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Front. Microbiol. | doi: 10.3389/fmicb.2018.01360

Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics

  • 1Department of Microbiology and Genetics, Universidad de Salamanca, Spain
  • 2Servicio de Bioinformática, NUCLEUS, Universidad de Salamanca, Spain
  • 3Bioinformatics & Systems Biology, Justus-Liebig-University, Germany
  • 4School of Natural & Environmental Sciences, Newcastle University, United Kingdom
  • 5CNRS-UMR5557 Ecologie Microbienne, Claude Bernard University Lyon 1, France

The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, 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 M. saelicesensis and M. noduli, ten strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of >99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09T and M. noduli GUI43T 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 gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene.
Overall results also supported the current classification of M. saelicesensis and M. noduli 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 in-vitro phenotypic assays performed at different times were compared with in-silico predictions based on genomic data. In-vitro 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 in-silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.

Keywords: Micromonospora, Genome sequencing, phylogenomic analysis, nitrogen-fixing nodule, Taxonomy, species delimitation

Received: 26 Apr 2018; Accepted: 05 Jun 2018.

Edited by:

Jesus L. Romalde, Universidade de Santiago de Compostela, Spain

Reviewed by:

Javier Pascual, Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Germany
Marc G. Chevrette, University of Wisconsin-Madison, United States  

Copyright: © 2018 Riesco, Carro, Román-Ponce, Prieto, Blom, Klenk, Normand and Trujillo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Martha E. Trujillo, Universidad de Salamanca, Department of Microbiology and Genetics, Salamanca, Spain, mett@usal.es