Publications in Peer Reviewed Scientific Journals

Publications in peer reviewed scientific journals:

1. Bottacini, F., Milani, C., Turroni, F., Sánchez, B., Foroni, E., Duranti, S., Serafini, F., Viappiani, A., Strati, F., Ferrarini, A., Delledonne, M., Henrissat, B., Coutinho, P., Fitzgerald, G.F., Margolles, A., van Sinderen, D., and Ventura, M. 2012. Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PloS One (in press). (IF: 4.3). 2. Alvarez-Martin, P., O'Connell-Motherway, M., Turroni, F., Foroni, E., Ventura, M., and van Sinderen, D. 2012. A two-component regulatory system controls serpin expression in Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. (in press). (IF: 3.778). 3. Ventura, M., Turroni, F., O’Connell Motherway, M., MacSharry, J., and van Sinderen, D. 2012. Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria. Trends in Microbiology (in press). (IF: 7.910). 4. Gueimonde, M., Bottacini, F., van Sinderen, D., Ventura, M., Margolles, A., and Sanchez, B. 2012. Genome sequence of the human breast-milk isolate Parascardovia denticolens IPLA 20019. J. Bacteriol (in press). (IF: 3.993). 5. Serafini, F., Turroni, F., Guglielmetti, S., Gioiosa, L., Foroni, E., Sanghez, V., Bartolomucci, A., O'Connell Motherway, M., Palanza, P., van Sinderen, D., and Ventura M. 2012. An efficient and reproducible method for transformation of genetically recalcitrant bifidobacteria. FEMS Microbiol. Lett. 333(2):146-52. (IF: 2.04). 6. Turroni, F., Strati, F., Foroni, E., Serafini, F., Duranti, S., van Sinderen D., and Ventura, M. 2012. Analysis of the predicted carbohydrate transport systems encoded by Bifidobacterium bifidum PRL2010. Appl. Environ. Microbiol. (in press). (IF: 3.778). 7. Turroni, F., Peano, C., Pass, D., Foroni, E., Severgnini, M., Claesson, M., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., Gueimonde, M., Margolles, A., De Bellis, G., O’Toole, P.W., van Sinderen, D., Marchesi, J., and Ventura, M. 2012. Diversity of bifidobacteria within the infant gut microbiota. PloS One (in press). (IF: 4.3). 8. González-Rodríguez, I., Sanchez, B., Ruiz, L., Turroni, F., Ventura, M., Ruas-Madiedo, P., Gueimonde, M., and Margolles, A. 2012. Role of extracellular transaldolase from Bifidobacterium bifidum in mucin adhesion and aggregation. Appl. Environ. Microbiol. (in press). (IF: 3.778). 9. Ruiz, L., Gueimonde, M., Ruas-Madiedo, P., Ribbera, A., de los Reyes-Gavilan, C., Ventura, M., Margolles, A., and Sanchez, B. 2012. Molecular clues to understand the aerotolerant phenotype of Bifidobacterium animalis subsp. lactis. Appl. Environ. Microbiol. 78(3):644-50. (IF: 3.778). 10. Ventura, M., Turroni, F., and van Sinderen, D. 2012. Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut. Bioengineered Bugs. 1;3(2). 11. Turroni, F., Foroni, E., Montanini, B., Viappiani, A., Strati, F., Duranti, F., Ferrarini, A., Delledonne, M., van Sinderen D., and Ventura M. 2011. Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative Real-Time PCR. Appl. Environ. Microbiol. 77(24):8578- 87. (IF: 3.778). 12. Bottacini, F., Dal Bello, F., Turroni, F., Milani, C., Duranti, S., Foroni, E., Viappiani, A., Strati, F., Mora, D., van Sinderen, D., and Ventura, M. 2011. Complete genome sequence of Bifidobacterium animalis subsp. lactis BLC1. J. Bacteriol. 193(22):6387-8. (IF: 3.993). 13. Turroni, F., Foroni, E., Serafini, F., Viappiani, A., Montanini, B., Bottacini, F., Ferrarini, A., Bacchini, P.L., Rota, C., Delledonne, M., Ottonello, S., van Sinderen, D. and Ventura, M. 2011. The ability of Bifidobacterium breve to grow on different milk types: exploring metabolism through genome analyses. Appl. Environ. Microbiol. 77(20):7408-17. (IF: 3.778). 14. Foroni, E., Serafini, F., Amidani, D., Turroni, F., He, F., Bottacini, F., O’Connell Motherway, M., Viappiani, A., Zhang, Z., Rivetti, C., van Sinderen, D. and Ventura, M. 2011. Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium. Microbial Cell Factories 10 Suppl 1:S16. (IF. 4.54). 15. O'Connell Motherway, M., Zomer, A., Leahy, S., Reunanen, J., Bottacini, F., Claesson, M.J., O’Brien, F., O’Flynn, K., Casey, P.C., Moreno-Munoz, J., Kearney, B., Houston, B., O’Mahony, C., Higgins, D.G., Shanahan F., Palva A., de Vos,W., Fitzgerald, G.F., Ventura, M., O’Toole, P.O., and van Sinderen D. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 108(27):11217-22 (IF: 9.432). 16. Turroni, F., Milani, C., van Sinderen, D., and Ventura, M. 2011. Genetic strategies for mucin metabolism in Bifidobacterium bifidum PRL2010: an example of possible human- microbe co-evolution. Gut Microbes 2(3):183-9. (IF: 2). 17. Serafini, F., Bottacini, F., Viappiani, A., Baruffini, E., Turroni, F., Foroni, E., Lodi, T., van Sinderen, D., and Ventura, M. 2011. Investigation of mupirocin susceptibility in bifidobacteria: physiological and genetic insights. Appl. Environ. Microbiol. 77(9):3141-6. (IF: 3.778). 18. Turroni, F., van Sinderen D., Ventura, M. 2011. Genomics and ecological overview of the genus Bifidobacterium. Int. J. Food Microbiol. 149(1):37-44. (IF: 3.143). 19. Cronin M, Ventura M, Fitzgerald GF, van Sinderen D. 2011. Progress in genomics, metabolism and biotechnology of bifidobacteria. Int. J. Food Microbiol. 149(1):4-18. (IF: 3.143). 20. Ventura, M., Sozzi, T., Turroni, F., Matteuzzi, D., and D. van Sinderen. 2011. The impact of bacteriophages on probiotic bacteria and gut microbiota diversity. Genes and Nutrition J., 6(3):205-7. 21. Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., Delledonne, M., Henrissat, B., Coutinho, P., Oggioni, M., Fitzgerald, G.F., Mills, D., Margolles, A., Kelly, D., van Sinderen, D., and Ventura, M. 2010. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 107(45):19514-9. (IF: 9.432). 22. Bottacini, F., Medini, D., Pavesi, A., Turroni, F., Foroni, E., Riley, D., Giubellini, V., Tettelin, H., van Sinderen, D., and Ventura, M. 2010. Comparative genomics of the genus Bifidobacterium. Microbiology 156(Pt 11):3243-54. (IF: 3.025). 23. Canchaya C, Giubellini V, Ventura M, de los Reyes-Gavilán CG, Margolles A. .Mosaic-like sequences containing transposon, phage, and plasmid elements among Listeria monocytogenes plasmids. 2010. Appl. Environ. Microbiol. 76:4851-7. (IF: 3.778). 24. Turroni, F., Foroni, E., O’Connel Motherway M., Bottacini, F., Giubellini, V., Zomer, A., Ferrarini, A., Delledonne, M., Zhang, Z., van Sinderen D., and Ventura M. 2010. Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Appl. Environ. Microbiol. 76(10):3206-19 (IF: 3.778). 25. Ventura, M., Turroni, F., Foroni, E., Duranti, E., Giubellini, V., Bottacini, F., and D. van Sinderen. 2010. Analyses of bifidobacterial prophage-like sequences. Antonie van Leeuwenhoek. 98(1):39-50 (IF: 1.964). 26. Ventura M., Turroni F., Zomer A., Foroni E., Giubellini V., Canchaya C., Bottacini F., Claesson, M.J., Zhang, Z., Mantzourani, M., Mulas L., Ferrarini A., Delledonne M., Henrissat B., Coutinho, P., Oggioni M., Gupta R.S., Beighton D., Fitzgerald G.F., O’Toole, P.W., and van Sinderen D.,. 2009 The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity Plos Genetics 12: e1000785 (IF:8.7) 27. Ventura, M., F. Turroni, G.L. Mendez, E. Foroni, A. Zomer, S. Duranti, V. Giubellini, F. Bottacini, P. Horvath, R. Barrangou, D.A. Sela, D.A. Mills and D. van Sinderen. 2009. Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl. Environ. Microbiol. 75:6929-6936 (IF: 3.778) 28. Turroni F, Marchesi, J.R., Foroni E, Gueimonde, M., Shanahan F, Margolles, A., van Sinderen D, Ventura M. 2009. Microbiomic analysis of the bifidobacterial population in the human distal gut. The ISME J. 3(6):745-51. (IF:5.029) 29. Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, Cagnasso P, Bizzarri B, De'angelis GL, Shanahan F, van Sinderen D, Ventura M. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75(6):1534-45 (IF: 3.778) 30. Ventura, M., O'Flaherty S., Claesson M.J., Turroni F, Klaenhammer T. R., van Sinderen D., and O'Toole P. W. 2009. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nature Microbiol. Rev 7(1):61-71 (IF: 14.959) 31. Ventura, M, Turroni, F., Canchaya, C., Vaughan, E.E., O’Toole, P.W., van Sinderen. D. 2009. Microbial diversity in the human intestine and novel insights from metagenomics. Frontiers in Bioscience 14:3214-21 (IF: 3.60). 32. Turroni, F., van Sinderen. D., Ventura, M. 2009. Bifidobacteria: from ecology to genomics. Frontiers in Bioscience 14:4673-84 (IF: 3.60). 33. Denou, E., Pridmore R.D., Ventura, M., Pittet, A.C., Zwahlen, M.C., Berger, B., Barretto, C., Panoff, J.M., Brussow, H. 2008. The role of prophage for genome diversification within a clonal lineage of Lactobacillus johnsonii. J. Bacteriol. 190(17):5806-13. (IF: 3.993). 34. Mayo, B., van Sinderen D., and Ventura M. 2008. Genome analysis of food grade lactic acid-producing bacteria: from basics to applications. Current Genomics. 9(3):169-83. (IF:0.98, this is a new Journal) 35. Turroni, F, Ribbera, A., Foroni, E., van Sinderen, D., and Ventura, M. 2008. Human gut microbiota and bifidobacteria: from composition to functionality. Antonie van Leeuwenhoek 94(1):35-50 (IF: 1.964). 36. Ventura M, Zomer A, Canchaya C, O'Connell-Motherway M, Kuipers O, Turroni F, Ribbera A, Foroni E, Buist G, Wegmann U, Shearman C, Gasson MJ, Fitzgerald GF, Kok J, van Sinderen D. 2007. Comparative analyses of prophage-like elements present in two Lactococcus lactis strains. Appl. Environ. Microbiol. 73:7771-80 (IF: 3.778). 37. Ventura, M., Canchaya, C., Tauch. A, Chandra G., Chater, K., Fitzgerald, G.F., and van Sinderen, D. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiology and Molecular Biology Reviews 71: 495-548 (IF: 15.864). 38. Ventura, M., O’Connell-Motherway, M., Leahy, S., Fitzgerald, G.F., and van Sinderen D. 2007. From bacterial genome to functionality: case bifidobacteria. Int. J. Food Microbiol. 120;2-12 (IF:2.608). 39. Lindner, J., Canchya, C., Zhang, Z., Neviani, E., Fitzgerald, G.F., van Sinderen, D., and Ventura, M.,. 2007 Exploiting Bifidobacterium genomes: the molecular basis of stress response. Int. J. Food Microbiol.120:13-24 (IF:2.608). 40. Ventura, M., Canchaya, C., Zhang, Z., Fitzgerald, G.F., and D. van Sinderen. 2007. Molecular characterization of the small heat shock-encoding gene, hsp20, from Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 73:4695-703. (IF: 3.778). 41. Wegmann U, O'connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, van Sinderen D, Kok J. 2007. The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363. J. Bacteriol. 189:3256-70. (IF: 3.993). 42. Ventura, M., Canchaya, C., Fitzgerald, G.F., Gupta, R.S., and van Sinderen D. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek, 91:351-372. (IF: 1.964). 43. Ventura, M., C. Canchaya, A. Del Casale, F. Dellaglio, E. Neviani, G. F. Fitzgerald and D. van Sinderen. 2006. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 30:734-59. (IF: 2.662). 44. Mahony, J., Deveau, H., McGrath, S., Ventura, M., Canchaya, C., Moineau, S., Fitzgerald, G.F. and D. van Sinderen. 2006. Sequence and comparative analysis of lactococcal bacteriophages jj50, 712 and P008: evolutionary insights into the 936 phage species. FEMS Microbiol. Lett., 261:253-61. (IF: 2.068). 45. Ventura, M., C. Canchaya, V. Bernini, G.F. Fitzgerald and D. Van Sinderen. 2006. How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators. FEMS Microbiol. Rev. 30:734-759. (IF: 8.691). 46. Ventura, M., C. Canchaya, V. Bernini, E. Altermann, R. Barrangou, S. Mc Grath, M. J. Claesson, Y. Li, S. Leahy, C. D. Walker, R. Zink, E. Neviani, J. Steele, J. Broadbent, T. R. Klaenhammer, G. F. Fitzgerald, P. O’Toole, and D. van Sinderen. 2006. Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius and Lactobacillus casei. Appl. Environ. Microbiol. 72:3131-3146. (IF: 3.778). 47. Ventura, M., C. Canchaya, V. Bernini, A. Del Casale, F. Dellaglio, E. Neviani, G. F. Fitzgerald and D. van Sinderen. 2005. Genetic characterization of hrcA locus in Bifidobacterium breve UCC 2003. Appl. Environ. Microbiol. 71:8998-9007. (IF: 3.778). 48. Ventura, M., Z. Ziding, J.G. Kenny, M. Cronin, C. Canchaya, G. F. Fitzgerald and D. van Sinderen. 2005. The ClgR protein regulates the transcription of the clpP operon in Bifidobacterium breve UCC 2003. J. Bacteriol. 187:8411-8426. (IF: 3.993). 49. Ventura, M., J.H. Lee, C. Canchaya, R. Zink, S. Leahy, J.A. Moreno- Munoz, M. O’Connell-Motherway, D. Higgins, G. F. Fitzgerald, D. J. O’Sullivan and D. van Sinderen. 2005. Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution and phylogenetic analysis. Appl. Environ. Microbiol. 71:8692-8705. (IF: 3.778). 50. Ventura, M, J.G. Kenny, Z. Zhang, G.F. Fitzgerald, and D. van Sinderen. 2005. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology. 151:2861-2872. (IF: 3.139). 51. Ventura, M., G.F. Fitzgerald, and D. van Sinderen. 2005. Genetic and transcriptional organization of the clpC locus in Bifidobacterium breve UCC 2003. Appl. Environ. Microbiol. 71:6282-6291. (IF: 3.778). 52. Ventura, M., R. Zink, G.F. Fitzgerald, and D. van Sinderen. 2005. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and its application in bifidobacterial tracing. Appl. Environ. Microbiol. 71:487-500. (IF: 3.778). 53. Ventura, M., C. Canchaya, R. Zink, G.F. Fitzgerald, and D. van Sinderen. 2004. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional and phylogenetic analysis. Appl. Environ. Microbiol. 70:6197-209. (IF: 3.778). 54. Ventura, M., D. van Sinderen, G.F. Fitzgerald, and R. Zink. 2004. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie van Leeuwenhoek. 86:205- 223 (review). (IF: 1.964). 55. Ventura, M. and H. Brüssow. 2004 Temporal transcription map of the virulent Streptococcus thermophilus bacteriophage Sfi19. Appl. Environ. Microbiol. 70:5041-5046. (IF: 3.778). 56. Masco L., M. Ventura, R. Zink, G. Huys and J. Swings. 2004. Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis comb. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis comb. nov. Int. J. Syst. Evol. Microbiol. 54:1137-43. (IF: 2.662). 57. Ventura M., C. Canchaya, D. van Sinderen, G.F. Fitzgerald, and R. Zink. 2004. Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon, its genetic structure, characterization and phylogenic analysis. Appl. Environ. Microbiol. 70:3110-3121. (IF: 3.778). 58. Ventura M., C. Canchaya, R.D. Pridmore, and H. Brüssow. 2004. The prophages of Lactobacillus johnsonii NCC533: comparative genomics, transcription and microarray analysis. Virology 320:229-242. (IF: 3.525). 59. Ventura M., and R. Zink. 2003. Comparative sequence analysis of the tuf and recA genes, as well as RFLP of the ITS-sequences supplies additional tools to discriminate Bifidobacterium lactis from Bifidobacterium animalis. Appl. Environ. Microbiol. 69:7517- 7522. (IF: 3.778). 60. Ventura M., C. Canchaya, V. Meylan, T.R. Klaenhammer, and R. Zink. 2003. Analysis, characterization and loci of the tuf genes in Lactobacillus and Bifidobacterium and their direct application for species identification. Appl. Environ. Microbiol. 69:6908-6922. (IF: 3.778). 61. Ventura M., C. Canchaya, M. Kleerebezem, W.M. de Vos, R.J. Siezen, and H. Brüssow. 2003. The prophage sequences of Lactobacillus plantarum strain WCFS1. Virology. 316:245-255. (IF: 3.525). 62. Ventura M., C. Canchaya, D. Pridmore, and H. Brüssow. 2003. Integration and distribution of Lactobacillus johnsonii prophages. J. Bacteriol. 185:4603-4608. (IF: 3.993). 63. Blatny J.M., M. Ventura, E.M. Rosenhaven, P.A. Risoen, M. Lunde, H. Brüssow, and I.F. Nes. 2003. Transcriptional and regulatory studies of the genetic elements involved in the lysogenic-lytic commitment and the identification of the Cro-like protein ORF76 of the temperate lactococcal bacteriophage ΦLC3. Mol. Gen. Genomics. 269:487-498. (IF: 2.345). 64. Jankovic I., M. Ventura, V. Meylan, M. Rouvet, and R. Zink. 2003. Contribution of Aggregation Promoting Factor (APF) to maintenance of cell shape in Lactobacillus gasseri 4B2. J. Bacteriol. 185:3288-3296. (IF: 3.993). 65. Ventura M., V. Meylan, and R. Zink. 2003. Identification and tracing of Bifidobacterium species by Enterobacterial Repetitive Intergenic Consensus (ERIC) Sequences. Appl. Environ. Microbiol. 69:4286-4301. (IF: 3.778). 66. Desiere F., S. Lucchini, C. Canchaya, M. Ventura & H. Brüssow. 2002. Comparative genomics of phages and prophages in lactic acid bacteria. Antonie van Leeuwenhoek. 82:73- 91. (review). (IF: 1.964). 67. Ventura M., and R. Zink. 2002. Specific identification and molecular typing analysis of Lactobacillus johnsonii by using PCR-based methods and pulsed-field gel electrophoresis. FEMS Microbiol. Lett. 217:141-154. (IF: 2.068). 68. Ventura M., and R. Zink. 2002. Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis. Appl. Environ. Microbiol. 68:6429-6434. (IF: 3.778). 69. Ventura M., I. Jankovic, D.C. Walker, R.D. Pridmore, and R. Zink. 2002. Identification and characterization of novel surface proteins in Lactobacillus johnsonii and Lactobacillus gasseri. Appl. Environ. Microbiol. 68:6172-6181. (IF: 3.778). 70. Ventura M., A. Bruttin, C. Canchaya, and H. Brüssow. 2002. Transcription analysis of Streptococcus thermophilus in the lysogenic state. Virology. 302:21-31. (IF: 3.525). 71. Ventura M., S. Foley, A. Bruttin, C. Canchaya, and H. Brüssow. 2002. Transcription mapping as a tool in phage genomics: the case of the temperate Streptococcus thermophilus phage Sfi21. Virology. 296:62-76. (IF: 3.525). 72. Ventura M., R. Reniero, and R. Zink. 2001. Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-PCR approach. Appl. Environ. Microbiol. 67:2760-2765. (IF: 3.778). 73. Ventura M., M. Elli, R. Reniero, R. Zink. 2001. Molecular microbial analysis of human intestinal Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiology ecology. 36:113-121. (IF: 3.157). 74. Ventura M., I. A. Casas, L. Morelli and M. L. Callegari. 2000. Rapid Amplified Ribosomal DNA Restriction Analysis (ARDRA) identification of Lactobacillus spp. isolated from fecal and vaginal samples. Systematic And Applied Microbiology. 23:504-509. (IF: 2.037). 75. Ventura M., L. Morelli and M. L. Callegari. 2000. S-layer gene as a molecular marker for identification of Lactobacillus helveticus. FEMS Microbiology Letters 189:275-279, 2000. (IF: 2.068). 76. Ventura M., M.L. Callegari, L. Morelli. 1999. Surface layer variations affecting phage adsorption on seven Lactobacillus helveticus strains. Annali di Microbiologia ed Enzimologia 49:55-63, 1999. (IF: 0.078).