{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["12"],"submitter":["Volpiano CG"],"pubmed_abstract":["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<sup>T</sup>\"), GCF_003024595.1 (\"<i>Mesorhizobium plurifarium</i> LMG 11,892<sup>T</sup>\"), GCF_003096615.1 (\"<i>Methylobacterium organophilum</i> DSM 760<sup>T</sup>\"), and GCF_000373025.1 (\"<i>R. gallicum</i> R-602 sp<sup>T</sup>\") 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<sup>T</sup> 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."],"journal":["Frontiers in microbiology"],"pagination":["614957"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8026895"],"repository":["biostudies-literature"],"pubmed_title":["Genomic Metrics Applied to <i>Rhizobiales</i> (<i>Hyphomicrobiales</i>): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains."],"pmcid":["PMC8026895"],"pubmed_authors":["Whitman WB","Beneduzi A","Vargas LK","Volpiano CG","de Souza EM","Passaglia LMP","Sant'Anna FH","Ambrosini A","Lisboa BB","de Sao Jose JFB"],"additional_accession":[]},"is_claimable":false,"name":"Genomic Metrics Applied to <i>Rhizobiales</i> (<i>Hyphomicrobiales</i>): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.","description":"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<sup>T</sup>\"), GCF_003024595.1 (\"<i>Mesorhizobium plurifarium</i> LMG 11,892<sup>T</sup>\"), GCF_003096615.1 (\"<i>Methylobacterium organophilum</i> DSM 760<sup>T</sup>\"), and GCF_000373025.1 (\"<i>R. gallicum</i> R-602 sp<sup>T</sup>\") 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<sup>T</sup> 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.","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021","modification":"2026-06-02T12:42:57.781Z","creation":"2022-02-11T07:02:17.542Z"},"accession":"S-EPMC8026895","cross_references":{"pubmed":["33841347"],"doi":["10.3389/fmicb.2021.614957"]}}