Áurea Simón-Soro, Inmaculada Tomás, Raúl Cabrera-Rubio, Bente Nyvad, Alex Mira Bacterial Geography of the Oral Cavity. J Dent Res. 2013 May 14. [Epub ahead of print]

Sánchez-Porro, C., R. de la Haba, N. Cruz-Hernández, J.M. González, C. Reyes-Guirao, L. Navarro-Sampedro, M. Carballo, A. Ventosa. 2013. Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae. Genome Announcements 1: e0008313.

Tormo-Más MA, Donderis J, García-Caballer M, Alt A, Mir-Sanchis I, Marina A, Penadés JR. 2013. Phage dUTPases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-like Mechanism. Mol Cell 49: 947–958.

Treuner-Lange A, Aguiluz K, van der Does C, Gómez-Santos N, Harms A, Schumacher D, Lenz P, Hoppert M, Kahnt J, Muñoz-Dorado J, and Søgaard-Andersen L. 2013. PomZ, a ParA-like protein, regulates Z-ring formation and cell division in Myxococcus xanthus. Molecular Microbiology 87: 235-253.

Lee CT, Pajuelo D, Llorens A, Chen YH, Leiro JM, Padrós F, Hor LI, Amaro. 2013. MARTX type III of Vibrio vulnificus is a virulence and survival factor. Environ Microbiol 15:419-32.

I. Brunet-Galmés , A.Busquets, A. Peña , M. Gomila, B. Nogales , E. García-Valdés, J. Lalucat, A. Bennasar , R. Bosch. 2013. Complete genome sequence of the naphthalene-degrading bacterium Pseudomonas stutzeri AN10 (CCUG 29243). J Bacteriol 194: 6642-6643.

J.A. Christie-Oleza, I. Brunet-Galmés, J. Lalucat, B. Nogales, R. Bosch. 2013. MiniUIB, a novel minitransposon-based system for stable insertion of foreign DNA into the genomes of Gram-negative and Gram-positive bacteria. Appl Environ Microbiol 79: 1629-1638.

M. Mulet, E. García-Valdés, J. Lalucat. 2013. Phylogenetic affiliation of Pseudomonas putida biovar A and B strains. Res Microbiol 164:351–359.

Gosalbes M. J., Llop S., Vallès Y., Moya A., Ballester F., Francino M. P. 2013. Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clinical and Experimental Allergy (43) 198-211.

Alfonso Benítez-Paez, Alex Mira, Inmaculada Tomás-García. 2013. Analysis of Bacteraemia Following Dental Extractions by 16S rDNA Pyrosequencing. PLoS One. 2013; 8(3): e57782.

Martínez-Abarca F, Martínez-Rodríguez L, López-Contreras JA, Jiménez-Zurdo JI and Toro N. 2013. Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium/Ensifer meliloti Strain GR4. Genome Announcements 1: e00174.

Toro, N and Martinez-Abarca, F. 2013. Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain revelas new varieties. PlosOne 8: e55102.

García-Heredia I., Rodriguez-Valera F., Martin-Cuadrado A-B. 2013. Novel group of Podovirus infecting the marine bacterium Alteromonas macleodii. To Bacgteriophage 3: e24766

Jiménez-Zurdo, J.I., Valverde, C., and Becker, A. 2013. Insights into the noncoding RNome of nitrogen-fixing endosymbiotic alpha-proteobacteria. Mol Plant-Microbe Interact 26, 160-16.

Quiles-Puchalt N, Tormo-Más MA, Campoy S, Alejandro Toledo-Arana A, Monedero V, Lasa I, Novick RP, Christie GE, Penadés JR. 2013. A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria. Nucleic Acid Research (in press).

González, J.M., M.C. Portillo, P. Belda-Ferre, A. Mira. 2012. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. Plos One 7: e29973.

Portillo, M.C., M. Santana, J.M. González. 2012. Presence and potencial role of thermophilic bacteria in temperate terrestrial environments. Naturwissenschaften 99: 43-53.

Zimmermann, J., M.C. Portillo, L. Serrano, J.M. González. 2012. Acidobacteria in freshwater ponds at Doñana National Park, Spain. Microbial Ecology 63: 844-855.

Mir-Sanchis I, Martínez-Rubio R, Martí M, Chen J, Lasa Í, Novick RP, Tormo-Más MÁ, Penadés JR. 2012. Control of Staphylococcus aureus pathogenicity island excision. Mol Microbiol 85: 833-845.

Gómez-Santos N, Treuner-Lange A, Moraleda-Muñoz A, García-Bravo E, García-Hernández R, Martínez-Cayuela M, Pérez J, Søgaard-Andersen L and Muñoz-Dorado J. 2012. A comprehensive set of integrative plasmid vectors for copper inducible gene expression in Myxococcus xanthus. Applied and Environmental Microbiology 78: 2515-2521.

Muñoz-Dorado J, Gómez-Santos N, and Pérez J. 2012. A novel mechanism of bacterial adaptation mediated by copper-dependent RNA polymerase s factors. Transcription 3: 63-67.

Skov, J., Kania, P.W., Holten-Andersen, L.; Fouz, B.; Buchmann, K. 2012. Immunomodulatory effects of dietary β-1,3-glucan from Euglena gracilis in rainbow trout (Oncorhynchus mykiss) immersion vaccinated against Yersinia ruckeri. Fish & Shellfish Immunology 33: 111-120.

Baker-Austin C, Lemm E, Hartnell R, Lowther J, Onley R, Amaro C, Oliver JD, and Lees D. 2012. pilF polymorphism-based real-time PCR to distinguish Vibrio vulnificus strains of human health relevance. Food Microbiol 30: 17-23.

M. Gomila, F. Renom, M.C. Gallegos, M. Garau, D. Guerrero, J.B. Soriano, J. Lalucat. 2012. Identification and diversity of multirresistent Corynebacterium striatum clinical isolates by MALDI-TOF mass spectrometry and by a multigene sequencing approach. BMC Microbiology 15: 52-60.

A. Busquets, A. Peña, M. Gomila, R. Bosch, B. Nogales, E. García-Valdés, J. Lalucat, A. Bennasar. 2012. Genome sequence of Pseudomonas stutzeri strain JM300 (DSM10701) a soil isolate and natural transformation model organism. J Bacteriol 194: 5477-5478.

M. Mulet, M. Gomila, C. Scotta, D. Sánchez, J. Lalucat, E. García-Valdés. 2012. Concordance between whole-cell matrix-assisted laser-desorption/ionization time of flight mass spectrometry and multi locus sequence analysis approaches in the species discrimination in the genus Pseudomonas. System Appl Microbiol 35: 455-464.

Vallès Y., Gosalbes M.J., de Vries L.E., Abellán J.J., Francino, M. P. 2012. Metagenomics and development of the gut microbiota in infants. Clinical Microbiology and Infection 18: 21-26.

Francino MP. 2012. The ecology of bacterial genes and the survival of the new. Int J of Evol Biology. Article ID 394026.

L.D. Alcaraz, P. Belda-Ferre, R. Cabrera, A. Simón, H. Romero , M. Pignatelli, A. Mira. 2012. Identifying a healthy oral microbiome through metagenomics. Clinical Microbiology and Infection 18:54-7.

Raul Cabrera-Rubio, M Carmen Collado, S Salminen, Mira A. 2012. The human milk microbiome changes over lactation time and is shaped by maternal weight and mode of delivery. Am J Clin Nutrition 96: 544-51.

Erik A. Pelve1, Ann-Christin Lindås, Anna Knöppel1, Alex Mira and Rolf Bernander. 2012. Four chromosome replication origins in the archaeon Pyrobaculum calidifontis. Molecular Microbiology 85:986-95.

Nyvad B, Crielaard W, Mira A, Takahashi N, Beighton D. 2012. Dental Caries from a Molecular Microbiological Perspective. Caries Res 47:89-102.

Torres-Cortes, G., Millan, V., Fernandez-Gonzalez, A.J., Aguirre-Garrido, J.F., Ramirez-Saad, H.C., Fernandez-Lopez, M., Toro, N. and Martinez-Abarca, F. 2012. Bacterial community in the rhizosphere of the cactus species Mammillaria carnea during dry and rainy seasons assessed by deep sequencing. Plant and Soil 357: 275-288.

del Val, C., Romero-Zaliz, R., Torres-Quesada, O., Peregrina, A., Toro, N., and Jiménez-Zurdo, J.I. 2012. A survey of sRNA families in α-proteobacteria. RNA Biol. 9, 119-129.

Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Mizuno CM, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. 2012. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol 4: 1360-1374.

Carolina MM, Rodriguez-Valera F, Garcia-Heredia I, Martin-Cuadrado AB, Ghai R. 2012. Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Applied and Environmental Microbiology 79: 688-95.

Gonzaga A, López-Pérez M, Martin-Cuadrado AB, Ghai R, Rodriguez-Valera F. 2012. Genome Announcement. Complete genome of the copiotrophic marine bacterium Alteromonas macleodii type strain ATCC 27126T. J Bacteriol 194: 6998.

López-Pérez M, Gonzaga A, Martin-Cuadrado AB, Onyshchenko O, Ghavidel A, Ghai R, Rodriguez-Valera F. 2012. Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Scientific Reports 2: 696.

Rohit Ghai, Claudia Mella Hernandez, Antonio Picazo, Carolina Megumi Mizuno, Karolina Ininbergs,Beatriz Díez, Ruben Valas, Christopher L. DuPont, Katherine D. McMahon, Antonio Camacho & Francisco Rodriguez-Valera. 2012. Metagenomes of mediterranean coastal lagoons. Scientific Reports : 490.

Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, Mira A, Antón J, Rodriguez-Valera F. 2012. Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS ONE 7: e33802.

Emanuele G. Biondi, Nicolás Toro, Marco Bazzicalupo and Francisco Martínez-Abarca. 2011. Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti. Mob Genet Elements 1: 2-7.

Nuria Gómez-Santos, Juana Pérez, María Celestina Sánchez-Sutil, Aurelio Moraleda-Muñoz, José Muñoz-Dorado. 2011. CorE from Myxococcus xanthus is a copper-dependent RNA polymerase sigma factor. PLoS Genet 7(6): e1002106

Rohit Ghai, Francisco Rodriguez-Valera, Katherine D. McMahon, Danyelle Toyama, Raquel Rinke, Tereza Cristina Souza de Oliveira, José Wagner Garcia, Fernando Pellon de Miranda, Flavio Henrique-Silva. 2011. Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River. PLoS ONE 6(8): e23785.

Rohit Ghai, Katherine D. McMahon, Francisco Rodriguez-Valera. 2011. Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC. Environmental Microbiology Reports 4: 29–35.

de Vries L. E., Valles Y., Agerso Y., Vaishampayan P. A., Kuehl J. V., Christensen H., Barlow M. and Francino, M. P. 2011. The Gut as Reservoir of Antibiotic Resistance: Microbial Diversity of Tetracycline Resistance in Mother and Infant. PloS ONE 6: e21644.

P. Belda-Ferre, L.D. Alcaraz, R. Cabrera, A. Simon-Soro, H. Romero, M. Pignatelli, A. Mira. 2011. The Oral Metagenome in Health and Disease. ISME Journal 6(1):46-56.

P. Belda-Ferre, R. Cabrera-Rubio, A. Moya, A. Mira. 2011. Mining virulence genes by metagenomics. PLoS One 6(10):e24975.

Barrientos-Duran A, Chillon I, Martinez-Abarca F, Toro N. 2011. Exon sequence requirements for excision in vivo of the bacterial group II intron RmInt1. BMC Mol Biol 12:24.

Molina-Sanchez MD, Barrientos-Duran A, Toro N. 2011. Relevance of the branch point adenosine, coordination loop, and 3' exon binding site for in vivo excision of the Sinorhizobium meliloti group II intron RmInt1. J Biol Chem 286: 21154-63.

Torres-Cortes G, Millan V, Ramirez-Saad HC, Nisa-Martinez R, Toro N, Martinez-Abarca F. 2011. Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ Microbiol. 13:1101-14.

Garcia-Rodriguez FM, Barrientos-Duran A, Diaz-Prado V, Fernandez-Lopez M, Toro N. 2011. Use of RmInt1, a group IIB intron lacking the intronencoded protein endonuclease domain, in gene targeting. Appl Environ Microbiol. 77:854-61.

Chillon I, Martinez-Abarca F, Toro N. 2011. Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior. Nucleic Acids Res. 39(3):1095-104.

Claudia Scotta, A. Bennasar, E.R.B. Moore, J. Lalucat, M. Gomila Taxonomic characterisation of ceftazidime-resistant Brevundimonas isolates and description of Brevundimonas faecalis sp. nov. Systematic and Applied Microbiology 34: 408-413.

Magdalena Mulet, Zoyla David, Balbina Nogales, Rafael Bosch, Jorge Lalucat, and Elena Garcia-Valdes. 2011 Pseudomonas Diversity in Crude-Oil-Contaminated Intertidal Sand Samples Obtained after the Prestige Oil Spill. Appl Environ Microbiol 77: 1076-85.

Sanjuan E, Gonzalez-Candelas F, Amaro C. 2011. Polyphyletic origin of Vibrio vulnificus biotype 2 as revealed by sequence-based analysis. Appl Environ Microbiol 77: 688-95.

Roig FJ, Gonzalez-Candelas F, Amaro C. 2011. Domain organization and evolution of multifunctional autoprocessing repeats-in-toxin (MARTX) toxin in Vibrio vulnificus. Appl Environ Microbiol 77: 657-68.

Cohn MT, Kjelgaard P, Frees D, Penades JR, Ingmer H. 2011. Clp-dependent proteolysis of the LexA N-terminal domain in Staphylococcus aureus. Microbiology 157: 677-84.

Guinane CM, Penades JR, Fitzgerald JR. 2011. The role of horizontal gene transfer in Staphylococcus aureus host adaptation. Virulence 2: 241-3.

Ferrer MD, Puchalt Q, Harwich M, Tormo-Mas MA, Campoy S, Barbe J, Lasa I, Novick RP, Christie GE, Penades JR. 2011. RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria. Nucleic Acids Res 39: 5866-78.

Lasa I, Toledo-Arana A, Dobin A, Villanueva M, Ruiz de los Mozos I, Vergara- Irigaray M, Segura V, Fagegaltier D, Penades JR, Valle J, Solano C and Gingeras TR. 2011. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A 108: 20172-7 (2011)

Ubeda C, Tormo-Mas MA, Penades JR, Novick RP. 2011. Structure-function analysis of the SaPIbov1 replication origin in Staphylococcus aureus. Plasmid 67: 183–190.

Portillo, M.C., Villahermosa, D., Corzo, A., Gonzalez, J.M. 2011. Microbial community fingerprints by Differential Display Denaturing Gradient Gel Electrophoresis (DD-DGGE). Appl Environ Microbiol 77: 351-354.

Rohit Ghai, Lejla Pašiæ, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno, Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa & Francisco Rodríguez-Valera. 2011. New Abundant Microbial Groups in Aquatic Hypersaline Environments. Sci Rep 1: 135.

M.A. Tormo-Más, I. Mir, A. Shrestha, S.M. Tallent, S. Campoy, I. Lasa, J. Barbe, R.P. Novick, G.E. Christie & J.R. Penadés. 2010. Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands. Nature 465:779–782.

  Rohit Ghai, Ana-Belén Martin-Cuadrado, Aitor Gonzaga Molto, Inmaculada García Heredia, Raúl Cabrera, Javier Martin, Miguel Verdú, Philippe Deschamps, David Moreira, Purificación López-García, Alex Mira and Francisco Rodriguez-Valera. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. The ISME Journal (2010), 1–13.

Isabel Chillón, Francisco Martínez-Abarca and Nicolás Toro. 2010. Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior. Nucleic Acids Research (2010), 1–10.

Aurelio Moraleda-Munoz, Juana Pérez, Antonio Luis Extremera, and José Muñoz-Dorado. 2010 Expression and Physiological Role of Three Myxococcus xanthus Copper-Dependent P1B-Type ATPases during Bacterial Growth and Development. Applied and Environmental Microbiology, ( 2010), 6077–6084.

Juana Pérez, José Muñoz-Dorado, Alfredo F. Braña, Lawrence J. Shimkets, Laura Sevillano and Ramón I. Santamaría. 2010. Myxococcus xanthus induces actinorhodin overproduction and aerial mycelium formation by Streptomyces coelicolor.. Microbial Biotechnology (2010) ,doi:10.1111/j.1751-7915.2010.00208.x

Aurelio Moraleda-Muñoz, Juana Pérez, Antonio Luis Extremera, and José Muñoz-Dorado. 2010. Differential Regulation of Six Heavy Metal Efflux Systems in the Response of Myxococcus xanthus to Copper. Applied and Environmental Microbiology, (2010), 6069–6076

Aurelio Moraleda-Muñoz, Antonio Luis Extremera, Juana Pérez, and José Muñoz-Dorado. 2010. Complexity of the Myxococcus xanthus copper response: differential regulation of six CBA-type heavy metal efflux systems. Applied and Environmental Microbiology, (2010), doi:10.1128/AEM.00755-10

Alex Mira, Ana B. Martín-Cuadrado, Giuseppe D’Auria, Francisco Rodríguez-Valera. 2010. The bacterial pan-genome: a new paradigm in microbiology. International microbiology (2010) 13:45-57.

Richard P. Novick, Gail E. Christie and José R. Penadés. 2010. The phage-related chromosomal islands of Gram-positive bacteria. Nature Reviews Microbiology (2010) 8, 541-551.

Viana, D., Blanco, J., Tormo-Más, M. Á., Selva, L., Guinane, C. M., Baselga, R., Corpa, J. M., Lasa, Í., Novick, R. P., Fitzgerald, J. R. and Penadés, J. R. 2010. Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPI-carried variants of von Willebrand factor-binding protein. Molecular Microbiology 77:1583–1594.

Roig, F., Gonzalez-Candelas, F.,Amaro, C. 2010. Rtx toxin variability in Vibrio vulnificus biotypes. Environmental microbiology reports, (2010)

Ramón I. Santamaría, José Muñoz-Dorado, Alfredo F Braña, Lawrence J. Shimkets, Laura Sevillano and Juana Pérez. 2010. Predatory Behaviour of Myxococcus xanthus over Streptomyces coelicolor induces overproduction of ACT and aerial mycelium formation.