The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotro... more The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic
Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, g... more Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13 Mb. We annotated mobile genetic elements and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.
Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City,... more Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City, Mexico, from a patient with a systemic infection, and its complete genome sequence was determined using PacBio single-molecule real-time technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.
Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting o... more Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyze alpha and beta diversity patterns of Rhizobiaceae communities from a conserved seasonally-dry tropical forest site in central Mexico and two nearby agricultural fields. Lineage-specific recA amplicon libraries were generated from soil DNA and their sequences compared with those from root-surface and nodule isolates recovered in trapping experiments from two native Acacia species and two Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A "rare biosphere"-like distribution of species was found in the three habitats. Multivariate statistical analyses demonst...
Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the s... more Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.
Current Plant Science and Biotechnology in Agriculture, 2005
... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level.... more ... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level. (RO Russo, in D. Werner and WE Newton (eds.) Nitrogen Fixation: Agriculture, Forestry, Ecology and the Environment, Kluwer, 2005) ...
We present evidence supporting the notion that codon usage (CU) compatibility between foreign gen... more We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.
Eguiarte, LE, V. Souza y X. Aguirre (Comps.): …, 2007
... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta ... more ... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta clasificaci??n ubica a la mayor??a de los rizobios en la subclase ?? de las Proteobacterias (Willems y Collins, 1993; Young, 1993; Mart??nez, 1994; Young y Haukka, 1996). ...
Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted ... more Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted in the identification of strain KIM-G1. Its rough colony appearance, flocculation in liquid culture, and Ndv(-) Fix(-) phenotype were indicative of a lipopolysaccharide (LPS) defect. Electrophoretic analysis of cell-associated polysaccharides showed that KIM-G1 produces only rough LPS. Composition analysis of purified LPS oligosaccharides from KIM-G1 indicated that it produces an intact LPS core trisaccharide (alpha-D-GalA-1-->4[alpha-D-GalA-1-->5]-Kdo) and tetrasaccharide (alpha-D-Gal-1-->6[alpha-D-GalA-1-->4]-alpha-D-Man-1-->5Kdo), strongly suggesting that the transposon insertion disrupted a locus involved in O-antigen biosynthesis. Five monosaccharides (Glc, Man, GalA, 3-O-Me-6-deoxytalose, and Kdo) were identified as the components of the repeating O unit of the smooth parent strain, KIM5s. Strain KIM-G1 was complemented with a 7.2-kb DNA fragment from KIM5s that, whe...
Zeitschrift für Naturforschung. C, Journal of biosciences
A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amp... more A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic fingerprinting (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis ARDRA. It was shown that the antagonistic strains are closely related, forming a separate cluster from other...
Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic t... more Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.
The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotro... more The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic
Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, g... more Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13 Mb. We annotated mobile genetic elements and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.
Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City,... more Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City, Mexico, from a patient with a systemic infection, and its complete genome sequence was determined using PacBio single-molecule real-time technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.
Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting o... more Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyze alpha and beta diversity patterns of Rhizobiaceae communities from a conserved seasonally-dry tropical forest site in central Mexico and two nearby agricultural fields. Lineage-specific recA amplicon libraries were generated from soil DNA and their sequences compared with those from root-surface and nodule isolates recovered in trapping experiments from two native Acacia species and two Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A "rare biosphere"-like distribution of species was found in the three habitats. Multivariate statistical analyses demonst...
Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the s... more Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.
Current Plant Science and Biotechnology in Agriculture, 2005
... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level.... more ... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level. (RO Russo, in D. Werner and WE Newton (eds.) Nitrogen Fixation: Agriculture, Forestry, Ecology and the Environment, Kluwer, 2005) ...
We present evidence supporting the notion that codon usage (CU) compatibility between foreign gen... more We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.
Eguiarte, LE, V. Souza y X. Aguirre (Comps.): …, 2007
... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta ... more ... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta clasificaci??n ubica a la mayor??a de los rizobios en la subclase ?? de las Proteobacterias (Willems y Collins, 1993; Young, 1993; Mart??nez, 1994; Young y Haukka, 1996). ...
Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted ... more Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted in the identification of strain KIM-G1. Its rough colony appearance, flocculation in liquid culture, and Ndv(-) Fix(-) phenotype were indicative of a lipopolysaccharide (LPS) defect. Electrophoretic analysis of cell-associated polysaccharides showed that KIM-G1 produces only rough LPS. Composition analysis of purified LPS oligosaccharides from KIM-G1 indicated that it produces an intact LPS core trisaccharide (alpha-D-GalA-1-->4[alpha-D-GalA-1-->5]-Kdo) and tetrasaccharide (alpha-D-Gal-1-->6[alpha-D-GalA-1-->4]-alpha-D-Man-1-->5Kdo), strongly suggesting that the transposon insertion disrupted a locus involved in O-antigen biosynthesis. Five monosaccharides (Glc, Man, GalA, 3-O-Me-6-deoxytalose, and Kdo) were identified as the components of the repeating O unit of the smooth parent strain, KIM5s. Strain KIM-G1 was complemented with a 7.2-kb DNA fragment from KIM5s that, whe...
Zeitschrift für Naturforschung. C, Journal of biosciences
A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amp... more A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic fingerprinting (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis ARDRA. It was shown that the antagonistic strains are closely related, forming a separate cluster from other...
Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic t... more Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.
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Papers by Pablo Vinuesa
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.