Taxonomic decisions on Rhizobiales order rested heavily on the interpretation of highly conserved 16S rRNA gene sequences and error-prone DNA-DNA hybridization experiments. Current pragmatic bacterial species definition considers that strains that present at least 95% of average nucleotide identity (ANI) belong to the same species. Here, we computed ANI from 520 genome sequence assemblies from type strains of species from the order Rhizobiales. Thresholds of ANI >=95 and percentage of conserved DNA >=0.7 were used to group the genomes using Maximal Clique Enumeration (MCE). Using this approach, we found that: i) there are synonymy between Aurantimonas manganoxydans and Aurantimonas coralicida, Chelativorans oligotrophicus and Chelativorans multitrophicus, Methylobacterium phyllosphaerae and Methylobacterium oryzae, Rhizobium fabae and Rhizobium pisi, Rhizobium azibense and Rhizobium gallicum, Rhizobium favelukesii and Rhizobium tibeticum, Rhodoplanes piscinae and Rhodoplanes serenus, and Brucella ceti, Brucella inopinata, Brucella microti, Brucella vulpis and Brucella melitensis; ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans, iii) “Rhizobium halotolerans” and “Bartonella mastomydis” should remain as not validly published species as they represent synonyms of other species already validated; iv) Bartonella vinsonii subsp. arupensis and Bartonella vinsonii subsp. berkhoffii do not belong to the same species; v) the genome accessions GCF_003024615.1 for Mesorhizobium loti LMG 6125T, GCF_003024595.1 for Mesorhizobium plurifarium LMG 11892T, GCF_003096615.1 for Methylobacterium organophilum DSM 760T, and GCF_000373025.1 for Rhizobium gallicum R-602 spT lack authenticity evidence; additionally, we provide an authentic genome for a type strain, SEMIA 4085T, of R. gallicum; vi) “Methylobacterium platani” SE2.11, "Xanthobacter autotrophicus" Py2 and "Aminobacter aminovorans" KCTC 2477 represent false type strains. Information of the general authenticity, completeness and contamination for the entire genome set is provided, which may be useful for researchers to select the best genome assemble for their purposes.
