Pablo Vinuesa

Pablo Vinuesa
Universidad Nacional Autónoma de México | UNAM · Centre for Genomic Sciences

Dr.

About

243
Publications
31,161
Reads
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4,298
Citations
Citations since 2016
81 Research Items
2399 Citations
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Introduction
Pablo Vinuesa currently works at the Center for Genomic Sciences, Universidad Nacional Autónoma de México (CCG-UNAM). Pablo is a microbiologist interested in genomics, ecology and evolution. He develops open-source software for microbial pan-genomics (GET_HOMOLOGUES) and phylogenomics (GET_PHYLOMARKERS), which is freely available at https://github.com/vinuesa For current projects and publications, please visit my personal website http://www.ccg.unam.mx/~vinuesa/. I do regularly tweet on diverse topics related to microbiology, genomics, statistics and computing @pvinmex
Additional affiliations
October 2001 - January 2016
Universidad Nacional Autónoma de México
Position
  • Professor (Full)
Description
  • I'm a microbiologist interested in host-microbe interactions, microbial ecology, genomics and evolution. Please visit my website for more details: http://www.ccg.unam.mx/~vinuesa/
October 1998 - August 2001
Philipps University of Marburg
Position
  • Research Assistant
Description
  • During this period I did Post-doctoral research in the groups of Prof. Herman Spaink (Istitute for Molecular Plant Sciences, Leiden, Holand)
October 1995 - September 1998
Philipps University of Marburg
Position
  • PhD Student
Description
  • PhD student, first with a DAAD scholarship (1995-1996) a then with EU-TMR scholarship (1997-1998), in the group of Prof. Dietrich Werner, at the Fachberich Biologie,

Publications

Publications (243)
Article
Full-text available
Mycobacterium tuberculosis is an acid-fast bacterium that causes tuberculosis worldwide. The role of epistatic interactions among different loci of the M. tuberculosis genome under selective pressure may be crucial for understanding the disease and the molecular basis of antibiotic resistance acquisition. Here, we analyzed polymorphic loci interact...
Chapter
The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for plants with large genomes or highly heterozygous species. Here, we describe a step-by-step protocol to analyze plant pangene sets with the s...
Article
Full-text available
Phages are generally described as species specific or even strain specific, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we isolated and c...
Article
Full-text available
Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and...
Preprint
Full-text available
Phages are generally described as species- or even strain-specific viruses, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we identified and...
Article
Pseudomonas aeruginosa is a Gram-negative bacterium frequently isolated from infected immunocompromised patients, and the strains are resistant to a broad spectrum of antibiotics. Recently, the use of phages has been proposed as an alternative therapy against multidrug-resistant bacteria. However, this approach may present various hurdles. This wor...
Article
Full-text available
Bioinformatic mining of the Streptomyces thermocarboxydus K155 genome predicted the presence of four synthases for the production of geosmin, hopene, albaflavenone, and a type B-type A diterpenoid system like that described for labdane-related diterpenoids (LRD). The lrd cluster was comprised by an operon of four genes (lrdABDC). This cluster seeme...
Article
Full-text available
The Salmonella enterica serovar Typhimurium sequence type 213 (ST213) emerged as a predominant genotype in Mexico. It is characterized by harboring multidrug resistance (MDR) IncC plasmids (previously IncA/C) and the lack of the Salmonella virulence plasmid (pSTV). Here we show that the D6-like plasmid prophage is present in most of the ST213 strai...
Article
Full-text available
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that...
Article
Full-text available
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal sta...
Article
Full-text available
The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain the...
Data
Comparison of the complete proteomes of the symbiotic plasmids of R. leguminosarum. Unidirectional BLASTp using the total predicted proteins of R. leguminosarum 3841 pRL10 symbiotic plasmid (illustrated by the red innermost circle) against the predicted proteins of others symbiotic plasmid indicated in the inset. Blast hits were recorded and showed...
Data
Correlation between ANIm and Gcov. (a) 102 Rhizobium and Sinorhizobium genomes, (b) 88 genomes, (c) 35 genomes of rC-I clade, and (d) 38 genomes o rC-II clade. Spearman r and p-values are indicated in the inset.
Data
Distribution of ANI values between pairs of genomes belonging to (a) 102 genomes, (b) 88 genomes, (c) and (e) 35 genomes of rC-I clade, and (d) and (f) 38 genomes o rC-II clade. Histograms show the frequency of pairwise comparisons within clades (turquoise color), and inter clades (pale red), distributed by segments of ANI values. In figures (e) an...
Data
The collection of genomes of Rhizobium and Sinorhizobium used in this study.
Data
Phylogenetic tree of ribosomal proteins of Rhizobium species. Ribosomal clades are indicated by Roman numerals (I to VI) enclosed in colored ellipses. Subclades appear with black ellipses within the clades. The tree was constructed using maximum likelihood in the MEGA software package, by using 58 concatenated ribosomal proteins (refer to section “...
Data
Genomic clusters of 102 Rhizobium and Sinorhizobium pairs obtained by pairwise ANIm comparisons.
Data
Correlation between ANIm and ANIb in pairwise comparison of 102 Rhizobium and Sinorhizobium genomes. Spearman r and p-values are shown.
Data
Phylogenetic families of RepB. Phylogenies were constructed with the maximum likelihood method and a bootstrap of n = 1000 replicates. Colors indicate the phylogenetic clades and their correspondence with the MCL clusters determined as indicated in the section “Materials and Methods” and Figure 5.
Data
Correlation between Gcov and phylogenetic distance. (a) 102 Rhizobium and Sinorhizobium genomes, (b) 88 genomes, (c) 35 genomes of rC-I clade, and (d) 38 genomes o rC-II clade. Spearman r and p-values are shown.
Data
Pairwise ANIm comparison between complete R. leguminosarum symbiotic plasmids. Only the genome sequences of R. leguminosarum listed in the GenBank up to 14-03-2019 were downloaded. The ANIm comparison were performed using JSspecies as described in the methods section. The heatmap show the values of the corrected Gcov% / ANIm%; the color scale key i...
Data
Bray Curtis dissimilarity index for accessory genes distribution within and between ribosomal clusters.
Article
Full-text available
Background: Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown. Results: We report here the ge...
Preprint
Full-text available
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments...
Data
Plasmids and acquired ARGs of the 32 Serratia spp. genomes. β-lactam resistance genes: blue, aminoglycoside resistance genes: red, macrolide resistance gene: yellow, sulfamide/trimethoprim resistance gene: pink, quaternary ammonium compounds: green.
Data
Total number of ARGs and efflux pumps identified in the 32 Serratia genomes. Genes found on the chromosome in white color, genes found on plasmids in orange color, genes found on transposons in blue color, genes found on probable genomic islands in purple color, regulatory genes in pink color and genes with mutations that confer resistance in green...
Data
Pairwise core-genome average nucleotide identity values from OMCL clusters (cgANIb-OMCL). The colors in the heat map represent pairwise ANI values, with a gradient from light yellow (high identity) to red (low identity).
Data
Venn analysis of the pan-genome of the 32 Serratia spp. genomes generated by COG and OMCL algorithms.
Data
Venn diagram of the consensus core-genome of the 32 Serratia spp. genomes generated by COG, OMCL, and BDBH algorithms.
Data
List of the 32 Serratia spp. genomes used in this study, source of isolation, geographic region, continent, NCBI genome reference number, and genome size.
Article
Full-text available
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 bi...
Preprint
Full-text available
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 bi...
Article
Full-text available
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....
Article
Full-text available
We present here the high-quality complete genome sequences of eight strains of Rhizobium -nodulating Phaseolus vulgaris . Comparative analyses showed that some of them belonged to different genomic and evolutionary lineages with common symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris specificity are reported here.
Article
Full-text available
Toxoplasma gondii is a protozoan parasite with a broad ecological valence, which has been detected in a wide range of hosts and landscapes. Although the genus is considered monospecific, in recent years it has been demonstrated to exhibit more genetic variability than previously known. In Mexico, there are few genotyping studies, which suggest that...
Working Paper
Full-text available
The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. S. 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 c...
Article
Full-text available
The whole-genome sequences of three strains of Rhizobium gallicum reported here support the concept that the distinct nodulation host ranges displayed by the symbiovars gallicum and phaseoli can be largely explained by different symbiotic plasmids.