Using molecular networking for microbial secondary metabolite bioprospecting

Metabolites

Volumn 6, Issue 1, 2016, Pages

  Purves, Kevin ^a   Macintyre, Lynsey ^b   Brennan, Debra ^a   Hreggviðsson, Guðmundur Ó ^c,d   Kuttner, Eva ^c   Ásgeirsdóttir, Margrét E ^c   Young, Louise C ^b   Green, David H ^a   Edrada Ebel, Ruangelie ^b   Duncan, Katherine R ^a  

^a SCOTTISH MARINE INSTITUTE   (United Kingdom)

^b UNIVERSITY OF STRATHCLYDE   (United Kingdom)

^c Matis ohf Iceland   (Iceland)

^d UNIVERSITY OF ICELAND   (Iceland)

Author keywords

Antarctica; Bacteria; Bioprospecting; Molecular networking; Secondary metabolites

Indexed keywords

ACTINOBACTERIA; ADENOCARCINOMA; ARTICLE; BACTERIUM ISOLATION; CELL VIABILITY; CONTROLLED STUDY; DNA EXTRACTION; FERMENTATION; FIRMICUTES; GENE SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; METABOLITE; METABOLOMICS; MICROBIAL DIVERSITY; MICROBIAL SECONDARY METABOLITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; TANDEM MASS SPECTROMETRY; TAXONOMIC IDENTIFICATION;

EID: 85006189714     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo6010002     Document Type: Article

References (95)

1. David, A.H. Streptomyces in Nature and Medicine: the Antibiotic Makers; Oxford University Press: Oxford, UK, 2007.
2. Kayser, O.; Kiderlen, A.F.; Croft, S.L. Natural products as antiparasitic drugs. Parasitol. Res. 2003, 90 (Suppl. 2), S55-S62. [CrossRef] [PubMed]
3. Wright, A.D.; Konig, G.M.; Angerhofer, C.K.; Greenidges, P.; Linden, A.; Desqueyroux-Faundez, R. Antimalarial Activity: The Search for Marine-Derived Natural Products with Selective Antimalarial Activity. J. Nat. Prod. 1996, 59, 710-716. [CrossRef] [PubMed]
4. Clark, B.R.; Engene, N.; Teasdale, M.E.; Rowley, D.C.; Matainaho, T.; Valeriote, F.A.; Gerwick,W.H. Natural products chemistry and taxonomy of the marine cyanobacterium Blennothrix cantharidosmum. J. Nat. Prod. 2008, 71, 1530-1537. [CrossRef] [PubMed]
5. Mann, J. Natural products as immunosuppressive agents. Nat. Prod. Rep. 2001, 18, 417-430. [CrossRef] [PubMed]
6. Miyanaga, A.; Janso, J.E.; McDonald, L.; He, M.; Liu, H.; Barbieri, L.; Eustáquio, A.S.; Fielding, E.N.; Carter, G.T.; Jensen, P.R.; et al. Discovery and assembly-line biosynthesis of the lymphostin pyrroloquinoline alkaloid family of mTOR inhibitors in Salinispora bacteria. J. Am. Chem. Soc. 2011, 133, 13311-13313. [CrossRef] [PubMed]
7. Simmons, T.L.; Andrianasolo, E.; McPhail, K.; Flatt, P.; Gerwick, W.H. Marine natural products as anticancer drugs. Mol. Cancer Ther. 2005, 4, 333-342. [PubMed]
8. Eustáquio, A.S.; McGlinchey, R.P.; Liu, Y.; Hazzard, C.; Beer, L.L.; Florova, G.; Alhamadsheh, M.M.; Lechner, A.; Kale, A.J.; Kobayashi, Y.; et al. Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine. Proc. Natl. Acad. Sci. USA. 2009, 106, 12295-12300.
9. Wyche, T.P.; Hou, Y.; Braun, D.; Cohen, H.C.; Xiong, M.P.; Bugni, T.S. First natural analogs of the cytotoxic thiodepsipeptide thiocoraline A from a marine Verrucosispora sp. J. Org. Chem. 2011, 76, 6542-6547. [CrossRef] [PubMed]
10. Kohanski, M.A.; Dwyer, D.J.; Collins, J.J. How antibiotics kill bacteria: From targets to networks. Nat. Rev. Microbiol. 2010, 8, 423-435. [CrossRef] [PubMed]
11. Lewis, K. Platforms for antibiotic discovery. Nat. Rev. Drug Discov. 2013, 12, 371-387. [CrossRef] [PubMed]
12. Chait, R.; Vetsigian, K.; Kishony, R. What counters antibiotic resistance in nature? Nat. Chem. Biol. 2012, 8, 2-5. [CrossRef] [PubMed]
13. Torella, J.P.; Chait, R.; Kishony, R. Optimal drug synergy in antimicrobial treatments. PLoS Comput. Biol. 2010. [CrossRef]
14. Sogin, M.L.; Morrison, H.G.; Huber, J.A.; MarkWelch, D.; Huse, S.M.; Neal, P.R.; Arrieta, J.M.; Herndl, G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. USA. 2006, 103, 12115-12120. [CrossRef] [PubMed]
15. Chu, H.; Fierer, N.; Lauber, C.L.; Caporaso, J.G.; Knight, R.; Grogan, P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 2010, 12, 2998-3006. [CrossRef] [PubMed]
16. Ganzert, L.; Bajerski, F.; Wagner, D. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland. FEMS Microbiol. Ecol. 2014, 89, 426-441. [CrossRef] [PubMed]
17. Steven, B.; Pollard, W.H.; Greer, C.W.; Whyte, L.G. Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic. Environ. Microbiol. 2008, 10, 3388-3403. [CrossRef] [PubMed]
18. Sunagawa, S.;Woodley, C.M.; Medina, M. Threatened corals provide underexplored microbial habitats. PLoS ONE 2010. [CrossRef] [PubMed]
19. Hentschel, U.; Piel, J.; Degnan, S.M.; Taylor, M.W. Genomic insights into the marine sponge microbiome. Nat. Rev. Microbiol. 2012, 10, 641-654. [CrossRef] [PubMed]
20. Yang, S.; Sun,W.; Tang, C.; Jin, L.; Zhang, F.; Li, Z. Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea. Microb. Ecol. 2013, 66, 189-199. [CrossRef] [PubMed]
21. Hochmuth, T.; Piel, J. Polyketide synthases of bacterial symbionts in sponges-Evolution-based applications in natural products research. Phytochemistry 2009, 70, 1841-1849. [CrossRef] [PubMed]
22. Montalvo, N.F.; Mohamed, N.M.; Enticknap, J.J.; Hill, R.T. Novel actinobacteria from marine sponges. Antonie Van Leeuwenhoek 2005, 87, 29-36. [CrossRef] [PubMed]
23. Duncan, K.R.; Haltli, B.; Gill, K.A.; Correa, H.; Berrué, F.; Kerr, R.G. Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada. J. Ind. Microbiol. Biotechnol. 2015, 42, 57-72. [CrossRef] [PubMed]
24. Bredholt, H.; Fjaervik, E.; Johnsen, G.; Zotchev, S.B. Actinomycetes from sediments in the Trondheim fjord, Norway: Diversity and biological activity. Mar. Drugs 2008, 6, 12-24. [CrossRef] [PubMed]
25. Riedlinger, J.; Reicke, A.; Zähner, H.; Krismer, B.; Bull, A.T.; Maldonado, L.A.;Ward, A.C.; Goodfellow, M.; Bister, B.; Bischoff, D.; et al. Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032. J. Antibiot. 2004, 57, 271-279. [CrossRef] [PubMed]
26. Williams, P.G.; Buchanan, G.O.; Feling, R.H.; Kauffman, C.A.; Jensen, P.R.; Fenical, W. New cytotoxic salinosporamides from the marine Actinomycete Salinispora tropica. J. Org. Chem. 2005, 70, 6196-6203. [CrossRef] [PubMed]
27. Bérdy, J. Bioactive microbial metabolites. J. Antibiot. 2005, 58, 1-26. [CrossRef] [PubMed]
28. Nithya, C.; Devi, M.G.; Karutha Pandian, S. A novel compound from the marine bacterium Bacillus pumilus S6-15 inhibits biofilm formation in gram-positive and gram-negative species. Biofouling 2011, 27, 519-528. [CrossRef] [PubMed]
29. Yang, S.-C.; Lin, C.-F.; Chang, W.-Y.; Kuo, J.; Huang, Y.-T.; Chung, P.-J.; Hwang, T.-L. Bioactive secondary metabolites of a marine Bacillus sp. inhibit superoxide generation and elastase release in human neutrophils by blocking formyl peptide receptor 1. Molecules 2013, 18, 6455-6468. [CrossRef] [PubMed]
30. Mondol, M.A.M.; Shin, H.J.; Islam, M.T. Diversity of secondary metabolites from marine Bacillus species: Chemistry and biological activity. Mar. Drugs 2013, 11, 2846-2872. [CrossRef] [PubMed]
31. Blunt, J.W.; Copp, B.R.; Hu,W.-P.; Munro, M.H.G.; Northcote, P.T.; Prinsep, M.R. Marine natural products. Nat. Prod. Rep. 2007, 24, 31-86. [CrossRef] [PubMed]
32. Pathom-aree, W.; Stach, J.E.M.; Ward, A.C.; Horikoshi, K.; Bull, A.T.; Goodfellow, M. Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench. Extremophiles 2006, 10, 181-189. [CrossRef] [PubMed]
33. Bazire, A.; Diab, F.; Jebbar, M.; Haras, D. Influence of high salinity on biofilm formation and benzoate assimilation by Pseudomonas aeruginosa. J. Ind. Microbiol. Biotechnol. 2007, 34, 5-8. [CrossRef] [PubMed]
34. Ballav, S.; Kerkar, S.; Thomas, S.; Augustine, N. Halophilic and halotolerant actinomycetes from a marine saltern of Goa, India producing anti-bacterial metabolites. J. Biosci. Bioeng. 2015, 119, 323-330. [CrossRef] [PubMed]
35. Starič, N.; Danevčič, T.; Stopar, D. Vibrio sp. DSM 14379 pigment production-A competitive advantage in the environment? Microb. Ecol. 2010, 60, 592-598.
36. McDougald, D.; Rice, S.A.; Barraud, N.; Steinberg, P.D.; Kjelleberg, S. Should we stay or should we go: Mechanisms and ecological consequences for biofilm dispersal. Nat. Rev. Microbiol. 2012, 10, 39-50. [CrossRef] [PubMed]
37. Penn, K.; Jenkins, C.; Nett, M.; Udwary, D.W.; Gontang, E.A.; McGlinchey, R.P.; Foster, B.; Lapidus, A.; Podell, S.; Allen, E.E.; et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009, 3, 1193-1203. [CrossRef] [PubMed]
38. Ziemert, N.; Lechner, A.; Wietz, M.; Millán-Aguiñaga, N.; Chavarria, K.; Jensen, P.R. Diversity and Evolution of Secondary Metabolism in the Marine Actinomycete Genus Salinispora. Proc. Natl. Acad. Sci. USA. 2014, 111, E1130-E1139. [CrossRef] [PubMed]
39. Bull, A.T. Clean technology: Industry and environment, a viable partnership? Biologist 2000, 47, 61-64. [PubMed]
40. Andrianasolo, E.H.; Haramaty, L.; Rosario-Passapera, R.; Vetriani, C.; Falkowski, P.; White, E.; Lutz, R. Ammonificins C and D, hydroxyethylamine chromene derivatives from a cultured marine hydrothermal vent bacterium, Thermovibrio ammonificans. Mar. Drugs 2012, 10, 2300-2311. [CrossRef] [PubMed]
41. Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B.S.; Yang, J.Y.; Kersten, R.D.; van der Voort, M.; Pogliano, K.; Gross, H.; Raaijmakers, J.M.; et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl. Acad. Sci. USA. 2012, 109, E1743-E1752. [CrossRef] [PubMed]
42. Frank, A.M.; Bandeira, N.; Shen, Z.; Tanner, S.; Briggs, S.P.; Smith, R.D.; Pevzner, P.A. Clustering millions of tandem mass spectra. J. Proteome Res. 2008, 7, 113-122. [CrossRef] [PubMed]
43. Nguyen, D.D.; Wu, C.-H.; Moree, W.J.; Lamsa, A.; Medema, M.H.; Zhao, X.; Gavilan, R.G.; Aparicio, M.; Atencio, L.; Jackson, C.; et al. MS/MS networking guided analysis of molecule and gene cluster families. Proc. Natl. Acad. Sci. USA. 2013, 110, E2611-E2620. [CrossRef] [PubMed]
44. Yang, J.Y.; Sanchez, L.M.; Rath, C.M.; Liu, X.; Boudreau, P.D.; Bruns, N.; Glukhov, E.; Wodtke, A.; de Felicio, R.; Fenner, A.; et al. Molecular Networking as a Dereplication Strategy. J. Nat. Prod. 2013, 76, 1686-1699. [CrossRef] [PubMed]
45. Duncan, K.R.; Crüsemann, M.; Lechner, A.; Sarkar, A.; Li, J.; Ziemert, N.;Wang, M.; Bandeira, N.; Moore, B.S.; Dorrestein, P.C.; et al. Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species. Chem. Biol. 2015, 22, 460-471. [CrossRef] [PubMed]
46. Kersten, R.D.; Ziemert, N.; Gonzalez, D.J.; Duggan, B.M.; Nizet, V.; Dorrestein, P.C.; Moore, B.S. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. Proc. Natl. Acad. Sci. USA. 2013, 110, E4407-E4416. [CrossRef] [PubMed]
47. 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. [CrossRef] [PubMed]
48. Briand, E.; Bormans, M.; Gugger, M.; Dorrestein, P.C.; Gerwick, W.H. Changes in secondary metabolic profiles of Microcystis aeruginosa strains in response to intraspecific interactions. Environ. Microbiol. 2015. [CrossRef] [PubMed]
49. Winnikoff, J.R.; Glukhov, E.; Watrous, J.; Dorrestein, P.C.; Gerwick, W.H. Quantitative molecular networking to profile marine cyanobacterial metabolomes. J. Antibiot. 2014, 67, 105-112. [CrossRef] [PubMed]
50. Fang, J.; Dorrestein, P.C. Emerging mass spectrometry techniques for the direct analysis of microbial colonies. Curr. Opin. Microbiol. 2014, 19, 120-129. [CrossRef] [PubMed]
51. Klitgaard, A.; Nielsen, J.B.; Frandsen, R.J.N.; Andersen, M.R.; Nielsen, K.F. Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization. Anal. Chem. 2015, 87, 6520-6526. [CrossRef] [PubMed]
52. Maldonado, L.A.; Stach, J.E.M.; Pathom-Aree, W.; Ward, A.C.; Bull, A.T.; Goodfellow, M. Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie Van Leeuwenhoek 2005, 87, 11-18. [CrossRef] [PubMed]
53. Duncan, K.; Haltli, B.; Gill, K.A.; Kerr, R.G. Bioprospecting from marine sediments of New Brunswick, Canada: Exploring the relationship between total bacterial diversity and actinobacteria diversity. Mar. Drugs 2014, 12, 899-925. [CrossRef] [PubMed]
54. Murray, A.E.; Grzymski, J.J. Diversity and genomics of Antarctic marine micro-organisms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2007, 362, 2259-2271. [CrossRef] [PubMed]
55. Nicholson,W.L.; Munakata, N.; Horneck, G.; Melosh, H.J.; Setlow, P. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol. Mol. Biol. Rev. 2000, 64, 548-572. [CrossRef] [PubMed]
56. Sneath, P. Longevity of microorganisms. Nature 1962, 195, 643-646. [CrossRef] [PubMed]
57. Haselwandter, K.; Ebner, M.R. Microorganisms surviving for 5300 years. FEMS Microbiol. Lett. 1994, 116, 189-193. [CrossRef] [PubMed]
58. Jensen, P.R.; Gontang, E.; Mafnas, C.; Mincer, T.J.; Fenical, W. Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ. Microbiol. 2005, 7, 1039-1048. [CrossRef] [PubMed]
59. Zhang, H.; Zhang, W.; Jin, Y.; Meifang, J.; Yu, X. A comparative study on the phylogenetic diversity of culturable actinobacteria isolated from five marine sponge species. Antonie Van Leeuwenhoek 2008, 93, 241-248. [CrossRef] [PubMed]
60. Maldonado, L.A.; Fragoso-Yáñez, D.; Pérez-García, A.; Rosellón-Druker, J.; Quintana, E.T. Actinobacterial diversity from marine sediments collected in Mexico. Antonie Van Leeuwenhoek 2009, 95, 111-120. [CrossRef] [PubMed]
61. Mincer, T.J.; Jensen, P.R.; Kauffman, C.A.; Fenical,W.Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments. Appl. Environ. Microbiol. 2002, 68, 5005-5011. [CrossRef] [PubMed]
62. Weyland, H. Actinomycetes of the bottom sediments of various seas. In Proceedings of the Colloque International de Bacteriologie Marine, Brest, France, 1-5 October 1986; pp. 73-79.
63. Sass, A.M.; McKew, B.A; Sass, H.; Fichtel, J.; Timmis, K.N.; McGenity, T.J. Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments. Saline Syst. 2008. [CrossRef] [PubMed]
64. Da Silva, M.A.C.; Cavalett, A.; Spinner, A.; Rosa, D.C.; Jasper, R.B.; Quecine, M.C.; Bonatelli, M.L.; Pizzirani-Kleiner, A.; Corção, G.; Lima, A.O.D.S. Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean. Springerplus 2013, 2, 127. [CrossRef] [PubMed]
65. Palomo, S.; González, I.; de La Cruz, M.; Martín, J.; Tormo, J.R.; Anderson, M.; Hill, R.T.; Vicente, F.; Reyes, F.; Genilloud, O. Sponge-derived Kocuria and Micrococcus spp. as sources of the new thiazolyl peptide antibiotic kocurin. Mar. Drugs 2013, 11, 1071-1086. [CrossRef] [PubMed]
66. Jensen, P.R.; Williams, P.G.; Oh, D.-C.; Zeigler, L.; Fenical, W. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl. Environ. Microbiol. 2007, 73, 1146-1152. [CrossRef] [PubMed]
67. Jensen, P.R.; Mafnas, C. Biogeography of the marine actinomycete Salinispora. Environ. Microbiol. 2006, 8, 1881-1888. [CrossRef] [PubMed]
68. Charlop-Powers, Z.; Owen, J.G.; Reddy, B.V.B.; Ternei, M.A; Brady, S.F. Chemical-biogeographic survey of secondary metabolism in soil. Proc. Natl. Acad. Sci. USA. 2014, 111, 3757-3762. [CrossRef] [PubMed]
69. Dunshee, B.R.; Leben, C.; Keitt, G.W.; Strong, F.M. The Isolation and Properties of Antimycin A. J. Am. Chem. Soc. 1949, 71, 2436-2437. [CrossRef]
70. Viegelmann, C.; Margassery, L.M.; Kennedy, J.; Zhang, T.; O'Brien, C.; O'Gara, F.; Morrissey, J.P.; Dobson, A.D.W.; Edrada-Ebel, R. Metabolomic profiling and genomic study of a marine sponge-associated Streptomyces sp. Mar. Drugs 2014, 12, 3323-3351. [CrossRef] [PubMed]
71. Liaw, C.-C.; Chen, P.-C.; Shih, C.-J.; Tseng, S.-P.; Lai, Y.-M.; Hsu, C.-H.; Dorrestein, P.C.; Yang, Y.-L. Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach. Sci. Rep. 2015. [CrossRef] [PubMed]
72. Vijayabharathi, R.; Bruheim, P.; Andreassen, T.; Raja, D.S.; Devi, P.B.; Sathyabama, S.; Priyadarisini, V.B. Assessment of resistomycin, as an anticancer compound isolated and characterized from Streptomyces aurantiacus AAA5. J. Microbiol. 2011, 49, 920-926. [CrossRef] [PubMed]
73. Schorn, M.; Zettler, J.; Noel, J.P.; Dorrestein, P.C.; Moore, B.S.; Kaysser, L. Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. ACS Chem. Biol. 2014, 9, 301-309. [CrossRef] [PubMed]
74. Ohba, M.; Mizuki, E.; Uemori, A. Parasporin, a new anticancer protein group from Bacillus thuringiensis. Anticancer Res. 2009, 29, 427-433. [PubMed]
75. Ma, E.L.; Choi, Y.J.; Choi, J.; Pothoulakis, C.; Rhee, S.H.; Im, E. The anticancer effect of probiotic Bacillus polyfermenticus on human colon cancer cells is mediated through ErbB2 and ErbB3 inhibition. Int. J. Cancer 2010, 127, 780-790. [PubMed]
76. Howe, J.A.; Shimmield, T.M.; Diaz, R. Deep-water sedimentary environments of the northwestern Weddell Sea and South Sandwich Islands, Antarctica. Deep Sea Res. 2004, 51, 1489-1514. [CrossRef]
77. Sea, N.W.; Howe, J.A.; Wilson, C.R.; Shimmield, T.M.; Diaz, R.J.; Carpenter, L.W. Recent deep-water sedimentation, trace metal and radioisotope geochemistry across the Southern Ocean and Northern Weddell Sea, Antarctica. Deep Sea Res. 2007, 54, 1652-1681.
78. Shiring, E.B.; Gottlieb, D. Methods for the Characterization of Streptomyces species. Int. J. Syst. Evol. Microbiol. 1966, 16, 313-340.
79. Macintyre, L.; Zhang, T.; Viegelmann, C.; Martinez, I.J.; Cheng, C.; Dowdells, C.; Abdelmohsen, U.R.; Gernert, C.; Hentschel, U.; Edrada-Ebel, R. Metabolomic tools for secondary metabolite discovery from marine microbial symbionts. Mar. Drugs 2014, 12, 3416-3448. [CrossRef] [PubMed]
80. Deutsch, E.W.; Mendoza, L.; Shteynberg, D.; Farrah, T.; Lam, H.; Sun, Z.; Nilsson, E.; Pratt, B.; Prazen, B.; Eng, J.K.; et al. A Guided Tour of the Trans-Proteomic Pipeline. Proteomics 2011, 10, 1150-1159. [CrossRef] [PubMed]
81. GNPS. The Future of Natural Products Research and Mass Spectrometry. Available online: http://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp (accessed on 7 January 2016).
82. Guthals, A.;Watrous, J.D.; Dorrestein, P.C.; Bandeira, N. The spectral networks paradigm in high throughput mass spectrometry. Mol. Biosyst. 2012, 8, 2535-2544. [CrossRef] [PubMed]
83. Keller, A.; Eng, J.; Zhang, N.; Li, X.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005. [CrossRef] [PubMed]
84. Smoot, M.E.; Ono, K.; Ruscheinski, J.; Wang, P.-L.; Ideker, T. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 2011, 27, 431-432. [CrossRef] [PubMed]
85. Cline, M.S.; Smoot, M.; Cerami, E.; Kuchinsky, A.; Landys, N.;Workman, C.; Christmas, R.; Avila-Campilo, I.; Creech, M.; Gross, B.; et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2007, 2, 2366-2382. [CrossRef] [PubMed]
86. Chambers, M.C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D.L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, B.; Egertson, J.; et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920. [CrossRef] [PubMed]
87. Pluskal, T.; Castillo, S.; Villar-Briones, A.; Oresic, M. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinform. 2010. [CrossRef] [PubMed]
88. Hopwood, D.A.; Bibb, M.J.; Chater, K.F.; Kieser, T.; Bruton, C.J.; Kieser, H.M.; Lydiate, D.J.; Smith, C.P.; Ward, J.M.; Schrempf, H. Genetic Manipulation of Streptomyces: A laboratory manual. Biochem. Educ. 1986. [CrossRef]
89. Weisburg, W.G.; Barns, S.M.; Pelletie, D.A; Lane, D.J. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 1991, 173, 697-703. [PubMed]
90. Sambrook, J.; Russel, D.W. Molecular Cloning: A Laboratory Manual; Cold pring Harbor Laboratory Press: New York, NY, USA, 2001.
91. Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28, 1647-1649. [CrossRef] [PubMed]
92. Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol. 1990, 215, 403-410. [CrossRef]
93. Thompson, J.D.; Higgins, D.G.; Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22, 4673-4680. [CrossRef] [PubMed]
94. Saitou, N.; Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406-425. [PubMed]
95. Jukes, T.H.; Cantor, C.R. Evolution of Protein Models; Academic Press: New York, NY, USA, 1969.