An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

Ramos, Patricia; Moreira-Filho, Carlos Alberto; Trappen, Stefanie Van; Swings, Jean; Vos, Paul De; Barbosa, Heloíza Ramos; Thompson, Cristiane C.; Vasconcelos, Ana Tereza Ribeiro de; Thompson, Fabiano L.

doi:10.1590/s0074-02762011000400003

Cited by 13 publications

(5 citation statements)

References 36 publications

(51 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Moreover, the supertree ( Figure 4C ) presented a clustering with a more recent hypothetical ancestor for the non-plant-associated group, thus excluding Xylella (in discordance with the two phylogenies discussed above). This result corroborates with that of other studies that show that Stenotrophomonas is phylogenetically closer to X. campestris than to Xylella (Ramos et al, 2011; Naushad and Gupta, 2013).…”

Section: Resultssupporting

confidence: 93%

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics

et al. 2019

View full text Add to dashboard Cite

Genomics research has produced an exponential amount of data. However, the genetic knowledge pertaining to certain phenotypic characteristics is lacking. Also, a considerable part of these genomes have coding sequences (CDSs) with unknown functions, posing additional challenges to researchers. Phylogenetically close microorganisms share much of their CDSs, and certain phenotypes unique to a set of microorganisms may be the result of the genes found exclusively in those microorganisms. This study presents the GTACG framework, an easy-to-use tool for identifying in the subgroups of bacterial genomes whose microorganisms have common phenotypic characteristics, to find data that differentiates them from other associated genomes in a simple and fast way. The GTACG analysis is based on the formation of homologous CDS clusters from local alignments. The front-end is easy to use, and the installation packages have been developed to enable users lacking knowledge of programming languages or bioinformatics analyze high-throughput data using the tool. The validation of the GTACG framework has been carried out based on a case report involving a set of 161 genomes from the Xanthomonadaceae family, in which 19 families of orthologous proteins were found in 90% of the plant-associated genomes, allowing the identification of the proteins potentially associated with adaptation and virulence in plant tissue. The results show the potential use of GTACG in the search for new targets for molecular studies, and GTACG can be used as a research tool by biologists who lack advanced knowledge in the use of computational tools for bacterial comparative genomics.

show abstract

Section: Resultssupporting

confidence: 93%

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics

et al. 2019

View full text Add to dashboard Cite

show abstract

“…However, DDH has several limitations, including low reproducibility among laboratories, high labour demand, cost and time consumption due to the need for hybridization of a large number of strains [ 23 , 25 ]. Furthermore, there is no database that allows the comparison of results from different studies [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

et al. 2015

View full text Add to dashboard Cite

BackgroundBiological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria.DescriptionClassification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species.ConclusionA database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.

show abstract

“…Six of these genes— atp D, gap A, gua A, pps A, nuo D, and rec A—were firstly employed for inferring the population structure of the genus Stenotrophomonas by Kaiser et al [16]. We also included the constitutive gene rpo A already used by our group [23]. …”

Section: Methodsmentioning

confidence: 99%

“…no. 10342020 Invitrogen Corporation, Carlsbad, CA), 25 mM of dNTPs, 10 mM of forward and reverse primers [16, 23], and water to adjust the final reaction volume to 50 μ L. The amount of DNA per reaction ranged from 20 to 40 ng depending on the size of the gene fragment to be amplified. The PCR reaction was performed for 40 cycles at the following temperatures: denaturation of DNA at 95°C/6 min, annealing at 62°C/15 sec, and extension at 72°C/1 min and 15 sec.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

Cerezer

Bando

Pasternak

et al. 2014

BioMed Research International

Self Cite

View full text Add to dashboard Cite

Stenotrophomonas ssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species, S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates of Stenotrophomonas spp. and, environmental and clinical strains of S. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process of Stenotrophomonas to different habitats. Two clinical isolates subgroups of S. maltophilia sharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partial ppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection with S. maltophilia was nosocomial or community-acquired.

show abstract

An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

Cited by 13 publications

References 36 publications

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

Contact Info

Product

Resources

About