.PMC8026895Whitman WBBeneduzi AVargas LKVolpiano CGde Souza EMPassaglia LMPSant'Anna FHAmbrosini ALisboa BBde Sao Jose JFBfalseGenomic Metrics Applied to <i>Rhizobiales</i> (<i>Hyphomicrobiales</i>): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.Taxonomic decisions within the order <i>Rhizobiales</i> 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 <i>Rhizobiales</i> 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 <i>Aminobacter lissarensis</i> and <i>Aminobacter carboxidus</i>, <i>Aurantimonas manganoxydans</i> and <i>Aurantimonas coralicida</i>, "<i>Bartonella mastomydis</i>," and <i>Bartonella elizabethae</i>, <i>Chelativorans oligotrophicus</i>, and <i>Chelativorans multitrophicus</i>, <i>Rhizobium azibense</i>, and <i>Rhizobium gallicum</i>, <i>Rhizobium fabae</i>, and <i>Rhizobium pisi</i>, and <i>Rhodoplanes piscinae</i> and <i>Rhodoplanes serenus</i>; (ii) <i>Chelatobacter heintzii</i> is not a synonym of <i>Aminobacter aminovorans</i>; (iii) "<i>Bartonella vinsonii</i>" subsp. <i>arupensis</i> and "<i>B. vinsonii</i>" subsp. <i>berkhoffii</i> represent members of different species; (iv) the genome accessions GCF_003024615.1 ("<i>Mesorhizobium loti</i> LMG 6,125^T"), GCF_003024595.1 ("<i>Mesorhizobium plurifarium</i> LMG 11,892^T"), GCF_003096615.1 ("<i>Methylobacterium organophilum</i> DSM 760^T"), and GCF_000373025.1 ("<i>R. gallicum</i> R-602 sp^T") are not from the genuine type strains used for the respective species descriptions; and v) "<i>Xanthobacter autotrophicus</i>" Py2 and "<i>Aminobacter aminovorans</i>" KCTC 2,477^T represent cases of misuse of the term "type strain". <i>Aminobacter heintzii</i> comb. nov. and the reclassification of <i>Aminobacter ciceronei</i> as <i>A. heintzii</i> 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.2021-01-01T00:00:00Z20212026-06-02T12:42:57.781Z2022-02-11T07:02:17.542ZS-EPMC80268953384134710.3389/fmicb.2021.614957