Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools

Abstract

BackgroundEvidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species.ResultsIn this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome.ConclusionOur ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0882-5) contains supplementary material, which is available to authorized users.

Pan-Resistome Insights into the Multidrug Resistance of Acinetobacter baumannii

“…Three strains (FDAARGOS_494, FDAARGOS_493, and FDAARGOS_560), previously identified as Acinetobacter sp., were grouped together and inside the A. baumannii clade, strongly suggesting that they are, in fact, of this same species. This taxonomic re-classification has already occurred in other cases of bacterial species [ 24 , 25 , 26 ]. More phylogenomic studies, including tetranucleotide analyses, Average Nucleotide Identity (ANI), and the presence and absence of species-specific genes evaluation, are needed to confirm this hypothesis and assure taxonomic reclassification based on genomic data and theoretical background [ 24 , 27 ].…”

Genetic and symbiotic characterization of rhizobia nodulating legumes in a mining area in southeast Brazil

“…This type of analysis was efficient in separating strains with greater potential for being new taxons. However, new studies that involve more comprehensive analyses of the genome of these microorganisms have become increasingly necessary for description of species (Konstantinidis and Tiedje, 2005;López-Guerrero et al, 2012;Okazaki et al, 2015;Kishi et al, 2016;Costa et al, 2018).…”

Pan-resistome insights into the multidrug resistance of Acinetobacter baumannii

“…Three strains (FDAARGOS_494, FDAARGOS_493, and FDAARGOS_560), previously identi ed as Acinetobacter sp., were grouped together and inside the A baumannii clade, strongly suggesting that they are, in fact, of this same species. This taxonomic re-classi cation has already occurred in other cases of bacterial species [27][28][29]. More phylogenomic studies, including tetranucleotide analyses, Average Nucleotide Identity (ANI), and the presence and absence of species-speci c genes evaluation, are needed to con rm this hypothesis and assure taxonomic reclassi cation based on genomic data and theoretical background [27,30].…”