Skip to main content Skip to section menu

Publications of INMARE Project



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


 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.

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.

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.


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

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.

Reen J, Shanahan R, Cano R, O’Gara F, & McGlacken GP. 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.


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


Reen FJ, Romano S, Dobson ADW, & 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.


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.


 Talens-Perales D, Górska A, Huson DH, Polaina J, Marín-Navarro J. Analysis of domain architecture and phylogenetics of family 2 glycoside hydrolases (GH2). 2016. PLoS One 11(12):e0168035.


 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.


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

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.

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


 Talens-Perales D, Górska A, Huson DH, Polaina J, & Marín-Navarro J. Analysis of domain architecture and phylogenetics of family 2 glycoside hydrolases (GH2). PLoS One 2016, 11:e0168035.

 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.


 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, 291:24200-24214. pii: jbc.M116.747527. DOI: 10.1074/jbc.M116.747527


 Martínez-Martínez M, Bargiela RM, 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: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing (TJ McGenity, KN Timmis and B Nogales eds.) (978-3-319-31421-1), 2017; pp-1-21; DOI: 10.1007/978-3-319-31421-1_211-1.

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


 Messina E, Sorokin DY, Kublanov IV, Toshchakov S, Lopatina A, Arcadi E, Smedile F, LaSpada G, LaCono 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.


 Thies S, Rausch SC, Kovacic F, Schmidt-Thaler A, Wilhelm S, Rosenau F, Daniel R, Streit W, Pietruszka J, & Jaeger KE. Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community. Sci Rep. 2016, 6, 27035. DOI:10.1038/srep27035.

Classen T, Kovacic F, Lauinger B, Pietruszka J, & Jaeger KE. Screening for enantioselective lipases. In: Hydrocarbon and Lipid Microbiology Protocols (TJ McGenity, KN Timmis, B Nogales eds.) 2016, Springer Protocols Handbooks, DOI 10.1007/8623_2016_218.

  Katzke N, Knapp A, Loeschcke A, Drepper T, & Jaeger KE. Novel Tools for the Functional Expression of Metagenomic DNA. Meth Mol Biol. 2016, 1539:159-196. DOI 10.1007/978-1-4939-6691-2_10.


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.

 Reen FJ & O’Gara F. Metagenomics as a tool for biodiscovery and enhancement of production of bioactives. In: The marine microbiome – an untold resource of biodiversity and biotechnological potential (L. Stahl, and MS Creitou eds.) Springer, 2016, ISBN 978-3-319-32998-7 ISBN 978-3-319-33000-6 (eBook).  DOI 10.1007/978-3-319-33000-6.

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


Reen FJ, Phelan JP, Gallagher L, Woods D, Shanahan RM, Cano R, Ó Muimhneacháin E, McGlacken GP & 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.

 Phelan JP, Reen FJ, O’Connor R. & 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.

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

 Ulluwishewa D, Wang L, Pereira C, Flynn S, Stick S, Reen FJ, Ramsay JP. & O’Gara F. Dissecting the regulation of bile-induced biofilm formation in Staphylococcus aureus. Microbiology 2016, DOI: 10.1099/mic.0.000317.

 Parages ML, Gutiérrez-Barranquero JA, Reen FJ, Dobson ADW. & O’Gara F. Integrated (Meta)Genomic and Synthetic Biology Approaches to Develop New Biocatalysts. Marine Drugs 2016, 14(3), 62.

  Romano S, Fernandez-Guerra S, Reen FJ, Glöckner FO, Crowley SP, O'Sullivan O, Cotter PD, Adams C, Dobson, ADW. & 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.

  Hennessy E, Adams C, Reen FJ. & 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.

 Buzid A, Shang F, Reen FJ, Ó Muimhneacháin E, Clarke SL, Zhou L, Luong JHT, O’Gara F, McGlacken GP, & Glennon JD. 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.

  Buzid A, Ó Muimhneacháin E, Reen FJ, Hayes P, Shang F, Clarke SL, O’Gara F, Sperry J, Luong JHT, Glennon JD. & McGlacken GP. 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.

  Reen FJ, Phelan JP, Woods DF, Shanahan R, Cano R, Clarke S, McGlacken GP. & O'Gara F. Harnessing bacterial signals for suppression of biofilm formation in the nosocomial fungal pathogen Aspergillus fumigatus. Frontiers Microbiol2016, DOI: 10.3389/fmicb.2016.02074.


  Reen FJ, Gutiérrez-Barranquero JA. & O’Gara F. Mining microbial signals for enhanced biodiscovery of secondary metabolites.  In: Methods in Molecular Biology”.  1539:287-300.  (WR Streit and R Daniel eds.) Springer Protocols. 2016, DOI: 10.1007/978-1-4939-6691-2_19. 


 Buzid A, Reen J, Langsi VK, Ó Muimhneacháin E, O’Gara F., Luong JHT, McGlacken GP. & Glennon JD. 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 Electrochem2017, DOI: 10.1002/celc.201600590.


 Shanahan RM, Reen FJ, Cano R, O’Gara F, & McGlacken GP. 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.

  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.

 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.

Rodrigues CJC, Pereira RFS, Fernandes P, Cabral JMS, & de Carvalho CCCR. Cultivation-based strategies to find efficient marine biocatalysts. Biotechnology Journal 2017, 12, 1700036. DOI: 10.1002/biot.201700036.

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.

 Poehlein A, Daniel R, Thürmer A, Bollinger A, Thies S, Katzke N, & Jaeger KE. First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045.Genome Announc. 2017, 5(32). pii: e00774-17. DOI: 10.1128/genomeA.00774-17.


 Santos-Moriano P, Fernandez-Arrojo L, Mengibar M, Belmonte-Reche E, Peñalver P, Acosta FN, Ballesteros AO, Morales JC, Kidibule P, Fernandez-Lobato M & Plou FJ. Enzymatic production of fully deacetylated chitooligosaccharides and their neuroprotective and anti-inflammatory properties, Biocatalysis and Biotransformation, 2017, 36:1, 57-67, DOI: 10.1080/10242422.2017.1295231.

Casa-Villegas M, Marín-Navarro J, & Polaina J. Synergies in coupled hydrolysis and fermentation of cellulose using a Trichoderma reesei enzyme preparation and a recombinant Saccharomyces cerevisiae strain. World J Microbiol Biotechnol. 2017, 33:140.

 Syranidou E, Karkanorachaki K, Amorotti F, Franchini M, Repouskou E, Kaliva M, Vamvakaki M, Kolvenbach B, Fava F, Corvini PF, & Kalogerakis N. Biodegradation of weathered polystyrene films in seawater microcosms. Sci Rep. 2017, 21;7(1):17991. DOI: 10.1038/s41598-017-18366-y.

Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciordia S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM & Koonin EV. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol. 2017, 2:17081. DOI: 10.1038/nmicrobiol.2017.81.

Bortoluzzi G, Romeo T, La Cono V, La Spada G, Smedile F, Esposito V, Sabatino G, Di Bella M, Canese S, Scotti G, Bo M, Giuliano L, Jones D, Golyshin PN, Yakimov MM, Andaloro F). Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago Geobiology. 2017, 15(5):664-677. doi: 10.1111/gbi.12237.

Chernikova TN, Dallimore J, Lünsdorf H, Heipieper HJ, & Golyshin PN. Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK. Int J Syst Evol Microbiol. 2017, 67(9):3310-3317. DOI: 10.1099/ijsem.0.002111.

 Toshchakov SV, Korzhenkov AA, Chernikova TN, Ferrer M, Golyshina OV, Yakimov MM, & Golyshin PN. The genome analysis of Oleiphilus messinensis ME102 (DSM 13489(T)) reveals backgrounds of its obligate alkane-devouring marine lifestyle. Mar Genomics. 2017, 36:41-47. DOI: 10.1016/j.margen.2017.07.005.

Bargiela R, & Ferrer M. Degradation newtowork reconstruction guided by metagenomic data. In: Metagenomics: methods and protocols (W Streit and R Daniel eds.), HumanaPress. 2017, pp. 145-157; DOI: 10.1007/978-1-4939-6682-0_8;

Distaso MA, Tran H, Ferrer M, & Golyshin PN. Metagenomic Mining of Enzyme Diversity. In: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing, pp.1-25 (TJ McGenity, KN Timmis and B Nogales eds.). 2017, pp. 1-23. DOI: 10.1007/978-3-319-31421-1_216-1;

 Bargiela R, Yakimov MM, Golyshin PN, & Ferrer M. Distribution of Hydrocarbon Degradation Pathways in the Sea. In: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Publisher: Springer International Publishing (TJ McGenity, KN Timmis and B Nogales eds.); 2017; pp. 1-23. DOI: 10.1007/978-3-319-31421-1_383-1;

 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), 2017, pp 167-184.

Méndez-García C, Bargiela R, Martínez-Martínez M, & Ferrer M. Metagenomic protocols and strategies. In: Metagenomics: Perspectives, Methods and Applications (Elsevier; ed. M Nagarajan). Academic Press (ISBN 978-0-08-102268-9), 2017, pp. 15-54.


Buzid, A., Luong, J.H.T., Reen, F.J., O’Gara, F., Glennon, J.D. and McGlacken, G.P. Rapid Electrochemical Detection of Pseudomonas aeruginosa Signaling Molecules by Boron-Doped Diamond Electrode. In Quorum Sensing – Methods and Protocols. Edited by Leoni L., and Rampioni, G. (Springer).  2017. Doi: 10.1007/978-1-4939-7309-5_9


Phelan, J.P., Reen, F.J., Caparros-Martin, J.A., O’Connor, R., and O’Gara, F Rethinking the bile acid/gut microbiome axis in cancer. Oncotarget, 1:8 (70): 115736 – 115747. doi: 10.18632/oncotarget.22803. eCollection 2017.


Gutiérrez-Barranquero, J.A., Reen, J.F., Parages, M.L., McCarthy, R., Dobson, D.W. and O’Gara, F. Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria.  Microb Biotechnol2017 Nov 3. doi: 10.1111/1751-7915.12867.

Chernikova TN, Kyrpides N, Bargiela R, Woyke T, Shapiro N, Whitman WB& Golyshin PN. Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated fromSeawater from the Menai Straits, Wales, United Kingdom. Genome Announc. 2018, 1;6(5). pii: e01444-17. DOI: 10.1128/genomeA.01444-17.


 Ferrer M, Sorokin DY, Wolf YI, Ciordia S, Mena MC, Bargiela R, Koonin EV, & Makarova KS. Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, aRepresentative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia". Genes (Basel). 2018, 23;9(2). pii: E28. DOI: 10.3390/genes9020028.

 Chiara M, Placido A, Picardi E, Ceci LR, Horner DS & Pesole G. A-GAME: improving the assembly of pooled functional metagenomics sequence data. BMC Genomics. 2018, 19(1):44. DOI: 10.1186/s12864-017-4369-z.

Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, & Amann RI. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J. 2018, 12(1):237-252. DOI: 10.1038/ismej.2017.165.


Kidibule PE, Santos-Moriano P, Jiménez-Ortega E, Ramírez-Escudero M, Limón MC, Remacha M, Plou FJ, Sanz-Aparicio J, & Fernández-Lobato M. Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity. Microb Cell Fact. 2018, 17(1):47. DOI: 10.1186/s12934-018-0895-x.

 Santiago G, Martínez-Martínez M, Alonso S, Bargiela R, Coscolín C, GolyshinPN, Guallar V & Ferrer M. Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry 2018, 57(15):2245-2255. DOI: 10.1021/acs.biochem.8b00274.


Ferrer M, Biocatalysis and Biotransformations. Catalysts 2018, 8(5), 216;

Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A,Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, DelPozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V,Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO,Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, GolyshinPN, Guallar V,  & Ferrer M, The Inmare Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol. 2018, 19;13(1):225-234. DOI: 10.1021/acschembio.     


Coscolín C, Martínez-Martínez M, Chow J, Bargiela R, García-Moyano A, Bjerga GEK, Bollinger A, Stokke R, Steen IH, Golyshina OV, Yakimov MM, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, & Ferrer M. Relationships between substrate promiscuity and chiral selectivity of esterases from phylogenetically and environmentally diverse microorganisms. Catalysts. 2018, 8(1).

Jakubovska J., Tauraitė D., Birštonas L., Meškys R. N4-acyl-2'-deoxycytidine-5'-triphosphates for the enzymatic synthesis of modified DNA. Nucleic Acids Res. 2018 doi: 10.1093/nar/gky435

 Ferrer, M., Méndez-García, C., Bargiela, R., Chow, J., Alonso, S., García-Moyano, A., et al. Decoding the Ocean’s Microbiological Secrets for Marine Enzyme Biodiscovery. FEMS Microbiol. Lett. 2018, DOI: 10.1093/femsle/fny285.

Bollinger, A., Thies, S., Katzke, N., and Jaeger, K.-E. The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena. Microb. Biotechnol. 2018, DOI: 10.1111/1751-7915.13288.

Jakubovska J., Tauraitė D., Meškys R. A versatile method for the UVA-induced cross-linking of acetophenone- or benzophenone-functionalized DNA. Sci Rep. 2018, 8: 16484. DOI:10.1038/s41598-018-34892.


Stanislauskienė R., Kutanovas S., Kalinienė L., Bratchikov M., Meškys R. Tetramethylpyrazine-inducible promoter region from Rhodococcus jostii TMP1. Molecules 2018, 23(7), 1530;

Aučynaitė, A.; Rutkienė, R.; Tauraitė, D.; Meškys, R.; Urbonavičius, J. Identification of a 2′-O-methyluridine nucleoside hydrolase using the metagenomic libraries. Molecules 2018, 23, 2904. .

Petkevičius V.; Vaitekūnas J.; Tauraitė D.; Stankevičiūtė J.; Šarlauskas J.; Čėnas N.; Meškys R. A biocatalytic synthesis of heteroaromatic N-oxides by whole cells of Escherichia coli expressing the multicomponent, soluble di-iron monooxygenase (SDIMO) PmlABCDEF. Adv Synth Catal 2019 DOI: 10.1002/adsc.201801491. This manuscript has been selected as a VIP (Very Important Publication) in Advanced Synthesis & Catalysis. That happens for a selected number of publications in Advanced Synthesis & Catalysis, which are considered by the referees, and also by the editorial office, to be of high significance. A special ASC Biocatalysis Issue will appear in June 2019 (as ASC Issue 11) and be presented at the BIOTRANS in Groningen in July 2019 ( This manuscript will be included in the Issue 11.


Časaitė V., Sadauskas M., Vaitekūnas J., Gasparavičiūtė R., Meškienė R., Skikaitė I., Sakalauskas I., Jakubovska J., Tauraitė D., Meškys R. Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase. MicrobiologyOpen 2019, e795. DOI: 10.1002/mbo3.795.


Šimoliūnas, E.; Truncaitė, L.; Rutkienė, R.; Povilonienė, S.; Goda, K.; Kaupinis, A.; Valius, M.; Meškys, R. The robust self-assembling tubular nanostructures formed by gp053 from phage vB_EcoM_FV3. Viruses 2019, 11, 50.


Špakova A., Šimoliūnas E., Batiuškaitė R., Pajeda S., Meškys R., Petraitytė-Burneikienė R. Self-assembly of tail tube protein of bacteriophage vB_EcoS_NBD2 into extremely long polytubes in E. coli and S. cerevisiae. Viruses 2019, 11, 208;

Urbelienė N., Kutanovas S., Meškienė R., Gasparavičiūtė R., Tauraitė D., Koplūnaitė M., Meškys R. Application of the uridine auxotrophic host and synthetic nucleosides for a rapid selection of hydrolases from metagenomic libraries. Microb Biotechnol. 2018, DOI: 10.1111/1751-7915.13316  (


Sorokin DY, Messina E, La Cono V, Ferrer M, Ciordia S, Mena MC, Toshchakov SV, Golyshin PN, Yakimov MM. Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes. Front Microbiol. 2018, 9:2359. doi: 10.3389/fmicb.2018.02359. eCollection.


Hajighasemi M, Tchigvintsev A, Nocek BP, Flick R, Popovic A, Hai T, Khusnutdinova AN, Brown G, Xu X, Cui H, Anstett J, Chernikova TN, Bruls T, Le Paslier D,Yakimov MM, Joachimiak A, Golyshina OV, Savchenko A, Golyshin PN, Edwards EA,Yakunin AF. Screening and characterization of novel polyesterases from environmentalmetagenomes with high hydrolytic activity against synthetic polyesters. Environ Sci Technol. 2018, doi: 10.1021/acs.est.8b04252.


 Ghuneim LJ, Jones DL, Golyshin PN, Golyshina OV. Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function. Front Microbiol. 2018, 9:1971. doi: 10.3389/fmicb.2018.01971. eCollection

Santiago G, Martínez-Martínez M, Alonso S, Bargiela R, Coscolín C,Golyshin PN, Guallar V, Ferrer M. Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry. 2018, 57(15):2245-2255. doi: 10.1021/acs.biochem.8b00274.Epub 2018 Mar 30.

Chow J, Danso D, Ferrer M. & Streit WR. The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli bioH-complementing esterase EstN1. Sci Rep. 2018, 8, Article number: 13823


Danso D, Schmeisser C, Chow J, Zimmermann W, Wei R, Leggewie C, Li X, Hazen T, Streit WR. New Insights into the Function and Global Distribution of olyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. Appl Environ Microbiol. 2018, 84 (8) e02773-17; DOI:10.1128/AEM.02773-17.

Molitor M, Bollinger A, Kubicki S, Loeschcke, A, Jaeger, K.-E., Thies, S. Agar plate-based screening methods for the identification of polyester hydrolysis by Pseudomonas species. Microb Biotechnol. 2019, DOI: 10.1111/1751-7915.13418.

Ferrer M., Biocatalysis and Biotransformation. Catalysts. 2018, 8-216.

Coscolín C, Beloqui A, Martínez-Martínez M, Bargiela R, Santiago G, Blanco RM, Delaittre G, Márquez-Álvarez C, Ferrer M. Controlled manipulation of enzyme specificity through immobilization-induced flexibility constraints.  Applied Catalysis A, General 2018, 565: 59-67.

Chow J, Danso D, Ferrer M, Streit WR. The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. Sci Rep. 2018, 8(1):13823. doi: 10.1038/s41598-018-32059-0.


Coscolín C, Katzke N, García-Moyano A, Navarro-Fernández J, Almendral D,Martínez-Martínez M, Bollinger A, Bargiela R, Gertler C, Chernikova TN, Rojo D,Barbas C, Tran H, Golyshina OV, Koch R, Yakimov MM, Bjerga GEK, Golyshin PN,Jaeger KE, Ferrer M. Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines. Appl Environ Microbiol. 2019, 85(2). pii: e02404-18. doi: 10.1128/AEM.02404-18.


Golyshin, P., Jaeger, K., Toshchakov, S., Golyshina, O., Chernikova, T., Yakimov, M., Ferrer, M. Aerobic Hydrocarbon-degrading Gammaproteobacteria - Oleiphilaceae and Relatives. In: Handbook of Hydrocarbon and Lipid Microbiology Series. Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes, Publisher: Springer.

International Publishing (ed. Terry J. McGenity); 2019, Accepted.


Reyes-Duarte D, Coscolín C, Martínez-Martínez M, Ferrer M, García-Arellano H. Functional-Based Screening Methods for Detecting Esterase and Lipase Activity Against Multiple Substrates. Methods Mol Biol. 2018; 1835:109-117.


Ferrer M, Golyshin PN and McMeel O. Innovation for new bio-based products from the ocean. Post on the Oxford University Press (OUP) web academic blog (web academic blog;; link:


Coscolín C, Bargiela R, Martínez-Martínez M, Alonso S, Chernikova TN, Hai T, Golyshina OV, Yakimov MM, Golyshin PN, Ferrer M. Hydrocarbon-degrading Microbes as Sources of New Biocatalysts. In: Handbook of Hydrocarbon and Lipid Microbiology Series. Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes, Publisher: Springer International Publishing (ed. Terry J. McGenity); 2018, pp 1-21 (DOI: 10.1007/978-3-319-60053-6_13-1).

Zeaiter Z., Mapelli F., Crotti E., Borin S. Methods for the genetic manipulation of marine bacteria. Electron. J Biotechnol. 2018, 33: 17-28. doi: 10.1016/j.ejbt.2018.03.003.


Reen, J.F., Gutiérrez-Barranquero, J.A., Parages, M.L., and O’Gara, F. Coumarin: a novel player in microbial quorum sensing and biofilm formation inhibition. Applied Microbiology and Biotechnology. 2018,


Ó Muimhneacháin E, Reen F.J., O'Gara F, McGlacken G.P. Analogues of Pseudomonas aeruginosa signalling molecules to tackle infections.  Org Biomol Chem. 2018, 16(2):169-179. doi: 10.1039/c7ob02395b.


Reen, F.J., McGlacken, G.P., and O’Gara, F.  The expanding horizon of alkyl quinolone signalling and communication in polycellular interactomes.  FEMS Microbiol Lett. 2018, May 1;365(9). doi: 10.1093/femsle/fny076.

Abreu Castilla, I., Woods, D.F., Reen, F.J. and O’Gara, F. Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies. Mar. Drugs 2018, 16, 227; doi:10.3390/md16070227.


Woods, D.F., Kozak, I.M., Flynn, S., and O’Gara, F. The microbiome of an active meat curing brine.  Front. Microbiol. 2019,| doi: 10.3389/fmicb.2018.03346


Gutiérrez-Barranquero, J.A., Reen, J.F., and O’Gara, F. Genome sequence of Paracoccus sp. JM45, a bacterial strain isolated from a marine sponge with a dual quorum sensing-quorum sensing inhibition activity.  American Society for Microbiology, 2019, Vol. 8, Issue 2, 1-3.


Gavin, D. P., Murphy, E. J., Foley, A. M., Abreu Castilla, I., Reen, F. J., Woods, D. F., Collins, S. G., O'Gara, F. and Maguire, A. Identification of an Esterase Isolated Using Metagenomic Technology which Displays an Unusual Substrate Scope and its Characterisation as an Enantioselective Biocatalyst, Adv. Synth.Catal. 2019, 361. 

Míguez, N., Gimeno-Pérez,M., Fernández-Polo, D., Cervantes,FV., Ballesteros,AO., Fernández-Lobato, M., Ribeiro, MH., Plou, F.J. Immobilization of the β-fructofuranosidase from Xanthophyllomyces dendrorhous by entrapment in polyvinyl alcohol and its application to neo-fructooligosaccharides production”. Catalysts 2018, 8(5), 201. Open access.


Santos-Moriano, P., Kidibule P., Míguez, N., Fernández-Arrojo, L. Ballesteros, A.O., Fernández-Lobato, M., Plou, F.J. “Tailored enzymatic synthesis of chitooligosaccharides with different deacetylation degree and their anti-inflammatory activity” Catalysts 2019, 9(5), 405; Open Access.







Site footer