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Items: 1 to 50 of 182

1.

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome.

Cabello-Yeves PJ, Rodriguez-Valera F.

Microbiome. 2019 Aug 22;7(1):117. doi: 10.1186/s40168-019-0731-5.

2.

Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea.

Kim JG, Kim SJ, Cvirkaite-Krupovic V, Yu WJ, Gwak JH, López-Pérez M, Rodriguez-Valera F, Krupovic M, Cho JC, Rhee SK.

Proc Natl Acad Sci U S A. 2019 Jul 30;116(31):15645-15650. doi: 10.1073/pnas.1905682116. Epub 2019 Jul 16.

PMID:
31311861
3.

Correction to: Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya.

Kim SJ, Kim JG, Lee SH, Park SJ, Gwak JH, Jung MY, Chung WH, Yang EJ, Park J, Jung J, Hahn Y, Cho JC, Madsen EL, Rodriguez-Valera F, Hyun JH, Rhee SK.

Microbiome. 2019 Mar 11;7(1):38. doi: 10.1186/s40168-019-0655-0.

4.

Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya.

Kim SJ, Kim JG, Lee SH, Park SJ, Gwak JH, Jung MY, Chung WH, Yang EJ, Park J, Jung J, Hahn Y, Cho JC, Madsen EL, Rodriguez-Valera F, Hyun JH, Rhee SK.

Microbiome. 2019 Feb 20;7(1):29. doi: 10.1186/s40168-019-0643-4. Erratum in: Microbiome. 2019 Mar 11;7(1):38.

5.

Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.

López-Pérez M, Jayakumar JM, Haro-Moreno JM, Zaragoza-Solas A, Reddi G, Rodriguez-Valera F, Shapiro OH, Alam M, Almagro-Moreno S.

MBio. 2019 Feb 19;10(1). pii: e02852-18. doi: 10.1128/mBio.02852-18.

6.

Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Mizuno CM, Guyomar C, Roux S, Lavigne R, Rodriguez-Valera F, Sullivan MB, Gillet R, Forterre P, Krupovic M.

Nat Commun. 2019 Feb 14;10(1):752. doi: 10.1038/s41467-019-08672-6.

7.

CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans.

Díez-Villaseñor C, Rodriguez-Valera F.

Nat Commun. 2019 Jan 17;10(1):294. doi: 10.1038/s41467-018-08167-w.

8.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

PMID:
30556814
9.

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes.

López-Pérez M, Haro-Moreno JM, de la Torre JR, Rodriguez-Valera F.

Environ Microbiol. 2019 Jun;21(6):1980-1988. doi: 10.1111/1462-2920.14462. Epub 2018 Dec 3.

PMID:
30370610
10.

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean.

Martinez-Hernandez F, Fornas Ò, Lluesma Gomez M, Garcia-Heredia I, Maestre-Carballa L, López-Pérez M, Haro-Moreno JM, Rodriguez-Valera F, Martinez-Garcia M.

ISME J. 2019 Jan;13(1):232-236. doi: 10.1038/s41396-018-0278-7. Epub 2018 Sep 18.

PMID:
30228380
11.

Ecological and genomic features of two widespread freshwater picocyanobacteria.

Cabello-Yeves PJ, Picazo A, Camacho A, Callieri C, Rosselli R, Roda-Garcia JJ, Coutinho FH, Rodriguez-Valera F.

Environ Microbiol. 2018 Oct;20(10):3757-3771. doi: 10.1111/1462-2920.14377. Epub 2018 Oct 2.

PMID:
30117250
12.

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment.

Haro-Moreno JM, López-Pérez M, de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F.

Microbiome. 2018 Jul 10;6(1):128. doi: 10.1186/s40168-018-0513-5.

13.

Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes.

Fernández-Ruiz I, Coutinho FH, Rodriguez-Valera F.

Front Microbiol. 2018 May 18;9:1033. doi: 10.3389/fmicb.2018.01033. eCollection 2018.

14.

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, Reinhardt R, Berman-Frank I, Rodriguez-Valera F, Hess WR.

ISME J. 2018 Apr;12(4):981-996. doi: 10.1038/s41396-017-0034-4. Epub 2018 Jan 15.

15.

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.

Carda-Diéguez M, Ghai R, Rodríguez-Valera F, Amaro C.

Microbiome. 2017 Dec 21;5(1):162. doi: 10.1186/s40168-017-0376-1.

16.

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling.

Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R.

ISME J. 2018 Mar;12(3):655-668. doi: 10.1038/s41396-017-0009-5. Epub 2017 Dec 5.

17.

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs.

Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F.

Front Microbiol. 2017 Nov 2;8:2131. doi: 10.3389/fmicb.2017.02131. eCollection 2017.

18.

Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal.

Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e02132-17. doi: 10.1128/AEM.02132-17. Print 2018 Jan 1.

19.

Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach.

Shevchenko V, Mager T, Kovalev K, Polovinkin V, Alekseev A, Juettner J, Chizhov I, Bamann C, Vavourakis C, Ghai R, Gushchin I, Borshchevskiy V, Rogachev A, Melnikov I, Popov A, Balandin T, Rodriguez-Valera F, Manstein DJ, Bueldt G, Bamberg E, Gordeliy V.

Sci Adv. 2017 Sep 22;3(9):e1603187. doi: 10.1126/sciadv.1603187. eCollection 2017 Sep.

20.

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters.

López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F.

PLoS Genet. 2017 Sep 25;13(9):e1007018. doi: 10.1371/journal.pgen.1007018. eCollection 2017 Sep.

21.

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs.

Cabello-Yeves PJ, Haro-Moreno JM, Martin-Cuadrado AB, Ghai R, Picazo A, Camacho A, Rodriguez-Valera F.

Front Microbiol. 2017 Jun 21;8:1151. doi: 10.3389/fmicb.2017.01151. eCollection 2017.

22.

Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface.

Bolhuis H, Martín-Cuadrado AB, Rosselli R, Pašić L, Rodriguez-Valera F.

BMC Genomics. 2017 Jul 3;18(1):510. doi: 10.1186/s12864-017-3892-2.

23.

Single-virus genomics reveals hidden cosmopolitan and abundant viruses.

Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M.

Nat Commun. 2017 Jun 23;8:15892. doi: 10.1038/ncomms15892.

24.

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

Melnikov I, Polovinkin V, Kovalev K, Gushchin I, Shevtsov M, Shevchenko V, Mishin A, Alekseev A, Rodriguez-Valera F, Borshchevskiy V, Cherezov V, Leonard GA, Gordeliy V, Popov A.

Sci Adv. 2017 May 12;3(5):e1602952. doi: 10.1126/sciadv.1602952. eCollection 2017 May.

25.

New insights into marine group III Euryarchaeota, from dark to light.

Haro-Moreno JM, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado AB.

ISME J. 2017 May;11(5):1102-1117. doi: 10.1038/ismej.2016.188. Epub 2017 Jan 13.

26.

Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.

López-Pérez M, Ramon-Marco N, Rodriguez-Valera F.

BMC Genomics. 2017 Jan 5;18(1):36. doi: 10.1186/s12864-016-3461-0.

27.

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

Ghai R, Mehrshad M, Mizuno CM, Rodriguez-Valera F.

ISME J. 2017 Jan;11(1):304-308. doi: 10.1038/ismej.2016.110. Epub 2016 Aug 9.

28.

Genomes of Abundant and Widespread Viruses from the Deep Ocean.

Mizuno CM, Ghai R, Saghaï A, López-García P, Rodriguez-Valera F.

MBio. 2016 Jul 26;7(4). pii: e00805-16. doi: 10.1128/mBio.00805-16.

29.

Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea.

López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F.

Front Microbiol. 2016 Jun 22;7:996. doi: 10.3389/fmicb.2016.00996. eCollection 2016.

30.

The discovery of CRISPR in archaea and bacteria.

Mojica FJ, Rodriguez-Valera F.

FEBS J. 2016 Sep;283(17):3162-9. doi: 10.1111/febs.13766. Epub 2016 Jun 15. Review.

31.

Pangenome Evolution in the Marine Bacterium Alteromonas.

López-Pérez M, Rodriguez-Valera F.

Genome Biol Evol. 2016 Jun 3;8(5):1556-70. doi: 10.1093/gbe/evw098.

32.

Thalassospira australica sp. nov. isolated from sea water.

Ivanova EP, López-Pérez M, Webb HK, Ng HJ, Dang TH, Zhukova NV, Mikhailov VV, Crawford RJ, Rodriguez-Valera F.

Antonie Van Leeuwenhoek. 2016 Aug;109(8):1091-100. doi: 10.1007/s10482-016-0710-9. Epub 2016 May 14.

PMID:
27180097
33.

Flexible genomic islands as drivers of genome evolution.

Rodriguez-Valera F, Martin-Cuadrado AB, López-Pérez M.

Curr Opin Microbiol. 2016 Jun;31:154-160. doi: 10.1016/j.mib.2016.03.014. Epub 2016 Apr 14. Review.

PMID:
27085300
34.

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.

Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G.

Front Microbiol. 2016 Feb 25;7:211. doi: 10.3389/fmicb.2016.00211. eCollection 2016.

35.

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea.

Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F.

Appl Environ Microbiol. 2016 Jan 4;82(5):1599-1612. doi: 10.1128/AEM.03381-15.

36.

Marine Group II Archaea, potentially important players in the global ocean carbon cycle.

Zhang CL, Xie W, Martin-Cuadrado AB, Rodriguez-Valera F.

Front Microbiol. 2015 Oct 13;6:1108. doi: 10.3389/fmicb.2015.01108. eCollection 2015. Review.

37.

Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern.

León MJ, Rodríguez-Olmos A, Sánchez-Porro C, López-Pérez M, Rodríguez-Valera F, Soliveri J, Ventosa A, Copa-Patiño JL.

Int J Syst Evol Microbiol. 2015 Dec;65(12):4638-43.

PMID:
26394793
38.

Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi.

Martin-Cuadrado AB, Pašić L, Rodriguez-Valera F.

BMC Genomics. 2015 Aug 13;16:603. doi: 10.1186/s12864-015-1794-8.

39.

Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone.

Kimes NE, López-Pérez M, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, Peix A, Rodriguez-Valera F, Velázquez E.

Syst Appl Microbiol. 2015 Jul;38(5):293-9. doi: 10.1016/j.syapm.2015.05.003. Epub 2015 May 29.

PMID:
26078205
40.

Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla).

Carda-Diéguez M, Mizuno CM, Ghai R, Rodriguez-Valera F, Amaro C.

Front Microbiol. 2015 Jan 29;6:3. doi: 10.3389/fmicb.2015.00003. eCollection 2015.

41.

Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.

Mizuno CM, Rodriguez-Valera F, Ghai R.

MBio. 2015 Feb 10;6(1). pii: e02083-14. doi: 10.1128/mBio.02083-14.

42.

Correction for López-Pérez et al., Genome Sequence of "Thalassospira australica" NP3b2T Isolated from St. Kilda Beach, Tasman Sea.

López-Pérez M, Rodriguez-Valera F, Webb HK, Crawford RJ, Ivanova EP.

Genome Announc. 2015 Jan 22;3(1). pii: e01453-14. doi: 10.1128/genomeA.01453-14. No abstract available.

43.

A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum.

Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F.

ISME J. 2015 Jul;9(7):1619-34. doi: 10.1038/ismej.2014.249. Epub 2014 Dec 23.

44.

Genome Sequence of "Thalassospira australica" NP3b2T Isolated from St. Kilda Beach, Tasman Sea.

López-Pérez M, Rodriguez-Valera F, Webb HK, Crawford RJ, Ivanova EP.

Genome Announc. 2014 Nov 13;2(6). pii: e01139-14. doi: 10.1128/genomeA.01139-14. Erratum in: Genome Announc. 2015 Jan 22;3(1):.

45.

Metagenomics of the mucosal microbiota of European eels.

Carda-Diéguez M, Ghai R, Rodriguez-Valera F, Amaro C.

Genome Announc. 2014 Nov 6;2(6). pii: e01132-14. doi: 10.1128/genomeA.01132-14.

46.

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.

Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F.

Mol Ecol. 2014 Dec;23(24):6073-90. doi: 10.1111/mec.12985. Epub 2014 Nov 21.

PMID:
25355242
47.

RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages.

Kimes NE, López-Pérez M, Ausó E, Ghai R, Rodriguez-Valera F.

BMC Genomics. 2014 Oct 26;15:938. doi: 10.1186/1471-2164-15-938.

48.

Metagenomics of ancient fermentation pits used for the production of chinese strong-aroma liquor.

Guo MY, Huo DQ, Ghai R, Rodriguez-Valera F, Shen CH, Zhang N, Zhang SY, Hou CJ.

Genome Announc. 2014 Oct 23;2(5). pii: e01045-14. doi: 10.1128/genomeA.01045-14.

49.

Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov.

Ivanova EP, López-Pérez M, Zabalos M, Nguyen SH, Webb HK, Ryan J, Lagutin K, Vyssotski M, Crawford RJ, Rodriguez-Valera F.

Antonie Van Leeuwenhoek. 2015 Jan;107(1):119-32. doi: 10.1007/s10482-014-0309-y. Epub 2014 Oct 19.

PMID:
25326795
50.

The Santa Pola saltern as a model for studying the microbiota of hypersaline environments.

Ventosa A, Fernández AB, León MJ, Sánchez-Porro C, Rodriguez-Valera F.

Extremophiles. 2014 Sep;18(5):811-24. doi: 10.1007/s00792-014-0681-6. Epub 2014 Aug 17. Review.

PMID:
25129545

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