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MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae.

Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E - PLoS ONE (2011)

Bottom Line: Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae.Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences.The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

View Article: PubMed Central - PubMed

Affiliation: Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain.

ABSTRACT
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

Show MeSH
Neighbour-joining phylogenetic tree based on atpD gene sequences (about 500 nt) showing the position of species included in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 2 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
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pone-0020223-g004: Neighbour-joining phylogenetic tree based on atpD gene sequences (about 500 nt) showing the position of species included in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 2 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.

Mentions: To compare the data obtained by MALDI-TOF MS analysis with those based on gene sequence analysis (figures 2, 3 and 4), a cluster analysis was performed based on a correlation matrix using the integrated tools of the MALDI Biotyper 2.0 software package. Figure 5 showed that the genus Rhizobium was divided into several clusters whose distribution basically coincided with that observed after rrs, recA and atpD gene analyses. The results evidenced that some reclassifications performed within genus Rhizobium are correct as occurs in the case of the former species Agrobacterium tumefaciens reclassified into A. radiobacter [28]. MALDI-TOF MS results confirmed that they are the same species since their type strains held in different collections matched with score values higher than 2 (Table 2A and 2B). These results are congruent with those obtained from recA and atpD gene analyses since these strains presented nearly identical sequences (figures 3 and 4). After reclassification of the complete genus Agrobacterium into Rhizobium, the current valid name for these species is Rhizobium radiobacter [3].


MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae.

Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E - PLoS ONE (2011)

Neighbour-joining phylogenetic tree based on atpD gene sequences (about 500 nt) showing the position of species included in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 2 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105015&req=5

pone-0020223-g004: Neighbour-joining phylogenetic tree based on atpD gene sequences (about 500 nt) showing the position of species included in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 2 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
Mentions: To compare the data obtained by MALDI-TOF MS analysis with those based on gene sequence analysis (figures 2, 3 and 4), a cluster analysis was performed based on a correlation matrix using the integrated tools of the MALDI Biotyper 2.0 software package. Figure 5 showed that the genus Rhizobium was divided into several clusters whose distribution basically coincided with that observed after rrs, recA and atpD gene analyses. The results evidenced that some reclassifications performed within genus Rhizobium are correct as occurs in the case of the former species Agrobacterium tumefaciens reclassified into A. radiobacter [28]. MALDI-TOF MS results confirmed that they are the same species since their type strains held in different collections matched with score values higher than 2 (Table 2A and 2B). These results are congruent with those obtained from recA and atpD gene analyses since these strains presented nearly identical sequences (figures 3 and 4). After reclassification of the complete genus Agrobacterium into Rhizobium, the current valid name for these species is Rhizobium radiobacter [3].

Bottom Line: Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae.Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences.The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

View Article: PubMed Central - PubMed

Affiliation: Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain.

ABSTRACT
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

Show MeSH