Pablo's research and teaching areas Salto de San Anton, Cuernavaca, Mexico

Research interests

Research in our group aims to learn how niche specialization, including host adaptation, drives speciation in selected alpha- and gamma-Proteobacteria.

We are also interested in studying the ecological genetics of microbial communities and populations found in ecosystems with contrasting levels of human perturbation (conserved vs. perturbed tropical forests, contaminated vs. pristine rivers soils irrigated with clean vs. polluted water). We have generated and analyzed large collections of rhizobial isolates from seasonally dry tropical forests, and other Proteobacteria (Enterobacteriaceae, Ochrobactrum, Pseudomonas and Stenotrophomonas) recovered from water bodies and soils with different degrees of residual contamination/perturbation. In this cotext we study how anthropogenic environmental perturbation affects the diversity, genomic structure and environmental distribution of these groups of bacteria and selected classes of accessory genes (i.e. symbiotic, virulence and antibiotic resistance genes). To reach this goal, we are currently preforming large-scale genome sequencing of selected isolates recovered in the context of an ecologically-explicit sampling scheme described above. We are particularly interested in better understanding the impact of anthropogenic environmental perturbation on the structure and evolution of the pan-genome of alpha- and gamma-Proteobacteria, focusing mainly on mobile genetic elements and associated adaptive loci such as symbiosis, virulence and resistance determinants. see publications.

Current research

Research in our group now focuses on comparative and functional genomics of Salmonella and Stenotrophomonas species to elucidate the evolutionary processess and molecular mechanisms underlying the origin of opportunistic pathogens and adaptation to anthropogenized habitats.

Of particular interest to us are functional and evolutionary analyses of mobile genetic elements, efflux pumps, resistance genes, secretion systems and the exoproteins they secrete.

Research in Vinuesa's lab is funded by CONACyT and PAPIIT grants.
We collaborate in a large CONACyT - Fronteras de la Ciencia grant (2017-2018) entitled "Descubriendo el impacto del genoma accesorio en la evolución de cepas atípicas de Salmonella Typhimurium causantes de infecciones sistémicas en México", together with Drs. Edmundo Calva, José Luis Puente and Claudia Silva from the Institute of Biotechnology (IBT-UNAM).

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Synopsis of research lines

Ecological and phenotypic differentiation in sympatric populations of environmental Stenotrophomonas
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 nosocomial pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). We have used the multispecies coalescent, coupled with Bayes factor analysis, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters, to delimit species borders, revealing that the Smc contains at least 5 significantly differentiated lineages. We demonstrated that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and beta-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests.
Comparative and functional genomics of Stenotrophomonas spp. to elucidate evolutionary process and molecular mechanisms underlying the emergence of opportunistic pathogens
We have recently sequenced, assembled and annotated the complete genomes of a large number of our environmental isolates of Stenotrophomonas isolates. Ongoing phylogenomic and comparative genomic analyses in our lab are revealing key evolutionary patterns that largely explain the origin of opportunistic pathogens within the genus. We are currently starting functional genomic studies to test experimentally some of the predictions made by our phylogenomic analyses.
Bioinformatic tools for microbial pangenomics and comparative transcriptomics
In collaboration with Dr. Bruno Contreras-Moreira, head of the Laboratory of Computational Biology at EEAD-CSIC, we develop bioinformatics and comparative genomics tools to identify optimal molecular markers for the above-mentioned tasks. We also develop software to aid in the analysis of large sequence datasets. Our primers4clades web server is a tool to design degenerate PCR primers from multiple sequence alignments of protein-coding sequences. We use the primers designed with our extended CODEHOP algorithm in our lineage-targeted metagenomics and MLSA studies.
In collaboration with Bruno, we have also developed the open-source GET_HOMOLOGUES software package for robust microbial pan-genomics. The GET_HOMOLOGUES_EST software package can be used to cluster and analyze eukaryotic pan-transcriptomes.
Diversity of rhizobial communities in seasonally-dry tropical forests and host-dependent microbiome assembly on legume roots
We have combined culture dependent and independent approaches to study Rhizobial populations and communities inhabiting the bulk soil, rhizosphere and nodules to unravel host effects on structuring rhizobial commmunities based on large sequece data sets. We use multilocus sequence analysis to infer species trees, estimate population genetic parameters and learn about the biogeography and environmental distribution of the isolates of our target organims. We're using a lineage-targeted metagenomics strategy based on the analysis of libraries from environmental amplicons generated with clade-specific PCR primers for high-resolution population and community analyses.

The following sections provide a list of selected publications and some details about our current research lines.

Selected publications (Google Scholar)

Reviews
  • Pablo Vinuesa* and Bruno Contreras-Moreira 2015. Chapter 27. Pangenomic analysis of the Rhizobiales using the GET_HOMOLOGUES software package. Pages 271-280 in Biological Nitrogen Fixation 7, Vol. I.. Frans J. de Bruijn Editor. Wiley/Blackwel
  • Vinuesa, P.*, and B. Contreras-Moreira. 2015. Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids. Methods Mol. Biol. 1231:203-232. PubMed PMID: 25343868
  • Bernardo Sachman-Ruíz, Bruno Contreras-Moreira, Enrique Zozaya, Cristina Martínez-Garza and Vinuesa, P*. 2011. primers4clades, a web server to design lineage-specific PCR primers for gene-targeted metagenomics. Chapter 51 in Frans J. de Bruijn (ed.), Handbook of Molecular Microbial Ecology vol.I: Metagenomics and Complementary Approaches. Wiley/Blackwell. ISBN: 978-0-470-64479-9. In press. July 2011. (PDF)
  • Vinuesa, P*. 2010. Multilocus Sequence Analysis and Bacterial Species Phylogeny Estimation.Chapter 3, pg. 41-64, in A. Oren and R. T. Papke (ed.), Molecular Phylogeny of Microorganisms. Caister Academic Press, Norfolk, UK. Abstract. ISBN: 978-1-904455-67-7.
  • Rademaker, H. J. M. Aarts and Vinuesa P. (2005). Molecular typing of environmental isolates. Chapter 4 in Molecular Microbial Ecology. Mark Osborn and Cindy Smith (eds). NY, Taylor & Francis. (PDF)
Papers
  • Pablo Vinuesa*, Luz Edith Ochoa-Sánchez and Bruno Contreras-Moreira (2018). 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 genus Stenotrophomonas. Front. Microbiol. 9:771 | doi: 10.3389/fmicb.2018.00771. | PubMed PMID: 29765358 | Part of the Research Topic: Microbial Taxonomy, Phylogeny and Biodiversity. | Source code on GitHub
  • Luz Edith Ochoa-Sanchez and Pablo Vinuesa* (2017). Evolutionary genetic analysis uncovers multiple species with distinct habitat preferences and antibiotic resistance phenotypes in the Stenotrophomonas maltophilia complex. Front. Microbiol. 8: 1548. https://doi.org/10.3389/fmicb.2017.01548 | PubMed PMID: 28861062 | latest manuscript version on bioRxiv.
  • Bruno Contreras-Moreira, Carlos Pérez Cantalapiedra, María Jesús García Pereira, Sean Gordon, John P Vogel, Ernesto Igartua, Ana M Casas and Pablo Vinuesa (2017). Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species. Front. in Plant Sci. 8: 184. Online Article, doi: 10.3389/fpls.2017.00184.
  • Fabiola Miranda-Sánchez, Javier Rivera and Pablo Vinuesa* 2016. Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ. Microbiol. 18(8): 2375-2391. doi: 10.1111/1462-2920.13061. Epub 2015 Dec 2. PMID:26395550|PDF
  • Olga M. Pérez Carrascal, David VanInsberghe, Soledad Juárez, Martin F. Polz, Pablo Vinuesa and Víctor González (2016). Population Genomics of the Symbiotic Plasmids of Sympatric Nitrogen-Fixing Rhizobium Species Associated with Phaseolus vulgaris. Environmental Microbiology. 18(8): 2660-2676. doi: 10.1111/1462-2920.13415. Epub 2016 Jul 12. PMID:27312778|PDF
  • Pablo Vinuesa*, Jose Puente, Edmundo Calva, Mussaret Zaidi, and Claudia Silva*. 2016. Complete genome sequence of Salmonella enterica serovar Typhimurium strain SO3 (sequence type 302) isolated from a baby with meningitis in Mexico. 4(2):e00285-16. doi:10. 1128/genomeA.00285-16. PMID:27103717|PDF
  • Pablo Vinuesa* and Luz E. Ochoa-Sánchez 2015. Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico, Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide Biosynthesis Gene Cluster. Genome Annoucements. Accepted on Oct. 17th, 2015. GenBank acc. no. CP012900.1, Assembly GCA_001314305.1, BioSample acc. SAMN04099006, BioProject acc. PRJNA296415
  • Claudia Silva*, Edmundo Calva, Juan J. Calva, Magdalena Wiesnera, Marcos Fernández-Mora, José L. Puente and Pablo Vinuesa*. 2015. Complete genome sequence of a human-invasive Salmonella Typhimurium strain of the emerging sequence type 213 harboring a multidrug resistance IncA/C plasmid and a blaCMY-2-carrying IncF plasmid. Genome Announcements. November/December 2015 vol. 3 no. 6 e01323-15 PubMed PMID:26564044
  • Ciro Cubillas, Pablo Vinuesa, Maria Luisa Tabche, Araceli Davalos, Vázquez A., Ismael Hernandez-Lucas, David Romero and Alejandro García-de los Santos. 2014. The cation diffusion facilitator protein EmfA of Rhizobium etli belongs to a novel subfamily of Mn2+/ Fe2+ transporters conserved in alpha-proteobacteria. Metallomics. Metallomics. 6(10):1808-1815. PubMed PMID: 25054342
  • Bruno Contreras-Moreira* and Pablo Vinuesa* (2013). GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pan-genome analysis. Appl. Env. Microbiol. 79(24):7696-7701. PubMed PMID: 24096415 | PDF | GET_HOMOLOGUES source code download.
  • Ciro Cubillas, Pablo Vinuesa, María Luisa Tabche and Alejandro García-de los Santos (2013). Phylogenomic analysis of Cation Diffusion Facilitator proteins uncovers Ni2+/Co2+ transporters. Metallomics 5(12):1634-1643. PubMED PMID: 24077251.
  • Contreras-Moreira, B., Sachman-Ruiz, B., Figueroa-Palacios, I., and Vinuesa, P*. (2009). primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucl. Acids Res. 37(Web Server issue):W95-W100. Epub 2009 May 21. (Advance Access published on May 21, 2009;) doi:10.1093/nar/gkp377.
  • Stephen P. Cummings, Prasad Gyaneshwar, Pablo Vinuesa, Mitchell Andrews, David Humphry, Geoffrey N. Elliott, Andrew Nelson, Caroline Orr, Deborah Pettitt, Gopit R. Shah, Scott Santos, Hari. B. Krishnan, David Odee, Fatima M. Moreira, Janet I. Sprent, J. Peter W. Young and Euan K. James* (2009). Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. (2009). Environ. Microbiol. 11(10):2510-2525. (PDF)
  • Miguel E. Rentería, Neha S. Gandhi, Pablo Vinuesa, Erik Helmerhorst, Ricardo L. Mancera (2008). A Comparative Structural Bioinformatics Analysis of the Insulin Receptor Family Ectodomain Based on Phylogenetic Information. PLoS ONE 3(11):e3667. doi:10.1371/journal.pone.0003667 (Open Access)
  • Vinuesa, P*., K. Rojas-Jiménez, B. Contreras-Moreira, S. K. Mahna, B. N. Prasad, H. Moe, S. B. Selvaraju, H. Thierfelder, and D. Werner. 2008. Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent.  Appl. Environ. Microbiol. 74(22):6987-6996 . doi:10.1128/AEM.00875-08 (PDF)
  • C. Sohlenkamp, K. A. Galindo-Lagunas, Z. Guan, P. Vinuesa, S. Robinson, J. Thomas-Oates, C. R. H. Raetz, and O. Geiger. (2007). The lipid lysyl-phosphatidylglycerol is present in membranes of Rhizobium tropici CIAT899 and confers increased resistance to polymyxin B under acidic growth conditions. Molec. Plant-Microbe Interact. 20(11):1421-1430. (PDF)
  • Silva, C, Vinuesa P,Eguiarte LE, Souza V, and Esperanza Martínez-Romero E (2005). Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes. Mol. Ecol. 14:4033-4050. (PDF)
  • Vinuesa P* , Silva C, Werner D, Martínez-Romero E (2005). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol. Phylogenet. Evol. 34(1):29-54. (PDF) NOTE: This paper ranks among the top-10 cited articles of MPE in the past 5 years! Extracted from Scopus (on Wed Jun 9 21:40:36 BST 2010)
  • Vinuesa P*, Silva C, Lorite, M J, Izaguirre-Mayoral, M L, Bedmar, E J, Martínez-Romero E (2005) Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst. Appl. Microbiol. 28:702-716. (PDF)
  • Vinuesa P* , León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A, Pérez-Galdona R, Werner D, Martínez-Romero E (2005). Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae:Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies a and Bradyrhizobiumgenospecies b. Int. J. Syst. Evol. Microbiol. 55:569-575. (PDF)
  • Rojas-Jiménez K, Sohlenkamp C, Geiger O, Martínez-Romero E, Werner D and Vinuesa P* (2005). A putative chloride channel and ornithine-containing membrane lipids of Rhizobium tropici CIAT899 are involved in symbiotic efficiency and acid tolerance. Mol. Plant-Microbe Interact. 18:1175-1185.(PDF)