InGEMICS-CM
MICROBIAL ENGINEERING,
HEALTH AND QUALITY OF LIFE
S2017/BMD-3691

Publications in 2018:

• de Lorenzo, V., y Schmidt, M. (2018) Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol 40: 170-180. doi: 10.1016/j.nbt.2017.05.001.
• Aparicio, T., de Lorenzo, V., y Martinez-Garcia, E. (2018) CRISPR/Cas9-based counterselection boosts recombineering efficiency in Pseudomonas putida. Biotechnol J 13: e1700161. doi: 10.1002/biot.201700161.
• Ricaurte, D.E., Martinez-Garcia, E., Nyerges, A., Pal, C., de Lorenzo, V., y Aparicio, T. (2018) A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. Microb Biotechnol 11: 176-188. doi: 10.1111/1751-7915.12846.
• Freitas, A.R., Tedim, A.P., Novais, C., Coque, T.M., y Peixe, L. (2018) Distribution of putative virulence markers in Enterococcus faecium: towards a safety profile review. J Antimicrob Chemother 73: 306-319. doi: 10.1093/jac/dkx387.
• Freitas, A.R., Novais, C., Duarte, B., Pereira, A.P., Coque, T.M., y Peixe, L. (2018) High rates of colonisation by ampicillin-resistant enterococci in residents of long-term care facilities in Porto, Portugal. Int J Antimicrob Agents 51: 503-507. doi: 10.1016/j.ijantimicag.2017.11.007.
• Gil-Bona, A., Amador-Garcia, A., Gil, C., y Monteoliva, L. (2018) The external face of Candida albicans: A proteomic view of the cell surface and the extracellular environment. J Proteomics 180: 70-79. doi: 10.1016/j.jprot.2017.12.002.
• Alcalde-Rico, M., y Martinez, J.L. (2018) Methods for measuring the production of quorum sensing signal molecules. Methods Mol Biol 1736: 1-15. doi: 10.1007/978-1-4939-7638-6_1.
• Leonardi, I., Li, X., Semon, A., Li, D., Doron, I., Putzel, G., Bar, A., Prieto, D., Rescigno, M., McGovern, D.P.B., Pla, J., y Iliev, I.D. (2018) CX3CR1(+) mononuclear phagocytes control immunity to intestinal fungi. Science 359: 232-236. doi: 10.1126/science.aao1503.
• Lanza, V.F., Baquero, F., Martinez, J.L., Ramos-Ruiz, R., Gonzalez-Zorn, B., Andremont, A., Sanchez-Valenzuela, A., Ehrlich, S.D., Kennedy, S., Ruppe, E., van Schaik, W., Willems, R.J., de la Cruz, F., y Coque, T.M. (2018) In-depth resistome analysis by targeted metagenomics. Microbiome 6: 11. doi: 10.1186/s40168-017-0387-y.
• Martinez, J.L. (2018) Ecology and evolution of chromosomal gene transfer between environmental microorganisms and pathogens. Microbiol Spectr 6. doi: 10.1128/microbiolspec.MTBP-0006-2016.
• Nikel, P.I., y de Lorenzo, V. (2018) Assessing carbon source-dependent phenotypic variability in Pseudomonas putida. Methods Mol Biol 1745: 287-301. doi: 10.1007/978-1-4939-7680-5_16.
• de Lorenzo, V. (2018) Environmental microbiology to the rescue of planet earth. Environ Microbiol doi: 10.1111/1462-2920.14105.
• de Lorenzo, V., Prather, K.L., Chen, G.Q., O'Day, E., von Kameke, C., Oyarzun, D.A., Hosta-Rigau, L., Alsafar, H., Cao, C., Ji, W., Okano, H., Roberts, R.J., Ronaghi, M., Yeung, K., Zhang, F., y Lee, S.Y. (2018) The power of synthetic biology for bioproduction, remediation and pollution control: The UN's Sustainable Development Goals will inevitably require the application of molecular biology and biotechnology on a global scale. EMBO Rep 19. doi: 10.15252/embr.201745658.
• Sanchez, M.B., y Martinez, J.L. (2018) Overexpression of the efflux pumps SmeVWX and SmeDEF is a major cause of resistance to co-trimoxazole in Stenotrophomonas maltophilia. Antimicrob Agents Chemother 62. doi: 10.1128/aac.00301-18.
• Baquero, F., y Gutierrez-Fuentes, J.A. (2018) Sciences unite in Spain to promote research for advancing society. Nature 556: 31. doi: 10.1038/d41586-018-04052-0.
• Baro, B., Jativa, S., Calabria, I., Vinaixa, J., Bech-Serra, J.J., de LaTorre, C., Rodrigues, J., Hernaez, M.L., Gil, C., Barcelo-Batllori, S., Larsen, M.R., y Queralt, E. (2018) SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast. Gigascience 7. doi: 10.1093/gigascience/giy047.
• Mingo, J., Rodriguez-Escudero, I., Luna, S., Fernandez-Acero, T., Amo, L., Jonasson, A.R., Zori, R.T., Lopez, J.I., Molina, M., Cid, V.J., y Pulido, R. (2018) A pathogenic role for germline PTEN variants which accumulate into the nucleus. Eur J Hum Genet doi: 10.1038/s41431-018-0155-x.
• Svenningsen, N.B., Martinez-Garcia, E., Nicolaisen, M.H., de Lorenzo, V., y Nybroe, O. (2018) The biofilm matrix polysaccharides cellulose and alginate both protect Pseudomonas putida mt-2 against reactive oxygen species generated under matric stress and copper exposure. Microbiology 164: 883-888. doi: 10.1099/mic.0.000667.
• Martinez-Garcia, L., Gonzalez-Alba, J.M., Baquero, F., Canton, R., y Galan, J.C. (2018) Ceftazidime is the key diversification and selection driver of VIM-type carbapenemases. MBio 9. doi: 10.1128/mBio.02109-17.
• Zuniga, A., Fuente, F., Federici, F., Lionne, C., Bonnet, J., de Lorenzo, V., y Gonzalez, B. (2018) An engineered device for indoleacetic acid production under quorum sensing signals enables Cupriavidus pinatubonensis JMP134 to stimulate plant growth. ACS Synth Biol 7: 1519-1527. doi: 10.1021/acssynbio.8b00002.
• Goni-Moreno, A., y de Lorenzo, V. (2018) Bio-algorithmic workflows for standardized synthetic biology constructs. Methods Mol Biol 1772: 363-372. doi: 10.1007/978-1-4939-7795-6_20.
• Sanchez-Pascuala, A., Nikel, P.I., y de Lorenzo, V. (2018) Re-factoring glycolytic genes for targeted engineering of catabolism in Gram-negative bacteria. Methods Mol Biol 1772: 3-24. doi: 10.1007/978-1-4939-7795-6_1.
• Nikel, P.I., y de Lorenzo, V. (2018) Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng doi: 10.1016/j.ymben.2018.05.005.
• Rodriguez-Escudero, I., Fernandez-Acero, T., Cid, V.J., y Molina, M. (2018) Heterologous mammalian Akt disrupts plasma membrane homeostasis by taking over TORC2 signaling in Saccharomyces cerevisiae. Sci Rep 8: 7732. doi: 10.1038/s41598-018-25717-w.
• Morales-Menchen, A., Navarro-Garcia, F., Guirao-Abad, J.P., Roman, E., Prieto, D., Coman, I.V., Pla, J., y Alonso-Monge, R. (2018) Non-canonical activities of Hog1 control sensitivity of Candida albicans to killer toxins from Debaryomyces hansenii. Front Cell Infect Microbiol 8: 135. doi: 10.3389/fcimb.2018.00135.
• O'Day, E., Hosta-Rigau, L., Oyarzun, D.A., Okano, H., de Lorenzo, V., von Kameke, C., Alsafar, H., Cao, C., Chen, G.Q., Ji, W., Roberts, R.J., Ronaghi, M., Yeung, K., Zhang, F., y Lee, S.Y. (2018) Are we there yet? How and when specific biotechnologies will improve human health. Biotechnol J doi: 10.1002/biot.201800195.
• Dvorak, P., y de Lorenzo, V. (2018) Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng 48: 94-108. doi: 10.1016/j.ymben.2018.05.019.
• Marin, E., Haesaert, A., Padilla, L., Adan, J., Hernaez, M.L., Monteoliva, L., y Gil, C. (2018) Unraveling Gardnerella vaginalis surface proteins using cell shaving proteomics. Front Microbiol 9: 975. doi: 10.3389/fmicb.2018.00975.
• Oravcova, V., Peixe, L., Coque, T.M., Novais, C., Francia, M.V., Literak, I., y Freitas, A.R. (2018) Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids. Environ Int 118: 125-133. doi: 10.1016/j.envint.2018.05.039.
• Roman, E., Huertas, B., Prieto, D., Diez-Orejas, R., y Pla, J. (2018) TUP1-mediated filamentation in Candida albicans leads to inability to colonize the mouse gut. Future Microbiol 13: 857-867. doi: 10.2217/fmb-2018-0012.
• Narciso-da-Rocha, C., Rocha, J., Vaz-Moreira, I., Lira, F., Tamames, J., Henriques, I., Martinez, J.L., y Manaia, C.M. (2018) Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant. Environ Int 118: 179-188. doi: 10.1016/j.envint.2018.05.040.
• Valderrama, M.J., Gonzalez-Zorn, B., de Pablo, P.C., Diez-Orejas, R., Fernandez-Acero, T., Gil-Serna, J., de Juan, L., Martin, H., Molina, M., Navarro-Garcia, F., Patino, B., Pla, J., Prieto, D., Rodriguez, C., Roman, E., Sanz-Santamaria, A.B., de Siloniz, M.I., Suarez, M., Vazquez, C., y Cid, V.J. (2018) Educating in antimicrobial resistance awareness: adaptation of the Small World Initiative program to service-learning. FEMS Microbiol Lett doi: 10.1093/femsle/fny161.
• Hernandez-Gonzalez, M., Bravo-Plaza, I., Pinar, M., de Los Rios, V., Arst, H.N., Jr., y Peñalva, M.A. (2018) Endocytic recycling via the TGN underlies the polarized hyphal mode of life. PLoS Genet 14: e1007291. doi: 10.1371/journal.pgen.1007291.
• Pantazopoulou, A., Galmarini, C.M., y Peñalva, M.A. (2018) Molecular basis of resistance to the microtubule-depolymerizing antitumor compound plocabulin. Sci Rep 8: 8616. doi: 10.1038/s41598-018-26736-3.
• Clemente, L.F., Hernaez, M.L., Ramos-Fernandez, A., Ligero, G., Gil, C., Corrales, F.J., y Marcilla, M. (2018) Identification of the missing protein hyaluronan synthase 1 in human mesenchymal stem cells derived from adipose tissue or umbilical cord. J Proteome Res. doi: 10.1021/acs.jproteome.8b00384.
• Hernandez-Gonzalez, M., Pantazopoulou, A., Spanoudakis, D., Seegers, C.L.C., y Peñalva, M.A. (2018) Genetic dissection of the secretory route followed by a fungal extracellular glycosyl hydrolase. Mol Microbiol. doi: 10.1111/mmi.14073.
• Novais, C., Campos, J., Freitas, A.R., Barros, M., Silveira, E., Coque, T.M., Antunes, P., y Peixe, L. (2018) Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal. Sci Total Environ 625: 1102-1112. doi: 10.1016/j.scitotenv.2017.12.265.
• Russo, N., Caggia, C., Pino, A., Coque, T.M., Arioli, S., y Randazzo, C.L. (2018) Enterococcus spp. in Ragusano PDO and Pecorino Siciliano cheese types: A snapshot of their antibiotic resistance distribution. Food Chem Toxicol 120: 277-286. doi: 10.1016/j.fct.2018.07.023.
• Chavarria, M., y de Lorenzo, V. (2018) The imbroglio of the physiological Cra effector clarified at last. Mol Microbiol 109: 273-277. doi: 10.1111/mmi.14080.
• Angers-Loustau, A., Petrillo, M., Bengtsson-Palme, J., Berendonk, T., Blais, B., Chan, K.G., Coque, T.M., Hammer, P., Hess, S., Kagkli, D.M., Krumbiegel, C., Lanza, V.F., Madec, J.Y., Naas, T., O'Grady, J., Paracchini, V., Rossen, J.W.A., Ruppe, E., Vamathevan, J., Venturi, V., y Van den Eede, G. (2018) The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Res 7: 459. doi: 10.12688/f1000research.14509.1.
• Torres, C., Alonso, C.A., Ruiz-Ripa, L., Leon-Sampedro, R., Del Campo, R., y Coque, T.M. (2018) Antimicrobial resistance in Enterococcus spp. of animal origin. Microbiol Spectr 6. doi: 10.1128/microbiolspec.ARBA-0032-2018.
• Viegas, S.C., Apura, P., Martinez-Garcia, E., de Lorenzo, V., y Arraiano, C.M. (2018) Modulating heterologous gene expression with portable mRNA-stabilizing 5'-UTR sequences. ACS Synth Biol 7: 2177-2188. doi: 10.1021/acssynbio.8b00191.
• Sanz-Garcia, F., Hernando-Amado, S., y Martinez, J.L. (2018) Mutation-driven evolution of Pseudomonas aeruginosa in the presence of either ceftazidime or ceftazidime-avibactam. Antimicrob Agents Chemother 62. doi: 10.1128/aac.01379-18.
• de Lorenzo, V. (2018) Evolutionary tinkering vs. rational engineering in the times of synthetic biology. Life Sci Soc Policy 14: 18. doi: 10.1186/s40504-018-0086-x.
• Blanco, P., Corona, F., y Martinez, J.L. (2018) Biolog phenotype microarray: a tool for the identification of multidrug resistance efflux pumps inducers. Antimicrob Agents Chemother. doi: 10.1128/aac.01263-18.
• Espeso, D.R., Martinez-Garcia, E., Carpio, A., y de Lorenzo, V. (2018) Dynamics of Pseudomonas putida biofilms in an upscale experimental framework. J Ind Microbiol Biotechnol 45: 899-911. doi: 10.1007/s10295-018-2070-0.
• Akkaya, O., Perez-Pantoja, D.R., Calles, B., Nikel, P.I., y de Lorenzo, V. (2018) The metabolic redox regime of Pseudomonas putida tunes its evolvability toward novel xenobiotic substrates. MBio 9. doi: 10.1128/mBio.01512-18.
• Baquero, F. (2018) Causality in biological transmission: Forces and energies. Microbiol Spectr 6. doi: 10.1128/microbiolspec.MTBP-0018-2016.
• Blanco, P., Sanz-Garcia, F., Hernando-Amado, S., Martinez, J.L., y Alcalde-Rico, M. (2018) The development of efflux pump inhibitors to treat Gram-negative infections. Expert Opin Drug Discov: 1-13. doi: 10.1080/17460441.2018.1514386.
• Perez-Pantoja, D., Kim, J., Platero, R., y de Lorenzo, V. (2018) The interplay of EIIA(Ntr) with C-source regulation of the Pu promoter of Pseudomonas putida mt-2. Environ Microbiol. doi: 10.1111/1462-2920.14410.
• Bernardini, A., Cuesta, T., Tomas, A., Bengoechea, J.A., Martinez, J.L., y Sanchez, M.B. (2018) The intrinsic resistome of Klebsiella pneumoniae. Int J Antimicrob Agents. doi: 10.1016/j.ijantimicag.2018.09.012.
• Ruppé, E., Ghozlane, A., Tap, J., Pons, N., Alvarez, A.-S., Maziers, N., Cuesta, T., Hernando-Amado, S., Clares, I., Martínez, J.L., Coque, T.M., Baquero, F., et al. (2018) Prediction of the intestinal resistome by a three-dimensional structure-based method. Nature Microbiology. doi: 10.1038/s41564-018-0292-6.

In bold, members of InGemics groups.