Stenotrophomonas daejeonensis sp. nov., isolated from sewage

Lee, Myungjin; Woo, Sung-Geun; Chae, Myoungsoo; Shin, Mincheol; Jung, Hae-Min; Ten, Leonid N.

doi:10.1099/ijs.0.017780-0

Cited by 32 publications

(23 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5, as previously defined (Ochoa-Sánchez and Vinuesa, 2017). Clade I groups environmental isolates, recovered from different ecosystems, mostly soils and plant surfaces, classified as S. ginsengisoli , S. koreensis (Yang et al, 2006), S. daejeonensis (Lee et al, 2011), S. nitritireducens (Finkmann et al, 2000), S. acidaminiphila (Labat et al, 2002), S. humi and S. terrae (Heylen et al, 2007). The recently described S. pictorum (Ouattara et al, 2017) is also included in clade I.…”

Section: Effect Of Tree-search Intensity On the Quality Of The Speciementioning

confidence: 96%

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Vinuesa

Ochoa-Sánchez

Contreras‐Moreira

2018

Preprint

View full text Add to dashboard Cite

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 14 misclassified RefSeq genome sequences, 12 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

show abstract

Section: Effect Of Tree-search Intensity On the Quality Of The Speciementioning

confidence: 96%

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Vinuesa

Ochoa-Sánchez

Contreras‐Moreira

2018

Preprint

View full text Add to dashboard Cite

show abstract

“…The first detected S. maltophilia species was initially described as Pseudomonas maltophilia in 1981, later reclassified as Xanthomonas maltophilia and finally classified as Stenotrophomonas maltophilia [2], [3], [4]. In the following years, additional species such as S. nitritireducens [5], S. rhizophila [6], S. acidaminiphila [7], S. koreensis [8], S. terrae and S. humi [9], S. chelatiphaga [10], S. ginsengisoli [11], S. daejonensis [12] as well as S. panachihumi [13], and S. pavanii [14] were described. S. dokdonensis was recently moved to the genus Pseudoxanthomonas [15], [16].…”

Section: Introductionmentioning

confidence: 99%

Genotyping of Environmental and Clinical Stenotrophomonas maltophilia Isolates and their Pathogenic Potential

Adámek

Overhage

Bathe³

et al. 2011

PLoS ONE

View full text Add to dashboard Cite

Stenotrophomonas maltophilia is a highly versatile species with useful biotechnological potential but also with pathogenic properties. In light of possible differences in virulence characteristics, knowledge about genomic subgroups is therefore desirable. Two different genotyping methods, rep-PCR fingerprinting and partial gyrB gene sequencing were used to elucidate S. maltophilia intraspecies diversity. Rep-PCR fingerprinting revealed the presence of 12 large subgroups, while gyrB gene sequencing distinguished 10 subgroups. For 8 of them, the same strain composition was shown with both typing methods. A subset of 59 isolates representative for the gyrB groups was further investigated with regards to their pathogenic properties in a virulence model using Dictyostelium discoideum and Acanthamoeba castellanii as host organisms. A clear tendency towards accumulation of virulent strains could be observed for one group with A. castellanii and for two groups with D. discoideum. Several virulent strains did not cluster in any of the genetic groups, while other groups displayed no virulence properties at all. The amoeba pathogenicity model proved suitable in showing differences in S. maltophilia virulence. However, the model is still not sufficient to completely elucidate virulence as critical for a human host, since several strains involved in human infections did not show any virulence against amoeba.

show abstract

“…Originally classified as Pseudomonas maltophilia and then Xanthomonas maltophilia, S. maltophilia belongs to the c-Proteobacteria and is the best known of the 11 species that form the genus Stenotrophomonas Lee et al, 2011;Ryan et al, 2009;Yi et al, 2010). In nature, S. maltophilia exists in a wide variety of environments, being found in water, soil and plant material (Denton & Kerr, 1998;Ryan et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Stenotrophomonas maltophilia strains replicate and persist in the murine lung, but to significantly different degrees

et al. 2011

View full text Add to dashboard Cite

The environmental bacterium Stenotrophomonas maltophilia is increasingly described as a multidrug-resistant pathogen of humans, being associated with pneumonia, among other diseases. But the degree to which S. maltophilia is capable of replicating in a mammalian host has been an issue of controversy. Using a model of intranasal inoculation into adult A/J mice, we now document that S. maltophilia strain K279a, the clinical isolate of S. maltophilia whose complete genome sequence was recently determined, is in fact capable of replicating in lungs, displaying as much as a 10-fold increase in c.f.u. in the first 8 h of infection. Importantly, as few as 104 c.f.u. deposited into the A/J lung was sufficient to promote bacterial outgrowth. Bacterial replication in the lungs of the A/J mice was followed by elevations in pro-inflammatory cytokines and also promoted resistance to subsequent challenge. We also found that DBA/2 mice were permissive for S. maltophilia K279a replication, although the level of growth and persistence in these animals was less than it was in the A/J mice. In contrast, the BALB/c and C57BL/6 mouse strains were non-permissive for S. maltophilia K279a growth. Interestingly, when five additional clinical isolates were introduced into the A/J lung, marked differences in survival were observed, with some strains being much less infective than K279a and others being appreciably more infective. These data suggest that the presence of major virulence determinants is variable among clinical isolates. Overall, this study confirms the infectivity of S. maltophilia for the mammalian host, and illustrates how both host and bacterial factors affect the outcome of Stenotrophomonas infection.

show abstract

Stenotrophomonas daejeonensis sp. nov., isolated from sewage

Abstract: A Gram-stain-negative, motile, aerobic bacterial strain, designated MJ03 T , was isolated from sewage and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ03T belongs to the family

Cited by 32 publications

References 27 publications

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

Genotyping of Environmental and Clinical Stenotrophomonas maltophilia Isolates and their Pathogenic Potential

Stenotrophomonas maltophilia strains replicate and persist in the murine lung, but to significantly different degrees

Contact Info

Product

Resources

About