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Publications of INMARE Project


Peer-reviewed papers and book chapters published/accepted

1. Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol. 2015 6, 1270. doi: 10.3389/fmicb.2015.01270.

2. Placido A, Hai T, Ferrer M, Chernikova TN, Distaso M, Armstrong D, Yakunin AF, Toshchakov SV, Yakimov MM, Kublanov IV, Golyshina OV, Pesole G, Ceci LR, Golyshin PN. Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase. Appl Microbiol Biotechnol. 2015 99(23), 10031-46. doi: 10.1007/s00253-015-6873-x.

3. Moridi N, Corvini PF, Shahgaldian P. Reversible Supramolecular Surface Attachment of Enzyme-Polymer Conjugates for the Design of Biocatalytic Filtration Membranes. Angew Chem Int Ed Engl. 2015 54(49), 14800-4. doi: 10.1002/anie.201507020.


4. Ferrer M, Bargiela R, Martínez-Martínez M, Mir J, Golyshina OV, Golyshin, PN. Biodiversity for Biocatalysis: a review for α/β-hydrolases of the esterase-lipase superfamily as case of study. Biocatal. Biotransform. 2015, 33, 235-249.

5. Bargiela R, Mapelli F, Rojo D, Chouaia B, Tornés J, Borin S, Richter M, Del Pozo MV, Cappello S, Gertler C, Genovese M, Denaro R, Martínez-Martínez M, Fodelianakis S, Amer RA, Bigazzi D, Han X, Chen J, Chernikova TN, Golyshina OV, Mahjoubi M, Jaouanil A, Benzha F, Magagnini M, Hussein E, Al-Horani F, Cherif A, Blaghen M, Abdel-Fattah YR, Kalogerakis N, Barbas C, Malkawi HI, Golyshin PN, Yakimov MM, Daffonchio D, Ferrer M. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sites are strongly linked to temperature. Sci. Rep. 2015, 5, 11651. DOI:10.1038/srep11651

6. Bargiela R, Herbst FA, Martínez-Martínez M, Seifert J, Rojo D, Cappello S, Genovese M, Crisafi F, Denaro R, Chernikova TN, Barbas C, von Bergen M, Yakimov MM, Ferrer M, Golyshin PN. Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation. Proteomics 2015, 15, 3508-3520. DOI: 10.1002/pmic.201400614.

7. Reen, J., Shanahan, R., Cano, R., O’Gara, F., and McGlacken, G.P. A structure activity-relationship study of the bacterial signal molecule HHQ reveals swarming motility inhibition in Bacillus atrophaeus. Organic and Biomolecular Chemistry 2015, 13, 5537-5541. DOI: 10.1039/C5OB00315F

8. Reen, F.J., Gutierrez-Barranquero, J., Adams, C. and O'Gara, F. Emerging Concepts promising New Horizons for Marine Biodiscovery and Synthetic Biology. Marine Drugs 2015, 13(5), 2924-2954.

9. Reen, F.J., Romano, S., Dobson, A.D.W. and O’Gara, F. The sound of silence: activating silent biosynthetic gene clusters in marine organisms. Marine Drugs 2015, 13(8), 4754-83. doi: 10.3390/md13084754.

10. Golyshina OV, Lünsdorf H, Kublanov IV, Goldenstein NI, Hinrichs KU, Golyshin PN. The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales. Int J Syst Evol Microbiol. 2016 66(1):332-40. doi: 10.1099/ijsem.0.000725.

11. Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol. 2016, 9(1),22-34. doi: 10.1111/1751-7915.12309.

12. Correro M. R, Moridi N, Schutzinger H, Sykora S, Ammann EM, Peters EH, Dudal Y, Corvini PF-X, Shahgaldian P. Enzyme Shielding in an Enzyme-thin and Soft Organosilica Layer. Angew. Chem. Int. Ed. 2016, 55, 6285-6289. DOI:10.1002/anie.201600590

13. Correro MR, Takacs M, Sykora S, Corvini PF-X, Shahgaldian P. Enzyme shielding in a biomimetic organosilica layer. RSC Adv. 2016, 6, 89966-89971. DOI: 10.1039/C6RA17775A

14. Chiara M, Placido A, Picardi E, Ceci LR, Horner, Pesole G. A-GAME: a Galaxy suite for Applied Metagenomics. Bioinformatics.(in press)

15. Peña-García C, Martínez-Martínez M, Reyes-Duarte D, Ferrer M. 2016. High throughput screening of esterases, lipases and phospholipases in mutant and metagenomic libraries: a review. Comb. Chem. High Throughput Screen 2016, 19, 605-615.

16. Martínez-Martínez M, Bargiela R, Ferrer M. Metagenomics and the search for industrial enzymes. In: Biotechnology of Microbial Enzymes, 1st Edition, Production, Biocatalysis and Industrial Applications. (G. Brahmachari, ed.; Academic Press; eBook ISBN: 9780128037461), 2016 pp. 167-184.

17. Ramírez-Escudero M, Del Pozo MV, Marín-Navarro J, González B, Golyshin PN, Polaina J, Ferrer M, Sanz-Aparicio J. Structural and functional characterization of a ruminal β-glycosidase defines a novel subfamily of glycosyl hydrolase family 3 with permuted domain topology. J. Biol. Chem. 2016 (in press) pii: jbc.M116.747527. DOI: 10.1074/jbc.M116.747527

18. Martínez-Martínez M, Bargiela R, Coscolín C, Navarro J, Golyshin PN, Ferrer M. Functionalization and modification of hydrocarbon-like molecules guided by metagenomics: esterases and lipases from the α/β-hydrolase fold superfamily and transaminases as study cases. In: “Hydrocarbon and Lipid Microbiology Protocols (Springer Protocols Handbooks; eds. Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales)”. In press.

19. Fernandes P, Enzymes in fish and seafood processing. Front. Bioeng. Biotechnol. 2016, 4, article 59, 1-14. doi: 10.3389/fbioe.2016.00059.

20. Messina E, Sorokin DY, Kublanov IV, Toshchakov S, Lopatina A, Arcadi E, Smedile F, La Spada G, La Cono V Yakimov MM Complete genome sequence of Halanaeroarchaeum sulfurireducens’ M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee. Stand Genomic Sci. 2016, 13, 11-35. doi: 10.1186/s40793-016-0155-9.

21. Thies S, Rausch SC, Kovacic F, et al. Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community. Sci Rep. 2016, 6, 27035. doi:10.1038/srep27035.

22. Classen T, Kovacic F, Lauinger B, Pietruszka J, Jaeger K-E. Screening for enantioselective lipases. In:, “Hydrocarbon and Lipid Microbiology Protocols” (T.J. McGenity, K.N. Timmis, B. Nogales eds.) 2016, Springer Protocols Handbooks, DOI 10.1007/8623_2016_218 in press

23. Katzke N, Knapp A, Loeschcke A, Drepper T, Jaeger K-E Novel Tools for the Functional Expression of Metagenomic DNA. Meth. Mol. Biol. 2016, 1539: DOI 10.1007/978-1-4939-6691-2_10, in press.

24. Yakimov MM, Crisafi F, Messina E, Smedile F, Lopatina A, Denaro R, Pieper DH, Golyshin PN, Giuliano L. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME. Environ Microbiol Rep. 2016 4, 508-19. doi: 10.1111/1758-2229.12424. Epub 2016 Jun 27. PubMed PMID: 27345842.

25. Rodrigues C.J.C., de Carvalho C.C.C.R. (in press). Desenvolvimento de bioprocessos com bactérias marinhas para aplicações industriais sustentáveis (Development of bioprocesses with marine bacteria for sustainable industrial applications), Proceedings of Jornadas do Mar 2016. Escola Naval, Lisbon, 8-11 November 2016.

26. Reen F.J. and F. O’Gara. Metagenomics as a tool for biodiscovery and enhancement of production of bioactives. In “The marine microbiome – an untold resource of biodiversity and biotechnological potential”. Edited by Stahl, L and Creitou, M.S. (Springer). 2016. ISBN 978-3-319-32998-7 ISBN 978-3-319-33000-6 (eBook). DOI 10.1007/978-3-319-33000-6.

27. Flynn, S., Woods, D., Ní Chróinín, M., Mullane, D., Adams, C., Reen, F.J. & F O’Gara. Bile Aspiration; a host factor modulating chronic respiratory infection. In “Bile Acids: Biosynthesis, Metabolic Regulation and Biological Functions”. (Ed. by Johnston, N. & Toohill, R.J). Nova Science Publishers. 2016, ISBN: 978-1-63484-075-0.

28. Reen, F.J., Phelan, J.P., Gallagher, L., Woods, D., Shanahan, R.M., Cano, R., Ó Muimhneacháin, E., McGlacken, G.P. and O’Gara, F. Exploiting interkingdom interactions for the development of small molecule inhibitors of Candida albicans biofilm formation. Antimicrob Agents Chemother. 2016, doi:10.1128/AAC.00190-16

29. Phelan, J.P., Reen F.J., O’Connor, R. and O’Gara, F. (). Bile acids destabilise HIF-1α and promote anti-tumour phenotypes in cancer cell models. BMC Cancer 2016, 16(1), 476. doi: 10.1186/s12885-016-2528-2.

30. Reen, F.J., Flynn, S., Woods, D., Dunphy, N., Ní Chróinín MN, Mullane D, Stick, S., Adams, C. and O’Gara, F. Bile signalling promotes chronic respiratory infections and antibiotic tolerance. Sci Rep. 2016, 6, 29768. doi: 10.1038/srep29768. PMID:27432520

31. Ulluwishewa, D., Wang, L., Pereira, C., Flynn, S., Stick, S., Reen, F.J., Ramsay, J.P. and O’Gara, F. Dissecting the regulation of bile-induced biofilm formation in Staphylococcus aureus. Microbiology 2016, doi: 10.1099/mic.0.000317. [Epub ahead of print].

32. Parages, M.L., Gutiérrez-Barranquero, J.A., Reen, F.J., Dobson, A.D.W. and O’Gara, F. Integrated (Meta)Genomic and Synthetic Biology Approaches to Develop New Biocatalysts. Marine Drugs 2016, 14(3), 62.

33. Romano, S., Fernandez-Guerra, S., Reen, F.J., Glöckner, F.O., Crowley, S.P., O'Sullivan, O, Cotter, P.D., Adams, C., Dobson, A.D.W. and O'Gara F. Comparative Genomic Analysis Reveals A Diverse Repertoire Of Genes Involved In Prokaryote-Eukaryote Interactions Within The Pseudovibrio Genus. Frontiers Microbiol. 2016, 7, 387.

34. Hennessy, E., Adams, C., Reen, F.J. and O’Gara, F. Is There Potential for Repurposing Statins as Novel Antimicrobials? Antimicrob Agents Chemother. 2016, 60(9), 5111-21. doi: 10.1128/AAC.00192-16. PMID: 27324773

35. Buzid, A., Shang, F., Reen, F.J., Ó Muimhneacháin, E., Clarke, S.L., Zhou, L., Luong, J.H.T., O’Gara, F., McGlacken. G.P., and Glennon, J.D. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode. Sci Rep. 2016, 6:30001. doi: 10.1038/srep30001. PMID:27427496

36. Buzid, A., Ó Muimhneacháin, E., Reen, F.J., Hayes, P., Shang, F., Clarke, O’Gara, F., Sperry, J., Luong, J.H.T., Glennon, J.D. and McGlacken. G.P. Synthesis and electrochemical detection of a thiazolyl-indole natural product isolated from the nosocomial pathogen Pseudomonas aeruginosa. Anal Bioanal Chem. 2016, 408(23), 6361-7. DOI: 10.1007/s00216-016-9749-8.

37. Reen, F.J., Phelan, J.P., Woods, D.F., Shanahan, R., Cano, R., Clarke, S., McGlacken, G.P. and O'Gara, F. Harnessing bacterial signals for suppression of biofilm formation in the nosocomial fungal pathogen Aspergillus fumigatus. Frontiers Microbiol. 2016, doi: 10.3389/fmicb.2016.02074. Pub Med ID: 28066389.

38. Reen, F.J., Gutiérrez-Barranquero and O’Gara, F. Mining microbial signals for enhanced biodiscovery of secondary metabolites. In “Methods in Molecular Biology”. 2016. 1539:287-300. (Ed. by W R. Streit and R. Daniel.) Springer Protocols. DOI: 10.1007/978-1-4939-6691-2_19. PMID: 27900698.

39. Buzid, A., Reen, F.J., Langsi, V.K., Ó Muimhneacháin, E., O’Gara, F., Luong, J.H.T, McGlacken, G.P. and Glennon, J.D. Direct and Rapid Electrochemical Detection of Pseudomonas aeruginosa Quorum Sensing Signaling Molecules in Bacterial Cultures and Cystic Fibrosis Sputum Samples through Cationic Surfactant-Assisted Membrane Disruption. Chem Electrochem. 2017, DOI: 10.1002/celc.201600590.

40. Shanahan, R.M., Reen, F.J., Cano, R., O’Gara, F., and McGlacken, G.P. The requirements at the C-3 position of alkylquinolones for signalling in Pseudomonas aeruginosa. Org Biomolec Chem. 2017, 15, 306-310. DOI: 10.1039/c6ob01930g.

41. Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. Sci Rep. 2017 7, 44103. doi: 10.1038/srep44103. PubMed PMID: 28272521; PubMed Central PMCID: PMC5341072.

42. Sorokin DY, Messina E, Smedile F, Roman P, Damsté JS, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Kublanov IV, Samarov NI, Toshchakov SV, La Cono V, Yakimov MM. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME J. 2017 doi: 10.1038/ismej.2016.203. [Epubahead of print] PubMed PMID: 28106880.

43. Rodrigues, C.J.C., Pereira R.F.S., Fernandes P, Cabral, J.M.S. de Carvalho C.C.C.R. Cultivation-based strategies to find efficient marine biocatalysts. Biotechnology Journal 2017, 12, 1700036 DOI: 10.1002/biot.201700036.

44. de Carvalho C.C.C.R. Whole cell biocatalysts: essential workers from Nature to the industry. Microbial Biotechnology 2017, 10(2), 250–263. Doi: 10.1111/1751-7915.12363.




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