Emerging concepts promising new horizons for marine biodiscovery and synthetic biology

Marine Drugs

Volumn 13, Issue 5, 2015, Pages 2924-2954

  Reen, F Jerry ^a   Gutiérrez Barranquero, José A ^a   Dobson, Alan D W ^a   Adams, Claire ^a   O'Gara, Fergal ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b CURTIN UNIVERSITY   (Australia)

Author keywords

Lantibiotics; Marine bioactives; Mimetics; Motif domain; Peptides; Quorum quenching; Quorum sensing; Signaling molecules

Indexed keywords

ANTI QUORUM SENSING COMPOUND; ANTIBIOFILM COMPOUND; ANTIBIOTIC AGENT; BACTERIOCIN; BL DZ 1; CYCLODEPSIPEPTIDE; DIPEPTIDE; HYDROXYAPATITE GOLD ARGININE NANOCOMPOSITE; LANTIBIOTIC; LINEAR DIPEPTIDE; MARINE PEPTIDE; MARINOPYRROLE A; NANOANTIBIOTIC; NANOCOMPOSITE; NISIN A; PEPTIDE; PEPTIDE NUCLEIC ACID; PEPTIDOMIMETIC AGENT; PIPERAZINEDIONE; PROTAMINE; SUBTILOMYCIN; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT;

ANTIBACTERIAL ACTIVITY; ANTIBIOFILM BIOACTIVITY; ANTIVIRULENCE BIOACTIVITY; BACTERIAL VIRULENCE; BIODIVERSITY; BIOINFORMATICS; BIOTECHNOLOGY; CELL COMMUNICATION; CHEMI INFORMATICS; CHEMICAL PROCEDURES; DATA MINING; DNA SEQUENCE; DRUG ACTIVITY; DRUG DESIGN; DRUG EFFICACY; DRUG IDENTIFICATION; DRUG MECHANISM; DRUG SAFETY; ECOLOGICAL PROCEDURES; GENOME; GENOMICS; HUMAN; INNOVATIVE BIOTECHNOLOGY; MARINE BIODISCOVERY; MARINE ENVIRONMENT; METAGENOME; METAGENOMICS; MICROBIAL DIVERSITY; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NANOBIOTECHNOLOGY; NONHUMAN; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; QUORUM SENSING; REVIEW; SIGNAL TRANSDUCTION; SINGLE CELL GENOMICS; STRUCTURE ACTIVITY RELATION; SYNTHETIC BIOLOGY; TANDEM CHEMICAL PROFILING; ANIMAL; AQUATIC SPECIES; CHEMISTRY; ECOSYSTEM; MARINE BIOLOGY; PROCEDURES;

BACTERIA (MICROORGANISMS);

ANIMALS; AQUATIC ORGANISMS; BIOLOGICAL PRODUCTS; ECOSYSTEM; HUMANS; MARINE BIOLOGY; PEPTIDES; SYNTHETIC BIOLOGY;

EID: 84930662401     PISSN: None     EISSN: 16603397     Source Type: Journal    
DOI: 10.3390/md13052924     Document Type: Review

References (148)

1. Fan, X.; Bai, L.; Zhu, L.; Yang, L.; Zhang, X. Marine algae-derived bioactive peptides for human nutrition and health. J. Agric. Food Chem. 2014, 62, 9211-9222.
2. Harnedy, P.A.; FitzGerald, R.J. Bioactive peptides from marine processing waste and shellfish: A review. J. Func. Foods 2012, 4, 6-24.
3. Kim, S.-K.; Wijesekaraa, I. Development and biological activities of marine-derived bioactive peptides: A review. J. Func. Foods 2012, 2, 1-9.
4. Ngo, D.H.; Vo, T.S.; Ngo, D.N.; Wijesekara, I.; Kim, S.K. Biological activities and potential health benefits of bioactive peptides derived from marine organisms. Int. J. Biol. Macromol. 2012, 51, 378-383.
5. Suarez-Jimenez, G.M.; Burgos-Hernandez, A.; Ezquerra-Brauer, J.M. Bioactive peptides and depsipeptides with anticancer potential: Sources from marine animals. Mar. Drugs 2012, 10, 963-986.
6. Tripathi, A.; Schofield, M.M.; Chlipala, G.E.; Schultz, P.J.; Yim, I.; Newmister, S.A.; Nusca, T.D.; Scaglione, J.B.; Hanna, P.C.; Tamayo-Castillo, G.; et al. Baulamycins A and B, broad-spectrum antibiotics identified as inhibitors of siderophore biosynthesis in Staphylococcus aureus and Bacillus anthracis. J. Am. Chem. Soc. 2014, 136, 1579-1586.
7. Zhang, X.; Jacob, M.R.; Rao, R.R.; Wang, Y.H.; Agarwal, A.K.; Newman, D.J.; Khan, I.A.; Clark, A.M.; Li, X.C. Antifungal cyclic peptides from the marine sponge. Res. Rep. Med. Chem. 2012, 2, 7-14.
8. Zheng, L.H.; Wang, Y.J.; Sheng, J.; Wang, F.; Zheng, Y.; Lin, X.K.; Sun, M. Antitumor peptides from marine organisms. Mar. Drugs 2011, 9, 1840-1859.
9. Martins, A.; Vieira, H.; Gaspar, H.; Santos, S. Marketed marine natural products in the pharmaceutical and cosmeceutical industries: Tips for success. Mar. Drugs 2014, 12, 1066-1101.
10. Dobretsov, S.; Teplitski, M.; Paul, V. Mini-review: Quorum sensing in the marine environment and its relationship to biofouling. Biofouling 2009, 25, 413-427.
11. Rocha-Martin, J.; Harrington, C.; Dobson, A.D.; O'Gara, F. Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar. Drugs 2014, 12, 3516-3559.
12. Iqbal, H.A.; Feng, Z.; Brady, S.F. Biocatalysts and small molecule products from metagenomic studies. Curr. Opin. Chem. Biol. 2012, 16, 109-116.
13. Kennedy, J.; Flemer, B.; Jackson, S.A.; Lejon, D.P.; Morrissey, J.P.; O'Gara, F.; Dobson, A.D. Marine metagenomics: New tools for the study and exploitation of marine microbial metabolism. Mar. Drugs 2010, 8, 608-628.
14. Tseng, C.H.; Tang, S.L. Marine microbial metagenomics: From individual to the environment. Int. J. Mol. Sci. 2014, 15, 8878-8892.
15. Wilson, M.C.; Piel, J. Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. Chem. Biol. 2013, 20, 636-647.
16. Bruns, A.; Cypionka, H.; Overmann, J. Cyclic Amp and Acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 2002, 68, 3978-3987.
17. Epstein, S.S. The phenomenon of microbial uncultivability. Curr. Opin. Microbiol. 2013, 16, 636-642.
18. Foster, K.R.; Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 2012, 22, 1845-1850.
19. Lee, H.S.; Kwon, K.K.; Kang, S.G.; Cha, S.S.; Kim, S.J.; Lee, J.H. Approaches for novel enzyme discovery from marine environments. Curr. Opin. Biotechnol. 2010, 21, 353-357.
20. Nichols, D.; Lewis, K.; Orjala, J.; Mo, S.; Ortenberg, R.; O'Connor, P.; Zhao, C.; Vouros, P.; Kaeberlein, T.; Epstein, S.S. Short peptide induces an "uncultivable" microorganism to grow in vitro. Appl. Environ. Microbiol. 2008, 74, 4889-4897.
21. Pham, V.H.; Kim, J. Cultivation of unculturable soil bacteria. Trends Biotechnol. 2012, 30, 475-484.
22. Puspita, I.D.; Kamagata, Y.; Tanaka, M.; Asano, K.; Nakatsu, C.H. Are uncultivated bacteria really uncultivable? Microbes Environ. 2012, 27, 356-366.
23. Pustam, A.; Smith, C.; Deering, C.; Grosicki, K.M.; Leng, T.Y.; Lin, S.; Yang, J.; Pink, D.; Gill, T.; Graham, L.; et al. Interactions of protamine with the marine bacterium, Pseudoalteromonas sp. NCIMB 2021. Lett. Appl. Microbiol. 2014, 58, 225-230.
24. Vartoukian, S.R.; Palmer, R.M.; Wade, W.G. Strategies for culture of "unculturable" bacteria. FEMS Microbiol. Lett. 2010, 309, 1-7.
25. Lazcano-Perez, F.; Roman-Gonzalez, S.A.; Sanchez-Puig, N.; Arreguin-Espinosa, R. Bioactive peptides from marine organisms: A short overview. Prot. Pept. Lett. 2012, 19, 700-707.
26. Kennedy, J.; Baker, P.; Piper, C.; Cotter, P.D.; Walsh, M.; Mooij, M.J.; Bourke, M.B.; Rea, M.C.; O'Connor, P.M.; Ross, R.P.; et al. Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from irish waters. Mar. Biotechnol. 2009, 11, 384-396.
27. Taylor, K.; McCullough, B.; Clarke, D.J.; Langley, R.J.; Pechenick, T.; Hill, A.; Campopiano, D.J.; Barran, P.E.; Dorin, J.R.; Govan, J.R. Covalent dimer species of β-defensin Defr1 display potent antimicrobial activity against multidrug-resistant bacterial pathogens. Antimicrob. Agents Chemother. 2007, 51, 1719-1724.
28. Thomas, S.; Karnik, S.; Barai, R.S.; Jayaraman, V.K.; Idicula-Thomas, S. CAMP: A useful resource for research on antimicrobial peptides. Nucleic Acids Res. 2010, 38, D774-D780.
29. Cleveland, J.; Montville, T.J.; Nes, I.F.; Chikindas, M.L. Bacteriocins: Safe, natural antimicrobials for food preservation. Int. J. Food Microbiol. 2001, 71, 1-20.
30. Cotter, P.D.; Hill, C.; Ross, R.P. Bacteriocins: Developing innate immunity for food. Nat. Rev. Microbiol. 2005, 3, 777-788.
31. Jack, R.W.; Tagg, J.R.; Ray, B. Bacteriocins of Gram-positive bacteria. Microbiol. Rev. 1995, 59, 171-200.
32. Knerr, P.J.; van der Donk, W.A. Discovery, biosynthesis, and engineering of lantipeptides. Annu. Rev. Biochem. 2012, 81, 479-505.
33. Line, J.E.; Svetoch, E.A.; Eruslanov, B.V.; Perelygin, V.V.; Mitsevich, E.V.; Mitsevich, I.P.; Levchuk, V.P.; Svetoch, O.E.; Seal, B.S.; Siragusa, G.R.; et al. Isolation and purification of enterocin E-760 with broad antimicrobial activity against Gram-positive and Gram-negative bacteria. Antimicrob. Agents Chemother. 2008, 52, 1094-1100.
34. Shokri, D.; Zaghian, S.; Khodabakhsh, F.; Fazeli, H.; Mobasherizadeh, S.; Ataei, B. Antimicrobial activity of a UV-stable bacteriocin-like inhibitory substance (BLIS) produced by Enterococcus faecium strain DSH20 against vancomycin-resistant enterococcus (VRE) strains. J. Microbiol. Immunol. Infect. 2014, 47, 371-376.
35. Piper, C.; Cotter, P.D.; Ross, R.P.; Hill, C. Discovery of medically significant lantibiotics. Curr. Drug Discov. Technol. 2009, 6, 1-18.
36. Cotter, P.D.; Ross, R.P.; Hill, C. Bacteriocins - A viable alternative to antibiotics? Nat. Rev. Microbiol. 2013, 11, 95-105.
37. Snyder, A.B.; Worobo, R.W. Chemical and genetic characterization of bacteriocins: Antimicrobial peptides for food safety. J. Sci. Food Agric. 2014, 94, 28-44.
38. Nguyen, V.D.; Pham, T.T.; Nguyen, T.H.; Nguyen, T.T.; Hoj, L. Screening of marine bacteria with bacteriocin-like activities and probiotic potential for ornate spiny lobster (Panulirus ornatus) juveniles. Fish Shellfish Immunol. 2014, 40, 49-60.
39. Haft, D.H.; Basu, M.K. Biological systems discovery in silico: Radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. J. Bacteriol. 2011, 193, 2745-2755.
40. Murphy, K.; O'Sullivan, O.; Rea, M.C.; Cotter, P.D.; Ross, R.P.; Hill, C. Genome mining for radical SAM protein determinants reveals multiple sactibiotic-like gene clusters. PLoS ONE 2011, 6, e20852.
41. Singh, M.; Sareen, D. Novel lant-associated lantibiotic clusters identified by genome database mining. PLoS ONE 2014, 9, e91352.
42. Van Heel, A.J.; Montalban-Lopez, M.; Kuipers, O.P. Evaluating the feasibility of lantibiotics as an alternative therapy against bacterial infections in humans. Expert Opin. Drug Metab. Toxicol. 2011, 7, 675-680.
43. Willey, J.M.; van der Donk, W.A. Lantibiotics: Peptides of diverse structure and function. Annu. Rev. Microbiol. 2007, 61, 477-501.
44. Cotter, P.D.; O'Connor, P.M.; Draper, L.A.; Lawton, E.M.; Deegan, L.H.; Hill, C.; Ross, R.P. Posttranslational conversion of L-serines to D-alanines is vital for optimal production and activity of the lantibiotic lacticin 3147. Proc. Natl. Acad. Sci. USA 2005, 102, 18584-18589.
45. Phelan, R.W.; Barret, M.; Cotter, P.D.; O'Connor, P.M.; Chen, R.; Morrissey, J.P.; Dobson, A.D.; O'Gara, F.; Barbosa, T.M. Subtilomycin: A new lantibiotic from Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans. Mar. Drugs 2013, 11, 1878-1898.
46. Deng, Y.; Li, C.Z.; Zhu, Y.G.; Wang, P.X.; Qi, Q.D.; Fu, J.J.; Peng, D.H.; Ruan, L.F.; Sun, M. ApnI, a transmembrane protein responsible for subtilomycin immunity, unveils a novel model for lantibiotic immunity. Appl. Environ. Microbiol. 2014, 80, 6303-6315.
47. Saude, A.C.; Ombredane, A.S.; Silva, O.N.; Barbosa, J.A.; Moreno, S.E.; Araujo, A.C.; Falcao, R.; Silva, L.P.; Dias, S.C.; Franco, O.L. Clavanin bacterial sepsis control using a novel methacrylate nanocarrier. Int. J. Nanomed. 2014, 9, 5055-5069.
48. Almeida, J.P.; Chen, A.L.; Foster, A.; Drezek, R. In vivo biodistribution of nanoparticles. Nanomedicine 2011, 6, 815-835.
49. Huh, A.J.; Kwon, Y.J. "Nanoantibiotics": A new paradigm for treating infectious diseases using nanomaterials in the antibiotics resistant era. J. Controll. Release 2011, 156, 128-145.
50. Vukomanovic, M.; Logar, M.; Skapina, S.D.; Suvorova, D. Hydroxyapatite/gold/arginine: Designing the structure to create antibacterial activity. J. Mater. Chem. B 2014, 2, 1557-1564.
51. Asmathunisha, N.; Kathiresan, K. A review on biosynthesis of nanoparticles by marine organisms. Colloids Surf. B Biointerfaces 2013, 103, 283-287.
52. Liddington, R.C. Structural basis of protein-protein interactions. Methods Mol. Biol. 2004, 261, 3-14.
53. Brady, R.M.; Baell, J.B.; Norton, R.S. Strategies for the development of conotoxins as new therapeutic leads. Mar. Drugs 2013, 11, 2293-2313.
54. Vagner, J.; Qu, H.; Hruby, V.J. Peptidomimetics, a synthetic tool of drug discovery. Curr. Opin. Chem. Biol. 2008, 12, 292-296.
55. Ruzza, P. Peptides and peptidomimetics in medicinal chemistry. In Medicinal Chemistry and Drug Design; Ekinci, D., Ed.; InTech: Rijeka, Croatia, 2012.
56. Som, A.; Navasa, N.; Percher, A.; Scott, R.W.; Tew, G.N.; Anguita, J. Identification of synthetic host defense peptide mimics that exert dual antimicrobial and anti-inflammatory activities. Clin. Vaccine Immunol. 2012, 19, 1784-1791.
57. Srinivas, N.; Jetter, P.; Ueberbacher, B.J.; Werneburg, M.; Zerbe, K.; Steinmann, J.; van der Meijden, B.; Bernardini, F.; Lederer, A.; Dias, R.L.; et al. Peptidomimetic antibiotics target outer-membrane biogenesis in Pseudomonas aeruginosa. Science 2010, 327, 1010-1013.
58. Avan, I.; Hall, C.D.; Katritzky, A.R. Peptidomimetics via modifications of amino acids and peptide bonds. Chem. Soc. Rev. 2014, 43, 3575-3594.
59. Dreyfuss, J.L.; Regatieri, C.V.; Lima, M.A.; Paredes-Gamero, E.J.; Brito, A.S.; Chavante, S.F.; Belfort, R., Jr.; Farah, M.E.; Nader, H.B. A heparin mimetic isolated from a marine shrimp suppresses neovascularization. J. Thromb. Haemost. 2010, 8, 1828-1837.
60. Doi, K.; Li, R.; Sung, S.S.; Wu, H.; Liu, Y.; Manieri, W.; Krishnegowda, G.; Awwad, A.; Dewey, A.; Liu, X.; et al. Discovery of marinopyrrole a (maritoclax) as a selective Mcl-1 antagonist that overcomes ABT-737 resistance by binding to and targeting Mcl-1 for proteasomal degradation. J. Biol. Chem. 2012, 287, 10224-10235.
61. Billard, C. BH3 mimetics: Status of the field and new developments. Mol. Cancer Ther. 2013, 12, 1691-1700.
62. Good, L.; Nielsen, P.E. Peptide nucleic acid (PNA) antisense effects in Escherichia coli. Curr. Issues Mol. Biol. 1999, 1, 111-116.
63. Worden, A.Z.; Chisholm, S.W.; Binder, B.J. In situ hybridization of Prochlorococcus and Synechococcus (marine cyanobacteria) spp. with rRNA-targeted peptide nucleic acid probes. Appl. Environ. Microbiol. 2000, 66, 284-289.
64. Wynendaele, E.; Bronselaer, A.; Nielandt, J.; D'Hondt, M.; Stalmans, S.; Bracke, N.; Verbeke, F.; van de Wiele, C.; de Tre, G.; de Spiegeleer, B. Quorumpeps database: Chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res. 2013, 41, D655-D659.
65. Bai, H.; You, Y.; Yan, H.; Meng, J.; Xue, X.; Hou, Z.; Zhou, Y.; Ma, X.; Sang, G.; Luo, X. Antisense inhibition of gene expression and growth in Gram-negative bacteria by cell-penetrating peptide conjugates of peptide nucleic acids targeted to rpoD gene. Biomaterials 2012, 33, 659-667.
66. Ghosal, A.; Nielsen, P.E. Potent antibacterial antisense peptide-peptide nucleic acid conjugates against Pseudomonas aeruginosa. Nucleic Acid Ther. 2012, 22, 323-334.
67. Good, L.; Awasthi, S.K.; Dryselius, R.; Larsson, O.; Nielsen, P.E. Bactericidal antisense effects of peptide-PNA conjugates. Nat. Biotechnol. 2001, 19, 360-364.
68. Kurupati, P.; Tan, K.S.; Kumarasinghe, G.; Poh, C.L. Inhibition of gene expression and growth by antisense peptide nucleic acids in a multiresistant β-lactamase-producing Klebsiella pneumoniae strain. Antimicrob. Agents Chemother. 2007, 51, 805-811.
69. Nekhotiaeva, N.; Awasthi, S.K.; Nielsen, P.E.; Good, L. Inhibition of Staphylococcus aureus gene expression and growth using antisense peptide nucleic acids. Mol. Ther. 2004, 10, 652-659.
70. Patenge, N.; Pappesch, R.; Krawack, F.; Walda, C.; Mraheil, M.A.; Jacob, A.; Hain, T.; Kreikemeyer, B. Inhibition of growth and gene expression by PNA-peptide conjugates in Streptococcus pyogenes. Mol. Ther. Nucleic Acids 2013, 2, e132.
71. Rajasekaran, P.; Alexander, J.C.; Seleem, M.N.; Jain, N.; Sriranganathan, N.; Wattam, A.R.; Setubal, J.C.; Boyle, S.M. Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages. Int. J. Antimicrob. Agents 2013, 41, 358-362.
72. Hatamoto, M.; Ohashi, A.; Imachi, H. Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology. Appl. Microbiol. Biotechnol. 2010, 86, 397-402.
73. Liu, B.R.; Liou, J.S.; Chen, Y.J.; Huang, Y.W.; Lee, H.J. Delivery of nucleic acids, proteins, and nanoparticles by arginine-rich cell-penetrating peptides in rotifers. Mar. Biotechnol. 2013, 15, 584-595.
74. Cook, L.C.; Federle, M.J. Peptide pheromone signaling in Streptococcus and Enterococcus. FEMS Microbiol. Rev. 2014, 38, 473-492.
75. Gram, L.; Grossart, H.P.; Schlingloff, A.; Kiorboe, T. Possible quorum sensing in marine snow bacteria: Production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl. Environ. Microbiol. 2002, 68, 4111-4116.
76. Mohamed, N.M.; Cicirelli, E.M.; Kan, J.; Chen, F.; Fuqua, C.; Hill, R.T. Diversity and quorum-sensing signal production of Proteobacteria associated with marine sponges. Environ. Microbiol. 2008, 10, 75-86.
77. Kjaerulff, L.; Nielsen, A.; Mansson, M.; Gram, L.; Larsen, T.O.; Ingmer, H.; Gotfredsen, C.H. Identification of four new agr quorum sensing-interfering cyclodepsipeptides from a marine Photobacterium. Mar. Drugs 2013, 11, 5051-5062.
78. Nielsen, A.; Mansson, M.; Bojer, M.S.; Gram, L.; Larsen, T.O.; Novick, R.P.; Frees, D.; Frokiaer, H.; Ingmer, H. Solonamide B inhibits quorum sensing and reduces Staphylococcus aureus mediated killing of human neutrophils. PLoS ONE 2014, 9, e84992.
79. Teasdale, M.E.; Donovan, K.A.; Forschner-Dancause, S.R.; Rowley, D.C. Gram-positive marine bacteria as a potential resource for the discovery of quorum sensing inhibitors. Mar. Biotechnol. 2011, 13, 722-732.
80. Decho, A.W.; Browne, K.A.; Zimmer-Faust, R.K. Chemical cues: Why basic peptides are signal molecules in marine environments. Limnol. Oceanogr. 1998, 43, 1410-1417.
81. Zhang, Y.; Yang, Y.; Woods, A.; Cotter, R.J.; Sun, Z. Resuscitation of dormant Mycobacterium tuberculosis by phospholipids or specific peptides. Biochem. Biophys. Res. Commun. 2001, 284, 542-547.
82. Kana, B.D.; Mizrahi, V. Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling. FEMS Immunol. Med. Microbiol. 2010, 58, 39-50.
83. Cummins, J.; Reen, F.J.; Baysse, C.; Mooij, M.J.; O'Gara, F. Subinhibitory concentrations of the cationic antimicrobial peptide colistin induce the pseudomonas quinolone signal in Pseudomonas aeruginosa. Microbiology 2009, 155, 2826-2837.
84. Furukawa, S.; Kuchma, S.L.; O'Toole, G.A. Keeping their options open: Acute versus persistent infections. J. Bacteriol. 2006, 188, 1211-1217.
85. Brogden, K.A.; Guthmiller, J.M.; Taylor, C.E. Human polymicrobial infections. Lancet 2005, 365, 253-255.
86. Peterson, M.M.; Mack, J.L.; Hall, P.R.; Alsup, A.A.; Alexander, S.M.; Sully, E.K.; Sawires, Y.S.; Cheung, A.L.; Otto, M.; Gresham, H.D. Apolipoprotein B is an innate barrier against invasive Staphylococcus aureus infection. Cell Host Microbe 2008, 4, 555-566.
87. Otto, M.; Sussmuth, R.; Vuong, C.; Jung, G.; Gotz, F. Inhibition of virulence factor expression in Staphylococcus aureus by the Staphylococcus epidermidis agr pheromone and derivatives. FEBS Lett. 1999, 450, 257-262.
88. Balaban, N.; Giacometti, A.; Cirioni, O.; Gov, Y.; Ghiselli, R.; Mocchegiani, F.; Viticchi, C.; del Prete, M.S.; Saba, V.; Scalise, G.; et al. Use of the quorum-sensing inhibitor RNAIII-inhibiting peptide to prevent biofilm formation in vivo by drug-resistant Staphylococcus epidermidis. J. Infect. Dis. 2003, 187, 625-630.
89. Ivanova, K.; Fernandes, M.M.; Tzanov, T. Current advances on bacterial pathogenesis inhibition and treatment strategies. In Microbial Pathogens and Strategies for Combating Them: Science, Technology and Education; Méndez-Vilas, A., Ed.; Formatex Research Center: Badajoz, Spain, 2013; Volume 4.
90. Giacometti, A.; Cirioni, O.; Gov, Y.; Ghiselli, R.; Del Prete, M.S.; Mocchegiani, F.; Saba, V.; Orlando, F.; Scalise, G.; Balaban, N.; et al. RNA III inhibiting peptide inhibits in vivo biofilm formation by drug-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2003, 47, 1979-1983.
91. Kiran, M.D.; Adikesavan, N.V.; Cirioni, O.; Giacometti, A.; Silvestri, C.; Scalise, G.; Ghiselli, R.; Saba, V.; Orlando, F.; Shoham, M.; et al. Discovery of a quorum-sensing inhibitor of drug-resistant Staphylococcal infections by structure-based virtual screening. Mol. Pharmacol. 2008, 73, 1578-1586.
92. Prasad, C. Bioactive cyclic dipeptides. Peptides 1995, 16, 151-164.
93. Schmitz, F.J.; Vanderah, D.J.; Hollenbeak, K.H.; Enwall, C.E.; Gopichand, Y.; Sengupta, P.K.; Hossain, M.B.; van der Helm, D. Metabolites from the marine sponge Tedania ignis. A new atisanediol and several known diketopiperazines. J. Organ. Chem. 1983, 48, 3941-3945.
94. Jayatilake, G.S.; Thornton, M.P.; Leonard, A.C.; Grimwade, J.E.; Baker, B.J. Metabolites from an Antarctic sponge-associated bacterium, Pseudomonas aeruginosa. J. Nat. Prod. 1996, 59, 293-296.
95. Stierle, A.C.; Cardellina, J.H., 2nd; Singleton, F.L. A marine micrococcus produces metabolites ascribed to the sponge Tedania ignis. Experientia 1988, 44, 1021.
96. De Rosa, S.; Mitova, M.; Tommonaro, G. Marine bacteria associated with sponge as source of cyclic peptides. Biomol. Eng. 2003, 20, 311-316.
97. Holden, M.T.; Ram Chhabra, S.; de Nys, R.; Stead, P.; Bainton, N.J.; Hill, P.J.; Manefield, M.; Kumar, N.; Labatte, M.; England, D.; et al. Quorum-sensing cross talk: Isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other Gram-negative bacteria. Mol. Microbiol. 1999, 33, 1254-1266.
98. Naik, D.N.; Wahidullah, S.; Meena, R.M. Attenuation of Pseudomonas aeruginosa virulence by marine invertebrate-derived Streptomyces sp. Lett. Appl. Microbiol. 2013, 56, 197-207.
99. Mansson, M.; Gram, L.; Larsen, T.O. Production of bioactive secondary metabolites by marine Vibrionaceae. Mar. Drugs 2011, 9, 1440-1468.
100. Mansson, M.; Nielsen, A.; Kjaerulff, L.; Gotfredsen, C.H.; Wietz, M.; Ingmer, H.; Gram, L.; Larsen, T.O. Inhibition of virulence gene expression in Staphylococcus aureus by novel depsipeptides from a marine Photobacterium. Mar. Drugs 2011, 9, 2537-2552.
101. Desriac, F.; Jegou, C.; Balnois, E.; Brillet, B.; Le Chevalier, P.; Fleury, Y. Antimicrobial peptides from marine Proteobacteria. Mar. Drugs 2013, 11, 3632-3660.
102. Curtis, M.M.; Russell, R.; Moreira, C.G.; Adebesin, A.M.; Wang, C.; Williams, N.S.; Taussig, R.; Stewart, D.; Zimmern, P.; Lu, B.; et al. QseC inhibitors as an antivirulence approach for Gram-negative pathogens. mBio 2014, 5, e02165.
103. Karavolos, M.H.; Winzer, K.; Williams, P.; Khan, C.M. Pathogen espionage: Multiple bacterial adrenergic sensors eavesdrop on host communication systems. Mol. Microbiol. 2013, 87, 455-465.
104. Rasko, D.A.; Sperandio, V. Anti-virulence strategies to combat bacteria-mediated disease. Nat. Rev. Drug Discov. 2010, 9, 117-128.
105. Dusane, D.H.; Pawar, V.S.; Nancharaiah, Y.V.; Venugopalan, V.P.; Kumar, A.R.; Zinjarde, S.S. Anti-biofilm potential of a glycolipid surfactant produced by a tropical marine strain of Serratia marcescens. Biofouling 2011, 27, 645-654.
106. Papa, R.; Parrilli, E.; Sannino, F.; Barbato, G.; Tutino, M.L.; Artini, M.; Selan, L. Anti-biofilm activity of the antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. Res. Microbiol. 2013, 164, 450-456.
107. Sayem, S.M.; Manzo, E.; Ciavatta, L.; Tramice, A.; Cordone, A.; Zanfardino, A.; de Felice, M.; Varcamonti, M. Anti-biofilm activity of an exopolysaccharide from a sponge-associated strain of Bacillus licheniformis. Microb. Cell Fact. 2011, 10, 74.
108. Thenmozhi, R.; Nithyanand, P.; Rathna, J.; Pandian, S.K. Antibiofilm activity of coral-associated bacteria against different clinical M serotypes of Streptococcus pyogenes. FEMS Immunol. Med. Microbiol. 2009, 57, 284-294.
109. Das, P.; Mukherjee, S.; Sen, R. Antiadhesive action of a marine microbial surfactant. Colloids Surf. B Biointerfaces 2009, 71, 183-186.
110. Dheilly, A.; Soum-Soutera, E.; Klein, G.L.; Bazire, A.; Compere, C.; Haras, D.; Dufour, A. Antibiofilm activity of the marine bacterium Pseudoalteromonas sp. Strain 3J6. Appl. Environ. Microbiol. 2010, 76, 3452-3461.
111. Rodrigues, S.; Paillard, C.; Dufour, A.; Bazire, A. Antibiofilm activity of the marine bacterium Pseudoalteromonas sp. 3J6 against Vibrio tapetis, the causative agent of brown ring disease. Probiotics Antimicrob. Proteins 2015, 7, 45-51.
112. Knight, R.; Jansson, J.; Field, D.; Fierer, N.; Desai, N.; Fuhrman, J.A.; Hugenholtz, P.; van der Lelie, D.; Meyer, F.; Stevens, R.; et al. Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 2012, 30, 513-520.
113. Suenaga, H. Targeted metagenomics: A high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ. Microbiol. 2012, 14, 13-22.
114. Wilson, M.C.; Mori, T.; Ruckert, C.; Uria, A.R.; Helf, M.J.; Takada, K.; Gernert, C.; Steffens, U.A.; Heycke, N.; Schmitt, S.; et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 2014, 506, 58-62.
115. Prakash, T.; Taylor, T.D. Functional assignment of metagenomic data: Challenges and applications. Brief. Bioinform. 2012, 13, 711-727.
116. Scholz, M.B.; Lo, C.C.; Chain, P.S. Next generation sequencing and bioinformatic bottlenecks: The current state of metagenomic data analysis. Curr. Opin. Biotechnol. 2012, 23, 9-15.
117. Teeling, H.; Glockner, F.O. Current opportunities and challenges in microbial metagenome analysis - A bioinformatic perspective. Brief. Bioinf. 2012, 13, 728-742.
118. Wooley, J.C.; Godzik, A.; Friedberg, I. A primer on metagenomics. PLoS Comput. Biol. 2010, 6, e1000667.
119. Wooley, J.C.; Ye, Y. Metagenomics: Facts and artifacts, and computational challenges&z.ast;. J. Comput. Sci. Technol. 2009, 25, 71-81.
120. Biggins, J.B.; Ternei, M.A.; Brady, S.F. Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. J. Am. Chem. Soc. 2012, 134, 13192-13195.
121. Gatte-Picchi, D.; Weiz, A.; Ishida, K.; Hertweck, C.; Dittmann, E. Functional analysis of environmental DNA-derived microviridins provides new insights into the diversity of the tricyclic peptide family. Appl. Environ. Microbiol. 2014, 80, 1380-1387.
122. Lim, F.Y.; Sanchez, J.F.; Wang, C.C.; Keller, N.P. Toward awakening cryptic secondary metabolite gene clusters in filamentous fungi. Methods Enzymol. 2012, 517, 303-324.
123. Luo, Y.; Huang, H.; Liang, J.; Wang, M.; Lu, L.; Shao, Z.; Cobb, R.E.; Zhao, H. Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster. Nat. Commun. 2013, 4, 2894.
124. Seyedsayamdost, M.R. High-throughput platform for the discovery of elicitors of silent bacterial gene clusters. Proc. Natl. Acad. Sci. USA 2014, 111, 7266-7271.
125. Blin, K.; Medema, M.H.; Kazempour, D.; Fischbach, M.A.; Breitling, R.; Takano, E.; Weber, T. AntiSMASH 2.0 - A versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 2013, 41, W204-W212.
126. Medema, M.H.; van Raaphorst, R.; Takano, E.; Breitling, R. Computational tools for the synthetic design of biochemical pathways. Nat. Rev. Microbiol. 2012, 10, 191-202.
127. Egan, F.; Reen, F.J.; O'Gara, F. Tle distribution and diversity in metagenomic datasets reveal niche specialization. Environ. Microbiol. Rep. 2014, 7, 194-203.
128. Macaulay, I.C.; Voet, T. Single cell genomics: Advances and future perspectives. PLoS Genet. 2014, 10, e1004126.
129. Xu, M.; Fujita, D.; Hanagata, N. Perspectives and challenges of emerging single-molecule DNA sequencing technologies. Small 2009, 5, 2638-2649.
130. Huang, S. Non-genetic heterogeneity of cells in development: More than just noise. Development 2009, 136, 3853-3862.
131. Luo, H.; Tolar, B.B.; Swan, B.K.; Zhang, C.L.; Stepanauskas, R.; Ann Moran, M.; Hollibaugh, J.T. Single-cell genomics shedding light on marine Thaumarchaeota diversification. ISME J. 2014, 8, 732-736.
132. Yoon, H.S.; Price, D.C.; Stepanauskas, R.; Rajah, V.D.; Sieracki, M.E.; Wilson, W.H.; Yang, E.C.; Duffy, S.; Bhattacharya, D. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 2011, 332, 714-717.
133. Roy, R.S.; Price, D.C.; Schliep, A.; Cai, G.; Korobeynikov, A.; Yoon, H.S.; Yang, E.C.; Bhattacharya, D. Single cell genome analysis of an uncultured heterotrophic Stramenopile. Sci. Rep. 2014, 4, 4780.
134. Barone, R.; de Santi, C.; Palma Esposito, F.; Tedesco, P.; Galati, F.; Visone, M.; DiScala, A.; de Pascale, D. Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery. Front. Mar. Sci. 2014, 1, 1-6.
135. Grindberg, R.V.; Ishoey, T.; Brinza, D.; Esquenazi, E.; Coates, R.C.; Liu, W.T.; Gerwick, L.; Dorrestein, P.C.; Pevzner, P.; Lasken, R.; et al. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS ONE 2011, 6, e18565.
136. Fjell, C.D.; Jenssen, H.; Hilpert, K.; Cheung, W.A.; Pante, N.; Hancock, R.E.W.; Cherkasov, A. Identification of novel antibacterial peptides by chemoinformatics and machine learning. J. Med. Chem. 2009, 52, 2006-2015.
137. Mitchell, J.B. Machine learning methods in chemoinformatics. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2014, 4, 468-481.
138. Frecer, V. QSAR analysis of antimicrobial and haemolytic effects of cyclic cationic antimicrobial peptides derived from protegrin-1. Bioorgan. Med. Chem. 2006, 14, 6065-6074.
139. Frecer, V.; Ho, B.; Ding, J.L. De novo design of potent antimicrobial peptides. Antimicrob. Agents Chemother. 2004, 48, 3349-3357.
140. Ostberg, N.; Kaznessis, Y. Protegrin structure-activity relationships: Using homology models of synthetic sequences to determine structural characteristics important for activity. Peptides 2005, 26, 197-206.
141. Sushko, Y.; Novotarskyi, S.; Korner, R.; Vogt, J.; Abdelaziz, A.; Tetko, I.V. Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process. J. Cheminf. 2014, 6, 48.
142. De Carvalho, C.C.; Fernandes, P. Production of metabolites as bacterial responses to the marine environment. Mar. Drugs 2010, 8, 705-727.
143. Kersten, R.D.; Yang, Y.L.; Xu, Y.; Cimermancic, P.; Nam, S.J.; Fenical, W.; Fischbach, M.A.; Moore, B.S.; Dorrestein, P.C. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 2011, 7, 794-802.
144. Medema, M.H.; Paalvast, Y.; Nguyen, D.D.; Melnik, A.; Dorrestein, P.C.; Takano, E.; Breitling, R. Pep2path: Automated mass spectrometry-guided genome mining of peptidic natural products. PLoS Comput. Biol. 2014, 10, e1003822.
145. Khalil, A.S.; Collins, J.J. Synthetic biology: Applications come of age. Nat. Rev. Genet. 2010, 11, 367-379.
146. Neumann, H.; Neumann-Staubitz, P. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl. Microbiol. Biotechnol. 2010, 87, 75-86.
147. Paddon, C.J.; Keasling, J.D. Semi-synthetic artemisinin: A model for the use of synthetic biology in pharmaceutical development. Nat. Rev. Microbiol. 2014, 12, 355-367.
148. Bloch, J.F.; Tardieu-Guigues, E. Marine biotechnologies and synthetic biology, new issues for a fair and equitable profit-sharing commercial use. Mar. Genomics 2014, 17, 79-83.