AUTHOR=Riesco Raúl , Carro Lorena , Román-Ponce Brenda , Prieto Carlos , Blom Jochen , Klenk Hans-Peter , Normand Philippe , Trujillo Martha E. 

TITLE=Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.01360

DOI=10.3389/fmicb.2018.01360

ISSN=1664-302X

ABSTRACT=<p>The type isolates of species <italic>Micromonospora saelicesensis</italic> and <italic>Micromonospora noduli</italic> are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes <italic>Lupinus angustifolius</italic> and <italic>Pisum sativum</italic>, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of <italic>M. saelicesensis</italic> and <italic>M. noduli</italic>, 10 strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either <italic>M. saelicensesis</italic> or <italic>M. noduli</italic>, based on a cut-off value of ≥99.5% were selected for whole-genome sequencing and compared with the type strains of <italic>M. saelicesensis</italic> Lupac 09<sup>T</sup> and <italic>M. noduli</italic> GUI43<sup>T</sup> using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and <italic>gyrB</italic> gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of <italic>M. saelicesensis</italic> and <italic>M. noduli</italic> as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of <italic>in vitro</italic> phenotypic assays performed at different times were compared with <italic>in silico</italic> predictions based on genomic data. <italic>In vitro</italic> phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of <italic>in silico</italic> predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining <italic>Micromonospora</italic> species at the genomic and phenotypic level.</p>