Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Rocha-Martin, Javier; Harrington, Catriona; Dobson, Alan; O'Gara, Fergal

doi:10.3390/md12063516

Cited by 84Microbial Natural Products and BiosynthesisMarine Sponges and Natural ProductsSynthesis and Biological Activity

Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Open access

Rocha-Martin, Javier, Harrington, Catriona, Dobson, Alan, O'Gara, Fergal·2014·Marine Drugs

DOI 10.3390/md12063516PMC PMC4071589

Open this paper in CoChat — free account Open PDF

Abstract

Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.3390/md12063516

Cites

236 of 236 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
The RAST Server: Rapid Annotations using Subsystems Technology
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T. L., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-75 · Cited by 11,777 · see citing works
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227 · see citing works
Marine natural products
Faulkner, D. J. (1990) · Natural Product Reports · doi:10.1039/np9900700269 · Cited by 4,880 · see citing works
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · cited 1× · see citing works
“67 × 10 30 cells [5].”
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376 · see citing works
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. B. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,683 · see citing works
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565 · see citing works
MEGAN analysis of metagenomic dataPreprint
Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007) · Genome Research · doi:10.1101/gr.5969107 · Cited by 3,293 · see citing works
National Center for Biotechnology Information
Gressner, A. M., & Arndt, T. (2019) · Springer Reference Medizin · doi:10.1007/978-3-662-48986-4_301184 · Cited by 2,610 · see citing works
Metagenomics: Application of Genomics to Uncultured Microorganisms
Handelsman, J. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.4.669-685.2004 · Cited by 2,454 · see citing works
Drug Discovery and Natural Products: End of an Era or an Endless Frontier?
Li, J. W.-H., & Vederas, J. C. (2009) · Science · doi:10.1126/science.1168243 · Cited by 2,056 · see citing works
Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
Muyzer, G., & Smalla, K. (1998) · Antonie van Leeuwenhoek · doi:10.1023/a:1000669317571 · Cited by 2,051 · see citing works
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
Medema, M. H., Blin, K., Cimermančič, P., de Jager, V., Zakrzewski, P., Fischbach, M. A., Weber, T., Eriko Takano, A., & Rainer Breitling, A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr466 · Cited by 2,013 · see citing works
Handbook of Hydrocarbon and Lipid Microbiology
Timmis, K. N. (2009) · Springer eBooks · doi:10.1007/978-3-540-77587-4 · Cited by 1,959 · see citing works
Microbial diversity and function in soil: from genes to ecosystems
Torsvik, V. L., & Øvreås, L. (2002) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(02)00324-7 · Cited by 1,927 · see citing works
GeneMark.hmm: new solutions for gene finding
Lukashin, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.4.1107 · Cited by 1,536 · see citing works
Programming cells by multiplex genome engineering and accelerated evolution
Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009) · Nature · doi:10.1038/nature08187 · Cited by 1,529 · see citing works
Assembly-Line Enzymology for Polyketide and Nonribosomal Peptide Antibiotics: Logic, Machinery, and Mechanisms
Fischbach, M. A., & Walsh, C. T. (2006) · Chemical Reviews · doi:10.1021/cr0503097 · Cited by 1,469 · see citing works
Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential
Taylor, M. W., Radax, R., Steger, D., & Wagner, M. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00040-06 · Cited by 1,463 · see citing works
Synthetic biology: applications come of age
Khalil, A. S., & Collins, J. J. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2775 · Cited by 1,385 · see citing works
The Biosynthetic Logic of Polyketide Diversity
Hertweck, C. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200806121 · Cited by 1,350 · see citing works
Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment
Kaeberlein, T., Lewis, K., & Epstein, S. S. (2002) · Science · doi:10.1126/science.1070633 · Cited by 1,239 · see citing works
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
Noguchi, H., Park, J., & Takagi, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl723 · Cited by 1,163 · see citing works
Growing Unculturable Bacteria
Stewart, E. J. (2012) · Journal of Bacteriology · doi:10.1128/jb.00345-12 · Cited by 1,154 · see citing works
Metagenomics: Genomic Analysis of Microbial Communities
Riesenfeld, C. S., Schloss, P. D., & Handelsman, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.091216 · Cited by 1,124 · see citing works
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
Rappé, M. S., Connon, S. A., Vergin, K. L., & Giovannoni, S. J. (2002) · Nature · doi:10.1038/nature00917 · Cited by 1,020 · see citing works
Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology
Smith, C. J., & Osborn, A. M. (2008) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2008.00629.x · Cited by 939 · see citing works
Next‐generation sequencing technologies for environmental DNA research
Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05538.x · Cited by 939 · see citing works
Exploring prokaryotic diversity in the genomic era.
Hugenholtz, P. (2002) · Genome biology · doi:10.1186/gb-2002-3-2-reviews0003 · Cited by 887 · see citing works
Manufacturing Molecules Through Metabolic Engineering
Keasling, J. D. (2010) · Science · doi:10.1126/science.1193990 · Cited by 829 · see citing works
Bacterioplankton Compositions of Lakes and Oceans: a First Comparison Based on Fluorescence In Situ Hybridization
Glöckner, F. O., Fuchs, B. M., & Amann, R. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.8.3721-3726.1999 · Cited by 817 · see citing works
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers
Blin, K., Medema, M. H., Kazempour, D., Fischbach, M. A., Rainer Breitling, A., Eriko Takano, A., & Weber, T. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt449 · Cited by 798 · see citing works
Cultivating the uncultured
Zengler, K., Toledo, G., Rappé, M., Elkins, J., Mathur, E. J., Short, J. M., & Keller, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252630999 · Cited by 796 · see citing works
Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms
Moter, A., & Göbel, U. B. (2000) · Journal of Microbiological Methods · doi:10.1016/s0167-7012(00)00152-4 · Cited by 786 · see citing works
Biosynthesis of Complex Polyketides in a Metabolically Engineered Strain of E. coli
Pfeifer, B. A., Admiraal, S. J., Gramajo, H. C., Cane, D. E., & Khosla, C. (2001) · Science · doi:10.1126/science.1058092 · Cited by 751 · see citing works
High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates
Connon, S. A., & Giovannoni, S. J. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.8.3878-3885.2002 · Cited by 742 · see citing works
A latitudinal diversity gradient in planktonic marine bacteria
Fuhrman, J. A., Steele, J. A., Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., & Brown, J. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803070105 · Cited by 733 · see citing works
Strategies for culture of ‘unculturable’ bacteria
Vartoukian, S. R., Palmer, R. M. J., & Wade, W. G. (2010) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2010.02000.x · Cited by 721 · see citing works
Marine sponges and their microbial symbionts: love and other relationships
Webster, N. S., & Taylor, M. W. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02460.x · Cited by 644 · see citing works
Polyketide and Nonribosomal Peptide Antibiotics: Modularity and Versatility
Walsh, C. T. (2004) · Science · doi:10.1126/science.1094318 · Cited by 631 · see citing works
Molecular Networking as a Dereplication Strategy
Yang, J. Y., Sanchez, L. M., Rath, C. M. B., Liu, X., Boudreau, P. D., Bruns, N., Glukhov, E., Wodtke, A., de Felício, R., Fenner, A. M., et al. (2013) · Journal of Natural Products · doi:10.1021/np400413s · Cited by 613 · see citing works
Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350
Ohnishi, Y., Ishikawa, J., Hara, H., Suzuki, H., Ikenoya, M., Ikeda, H., Yamashita, A., Hattori, M., & Horinouchi, S. (2008) · Journal of Bacteriology · doi:10.1128/jb.00204-08 · Cited by 564 · see citing works
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., et al. (2011) · Science · doi:10.1126/science.1205822 · Cited by 550 · see citing works
IMG 4 version of the integrated microbial genomes comparative analysis system
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Woyke, T., Huntemann, M., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt963 · Cited by 546 · see citing works
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica
Udwary, D., Allen, L. Z., Asolkar, R. N., Singan, V. R., Lapidus, A. L., Fenical, W., Jensen, P. R., & Moore, B. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700962104 · Cited by 537 · see citing works
High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment
DeSantis, T. Z., Brodie, E., Parker, J. M., Zubieta, I. X., Piceno, Y. M., & Andersen, G. L. (2007) · Microbial Ecology · doi:10.1007/s00248-006-9134-9 · Cited by 509 · see citing works
Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead
Konstantinidis, K. T., & Tiedje, J. M. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.08.006 · Cited by 499 · see citing works
Isolation of Antibiotics Turbomycin A and B from a Metagenomic Library of Soil Microbial DNA
Gillespie, D. E., Brady, S. F., Bettermann, A. D., et al. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.9.4301-4306.2002 · Cited by 495 · see citing works
Marine natural products
Blunt, J. W., Copp, B. R., Keyzers, R. A., Munro, M. H. G., & Prinsep, M. R. (2014) · Natural Product Reports · doi:10.1039/c3np70117d · Cited by 488 · see citing works
Marine natural products
Blunt, J. W., Copp, B. R., Keyzers, R. A., Munro, M. H. G., & Prinsep, M. R. (2011) · Natural Product Reports · doi:10.1039/c2np00090c · Cited by 482 · see citing works
BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides
van Heel, A. J., de Jong, A., Montalbán‐López, M., Kok, J., & Kuipers, O. P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt391 · Cited by 477 · see citing works
Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization
Cottrell, M. T., & Kirchman, D. L. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.12.5116-5122.2000 · Cited by 456 · see citing works
Cloning and Heterologous Expression of the Epothilone Gene Cluster
Tang, L., Shah, S. J., Chung, L., et al. (2000) · Science · doi:10.1126/science.287.5453.640 · Cited by 424 · see citing works
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts
Webster, N. S., Taylor, M. W., Behnam, F., Lücker, S., Rattei, T., Whalan, S., Horn, M., & Wagner, M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02065.x · Cited by 420 · see citing works
Marine Sponges as Pharmacy
Sipkema, D., Franssen, M. C. R., Osinga, R., TRAMPER, J., & Wijffels, R. H. (2005) · Marine Biotechnology · doi:10.1007/s10126-004-0405-5 · Cited by 419 · see citing works
Metaproteomics: studying functional gene expression in microbial ecosystems
Wilmes, P., & Bond, P. L. (2006) · Trends in Microbiology · doi:10.1016/j.tim.2005.12.006 · Cited by 416 · see citing works
CAMERA: A Community Resource for Metagenomics
Seshadri, R., Kravitz, S. A., Smarr, L. L., Gilna, P., & Frazier, M. E. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050075 · Cited by 394 · see citing works
Immense essence of excellence: Marine microbial bioactive compounds
Bhatnagar, I., & Kim, S.-K. (2010) · Marine Drugs · doi:10.3390/md8102673 · Cited by 384 · see citing works
SAR11 marine bacteria require exogenous reduced sulphur for growth
Tripp, H. J., Kitner, J. B., Schwalbach, M. S., Dacey, J. W. H., Wilhelm, L., & Giovannoni, S. J. (2008) · Nature · doi:10.1038/nature06776 · Cited by 378 · see citing works
BACTIBASE second release: a database and tool platform for bacteriocin characterization
Hammami, R., Zouhir, A., Lay, C., Hamida, J. B., & Fliss, I. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-22 · Cited by 370 · see citing works
Ecophysiological Interaction between Nitrifying Bacteria and Heterotrophic Bacteria in Autotrophic Nitrifying Biofilms as Determined by Microautoradiography-Fluorescence In Situ Hybridization
Kindaichi, T., Ito, T., & Okabe, S. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.3.1641-1650.2004 · Cited by 368 · see citing works
Optimization of Terminal-Restriction Fragment Length Polymorphism Analysis for Complex Marine Bacterioplankton Communities and Comparison with Denaturing Gradient Gel Electrophoresis
Moeseneder, M. M., Arrieta, J. M., Muyzer, G., et al. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.8.3518-3525.1999 · Cited by 358 · see citing works
Microbes and Microbial Technology
Ahmad, I., Ahmed, F. K., & Pichtel, J. (2011) · Springer eBooks · doi:10.1007/978-1-4419-7931-5 · Cited by 353 · see citing works
Microarrays for bacterial detection and microbial community analysis
Zhou, J. Z. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00052-3 · Cited by 348 · see citing works
Biocatalytic retrosynthesis
Turner, N. J., & O’Reilly, E. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1235 · Cited by 347 · see citing works
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea
Sowell, S. M., Wilhelm, L., Norbeck, A. D., et al. (2008) · The ISME Journal · doi:10.1038/ismej.2008.83 · Cited by 338 · see citing works
Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment
Rastogi, G., & Sani, R. K. (2011) · Springer eBooks · doi:10.1007/978-1-4419-7931-5_2 · Cited by 332 · see citing works
A genomics-guided approach for discovering and expressing cryptic metabolic pathways
Zazopoulos, E., Huang, K.-X., Staffa, A., Liu, W., Bachmann, B. O., Nonaka, K., Ahlert, J., Thorson, J. S., Shen, B., & Farnet, C. M. (2003) · Nature Biotechnology · doi:10.1038/nbt784 · Cited by 317 · see citing works
Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions
Schut, F., de Vries, E. J., Gottschal, J. C., Robertson, B. R., Harder, W., Prins, R. A., & Button, D. K. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.7.2150-2160.1993 · Cited by 310 · see citing works
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
Morris, R. M., Nunn, B. L., Frazar, C. D., Goodlett, D. R., Ting, Y. S., & Rocap, G. (2010) · The ISME Journal · doi:10.1038/ismej.2010.4 · Cited by 293 · see citing works
Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
Stepanauskas, R., & Sieracki, M. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700496104 · Cited by 285 · see citing works
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
Bernal, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.126 · Cited by 285 · see citing works
A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters
Williams, T. J., Long, E., Evans, F. F., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.28 · Cited by 277 · see citing works
Automated genome mining for natural products
Li, M. H., Ung, P. M. U., Zajkowski, J., et al. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-185 · Cited by 276 · see citing works
Single-cell genomics reveals the lifestyle of <i>Poribacteria</i> , a candidate phylum symbiotically associated with marine sponges
Siegl, A., Kamke, J., Hochmuth, T., Piel, J., Richter, M., Liang, C., Dandekar, T., & Hentschel, U. (2011) · The ISME Journal · doi:10.1038/ismej.2010.95 · Cited by 276 · see citing works
Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats
Nübel, U., García‐Pichel, F., Kühl, M., & Gerard Muyzer, C. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.2.422-430.1999 · Cited by 268 · see citing works
Novel Natural Products from Soil DNA Libraries in a Streptomycete Host
Wang, G.-Y.-S., Graziani, E. I., Waters, B., et al. (2000) · Organic Letters · doi:10.1021/ol005860z · Cited by 264 · see citing works
Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms
Radajewski, S. M., McDonald, I. R., & Murrell, J. C. (2003) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(03)00064-8 · Cited by 261 · see citing works
Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy
Heyndrickx, M., Vauterin, L., Vandamme, P. A. R., Kersters, K., & Vos, P. D. (1996) · Journal of Microbiological Methods · doi:10.1016/0167-7012(96)00916-5 · Cited by 259 · see citing works
Coupling 16S‐ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series
Brown, M. V., Schwalbach, M. S., Hewson, I., & Fuhrman, J. A. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00835.x · Cited by 255 · see citing works
NCBI (National Center for Biotechnology Information)
Stoesser, G. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/0471650129.dob0477 · Cited by 252 · see citing works
Diversity of Secondary Metabolites from Marine Bacillus Species: Chemistry and Biological Activity
Mondol, M. A. M., Shin, H. Y., & Islam, T. (2013) · Marine Drugs · doi:10.3390/md11082846 · Cited by 250 · see citing works
Metabolic engineering of Agrobacterium sp. strain ATCC 31749 for production of an α-Gal epitope
Ruffing, A. M., & Chen, R. R. (2010) · Microbial Cell Factories · doi:10.1186/1475-2859-9-1 · Cited by 248 · see citing works
Synthesis of Methyl Halides from Biomass Using Engineered Microbes
Bayer, T. S., Widmaier, D. M., Temme, K., Mirsky, E. A., Santi, D. V., & Voigt, C. A. (2009) · Journal of the American Chemical Society · doi:10.1021/ja809461u · Cited by 241 · see citing works
Exploring Nitrilase Sequence Space for Enantioselective Catalysis
Robertson, D. E., Chaplin, J. A., DeSantis, G., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.4.2429-2436.2004 · Cited by 231 · see citing works
Engineered Biosynthesis of a Complete Macrolactone in a Heterologous Host
Kao, C. M., Katz, L., & Khosla, C. (1994) · Science · doi:10.1126/science.8036492 · Cited by 229 · see citing works
Marine Biocatalysts: Enzymatic Features and Applications
Trincone, A. (2011) · Marine Drugs · doi:10.3390/md9040478 · Cited by 228 · see citing works
Viable but nonculturable bacteria: a survival strategy
Colwell, R. R. (2000) · Journal of Infection and Chemotherapy · doi:10.1007/pl00012151 · Cited by 224 · see citing works
Total biosynthesis of antitumor nonribosomal peptides in Escherichia coli
Watanabe, K., Hotta, K., Praseuth, A. P., Koketsu, K., Migita, A., Boddy, C. N. C., Wang, C. C. C., Oguri, H., & Oikawa, H. (2006) · Nature Chemical Biology · doi:10.1038/nchembio803 · Cited by 223 · see citing works
The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function
Adamczyk, J., Hesselsøe, M., Iversen, N., et al. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.11.6875-6887.2003 · Cited by 221 · see citing works
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Yu, Y., Breitbart, M., McNairnie, P., & Rohwer, F. L. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-57 · Cited by 213 · see citing works
Meta-omic Characterization of the Marine Invertebrate Microbial Consortium That Produces the Chemotherapeutic Natural Product ET-743
Rath, C. M. B., Janto, B., Earl, J., Ahmed, A., Hu, F. Z., Hiller, N. L., Dahlgren, M., Kreft, R., Yu, F., Wolff, J. J., et al. (2011) · ACS Chemical Biology · doi:10.1021/cb200244t · Cited by 208 · see citing works
Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor
Williamson, L. L., Borlee, B. R., Schloss, P. D., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.10.6335-6344.2005 · Cited by 199 · see citing works
Dominant marine bacterioplankton species found among colony-forming bacteria
Pinhassi, J., Zweifel, U., & Hagström, Å. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.9.3359-3366.1997 · Cited by 199 · see citing works
Statistical Research on Marine Natural Products Based on Data Obtained between 1985 and 2008
Hu, G., Yuan, J. X., Sun, L., She, Z., Wu, J., Lan, X., Zhu, X., Lin, Y., & Chen, S.-P. (2011) · Marine Drugs · doi:10.3390/md9040514 · Cited by 190 · see citing works
Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment
Hårdeman, F., & SjÃ¶ling, S. (2006) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2006.00206.x · Cited by 181 · see citing works
Molecular Basis for Chloronium-mediated Meroterpene Cyclization
Winter, J. M., Moffitt, M. C., Zazopoulos, E., et al. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m611046200 · Cited by 181 · see citing works
SBSPKS: structure based sequence analysis of polyketide synthases
Anand, S., Prasad, M., Yadav, G., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq340 · Cited by 181 · see citing works
Biosynthesis of natural products by microbial iterative hybrid PKS–NRPS
Fisch, K. M. (2013) · RSC Advances · doi:10.1039/c3ra42661k · Cited by 168 · see citing works
Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism
Kennedy, J., Flemer, B., Jackson, S. A., Lejon, D. P. H., Morrissey, J. P., O’Gara, F., & Dobson, A. D. W. (2010) · Marine Drugs · doi:10.3390/md8030608 · Cited by 165 · see citing works
Self-citation
Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis The DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642.
Urakawa, H., Kita-Tsukamoto, K., & Ohwada, K. (1999) · Microbiology · doi:10.1099/00221287-145-11-3305 · Cited by 161 · see citing works
Production of a New Thiopeptide Antibiotic, TP-1161, by a Marine Nocardiopsis Species
Engelhardt, K., Degnes, K. F., Kemmler, M., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00741-10 · Cited by 159 · see citing works
Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR
Neilan, B. A. (1995) · Applied and Environmental Microbiology · doi:10.1128/aem.61.6.2286-2291.1995 · Cited by 157 · see citing works
Heterologous Production of Epothilone C and D in Escherichia coli
Mutka, S. C., Carney, J. R., Liu, Y., et al. (2006) · Biochemistry · doi:10.1021/bi052075r · Cited by 153 · see citing works
The chemical biology of modular biosynthetic enzymes
Meier, J. L., & Burkart, M. D. (2009) · Chemical Society Reviews · doi:10.1039/b805115c · Cited by 152 · see citing works
The granaticin biosynthetic gene cluster of Streptomyces violaceoruber Tü22: sequence analysis and expression in a heterologous host
Ichinose, K., Bedford, D. J., Tornus, D., Bechthold, A., Bibb, M. J., Revill, W. P., Floss, H. G., & Hopwood, D. A. (1998) · Chemistry & Biology · doi:10.1016/s1074-5521(98)90292-7 · Cited by 151 · see citing works
Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing
Wellington, E. M. H., Berry, A. E., & Krsek, M. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00066-3 · Cited by 150 · see citing works
Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition
Fu, J., Wenzel, S. C., Perlova, O., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn499 · Cited by 148 · see citing works
Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites
Feng, Z., Kallifidas, D., & Brady, S. F. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103921108 · Cited by 147 · see citing works
Methods and options for the heterologous production of complex natural products
Zhang, H., Boghigian, B. A., Armando, J. W., & Pfeifer, B. A. (2010) · Natural Product Reports · doi:10.1039/c0np00037j · Cited by 147 · see citing works
A proteomics approach to discovering natural products and their biosynthetic pathways
Bumpus, S. B., Evans, B. S., Thomas, P. M., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1565 · Cited by 143 · see citing works
Identification of two novel esterases from a marine metagenomic library derived from South China Sea
Chu, X., He, H., Guo, C., et al. (2008) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-008-1566-3 · Cited by 139 · see citing works
Combinatorial biosynthesis of polyketides — a perspective
Wong, F. T., & Khosla, C. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.01.018 · Cited by 138 · see citing works
Heterologous expression of natural product biosynthetic gene clusters in Streptomyces coelicolor: from genome mining to manipulation of biosynthetic pathways
Gomez‐Escribano, J. P., & Bibb, M. J. (2013) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-013-1348-5 · Cited by 134 · see citing works
Engineering Fluorometabolite Production: Fluorinase Expression in Salinispora tropica Yields Fluorosalinosporamide
Eustáquio, A. S., O’Hagan, D., & Moore, B. S. (2010) · Journal of Natural Products · doi:10.1021/np900719u · Cited by 133 · see citing works
Kinase Inhibitors of Marine Origin
Bharate, S. B., Sawant, S. D., Singh, P. P., & Vishwakarma, R. A. (2013) · Chemical Reviews · doi:10.1021/cr300410v · Cited by 130 · see citing works
A bacterial laccase from marine microbial metagenome exhibiting chloride tolerance and dye decolorization ability
Fang, Z., Tong-liang, L., Wang, Q., et al. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2934-3 · Cited by 129 · see citing works
Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules
Banik, J. J., & Brady, S. F. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.08.012 · Cited by 126 · see citing works
Biosynthesis of Yersiniabactin, a Complex Polyketide-Nonribosomal Peptide, Using Escherichia coli as a Heterologous Host
Pfeifer, B. A., Wang, C. C. C., Walsh, C. T., & Khosla, C. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.11.6698-6702.2003 · Cited by 126 · see citing works
Metagenomic approaches to natural products from free-living and symbiotic organisms
Brady, S. F., Simmons, L., Kim, J. H., & Schmidt, E. W. (2009) · Natural Product Reports · doi:10.1039/b817078a · Cited by 125 · see citing works
Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters
Ichinose, K., Ozawa, M., Itou, K., Kunieda, K., & Ebizuka, Y. (2003) · Microbiology · doi:10.1099/mic.0.26310-0 · Cited by 122 · see citing works
Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase
Zhang, W., Ames, B. D., Tsai, S., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.4.2573-2580.2006 · Cited by 121 · see citing works
Culture-Dependent and -Independent Characterization of Microbial Communities Associated with a Shallow Submarine Hydrothermal System Occurring within a Coral Reef off Taketomi Island, Japan
Hirayama, H., Sunamura, M., Takai, K., Nunoura, T., Noguchi, T., Oida, H., Furushima, Y., Yamamoto, H., Oomori, T., & Horikoshi, K. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01258-07 · Cited by 118 · see citing works
Characterization of the Dominant and Rare Members of a Young Hawaiian Soil Bacterial Community with Small-Subunit Ribosomal DNA Amplified from DNA Fractionated on the Basis of Its Guanine and Cytosine Composition
Nüsslein, K. R., & Tiedje, J. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.4.1283-1289.1998 · Cited by 117 · see citing works
Diversity and Biocatalytic Potential of Epoxide Hydrolases Identified by Genome Analysis
van Loo, B., Kingma, J., Arand, M., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.4.2905-2917.2006 · Cited by 116 · see citing works
Sustainable production of biologically active molecules of marine based origin
Murray, P., Moane, S., Collins, C., Beletskaya, T., Thomas, O., Duarte, A. W. F., Nobre, F. S., Dayo-Owoyemi, I., Pagnocca, F. C., Sette, L. D., et al. (2013) · New Biotechnology · doi:10.1016/j.nbt.2013.03.006 · Cited by 114 · see citing works
Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules
Kersten, R. D., Ziemert, N., Gonzalez, D. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315492110 · Cited by 113 · see citing works
Combinatorial biosynthesis for drug development
Menzella, H. G., & Reeves, C. D. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.05.005 · Cited by 109 · see citing works
Integrated metagenomic and metaproteomic analyses of an ANME‐1‐dominated community in marine cold seep sediments
Stokke, R., Roalkvam, I., Lanzén, A., Haflidason, H., & Steen, I. H. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02716.x · Cited by 108 · see citing works
Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico
Wu, L., Kellogg, L. E., Devol, A. H., Tiedje, J. M., & Zhou, J. Z. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02751-07 · Cited by 106 · see citing works
Expression of a functional fungal polyketide synthase in the bacterium Streptomyces coelicolor A3(2)
Bedford, D. J., Schweizer, E., Hopwood, D. A., et al. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.15.4544-4548.1995 · Cited by 106 · see citing works
A comparison of stable‐isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate‐reducing marine sediment enrichment slurries
Webster, G., Watt, L. C., Rinna, J., et al. (2006) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01048.x · Cited by 102 · see citing works
A Genomic Screening Approach to the Structure‐Guided Identification of Drug Candidates from Natural Sources
Hornung, A., Bertazzo, M., Dziarnowski, A., et al. (2007) · ChemBioChem · doi:10.1002/cbic.200600375 · Cited by 101 · see citing works
Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria
Al-Awadhi, H. A., Dashti, N., Khanafer, M., et al. (2013) · SpringerPlus · doi:10.1186/2193-1801-2-369 · Cited by 100 · see citing works
Diversity of microbes associated with the marine sponge, Haliclona simulans , isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome
Kennedy, J., Codling, C. E., Jones, B. V., Dobson, A. D. W., & Marchesi, J. R. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01614.x · Cited by 99 · see citing works
Self-citation
Cultivating previously uncultured soil bacteria using a soil substrate membrane system
Ferrari, B. C., Winsley, T. J., Gillings, M. R., & Binnerup, S. J. (2008) · Nature Protocols · doi:10.1038/nprot.2008.102 · Cited by 98 · see citing works
Subtilomycin: A New Lantibiotic from Bacillus subtilis Strain MMA7 Isolated from the Marine Sponge Haliclona simulans
Phelan, R. W., Barret, M., Cotter, P. D., et al. (2013) · Marine Drugs · doi:10.3390/md11061878 · Cited by 98 · see citing works
Heterologous production of daptomycin in Streptomyces lividans
Penn, J., Li, X., Whiting, A., et al. (2005) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-005-0033-8 · Cited by 97 · see citing works
Examining the Fish Microbiome: Vertebrate-Derived Bacteria as an Environmental Niche for the Discovery of Unique Marine Natural Products
Sanchez, L. M., Wong, W. R., Riener, R. M., Schulze, C. J., & Linington, R. G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035398 · Cited by 96 · see citing works
Heterologous Expression of Novobiocin and Clorobiocin Biosynthetic Gene Clusters
Eustáquio, A. S., Gust, B., Galm, U., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.5.2452-2459.2005 · Cited by 96 · see citing works
Carrier Protein Structure and Recognition in Polyketide and Nonribosomal Peptide Biosynthesis
Lai, J. R., Koglin, A., & Walsh, C. T. (2006) · Biochemistry · doi:10.1021/bi061979p · Cited by 94 · see citing works
GC Fractionation Enhances Microbial CommunityDiversity Assessment and Detection of Minority Populations ofBacteria by Denaturing Gradient GelElectrophoresis
Holben, W. E., Feris, K. P., Kettunen, A., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.4.2263-2270.2004 · Cited by 94 · see citing works
Phylogenetic and Functional Metagenomic Profiling for Assessing Microbial Biodiversity in Environmental Monitoring
Kisand, V., Valente, A., Lahm, A., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043630 · Cited by 93 · see citing works
Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection
Carr, P. A., Wang, H. H., Sterling, B., Isaacs, F. J., Lajoie, M. J., Xu, G. J., Church, G. M., & Jacobson, J. M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks455 · Cited by 93 · see citing works
Genetic diversity of total, active and culturable marine bacteria in coastal seawater
Bernard, L., Schäfer, H., Joux, F., et al. (2000) · Aquatic Microbial Ecology · doi:10.3354/ame023001 · Cited by 92 · see citing works
In Vivo Production of Artificial Nonribosomal Peptide Products in the Heterologous Host Escherichia coli
Gruenewald, S., Mootz, H. D., Stehmeier, P., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.6.3282-3291.2004 · Cited by 91 · see citing works
Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans
Selvin, J., Kennedy, J., Lejon, D. P. H., et al. (2012) · Microbial Cell Factories · doi:10.1186/1475-2859-11-72 · Cited by 90 · see citing works
Multiplexing of Combinatorial Chemistry in Antimycin Biosynthesis: Expansion of Molecular Diversity and Utility
Yan, Y., Chen, J., Zhang, L., et al. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201305569 · Cited by 90 · see citing works
Non-ribosomal peptide synthetase module fusions to produce derivatives of daptomycin in Streptomyces roseosporus
Doekel, S., Gal, M.-F. C.-L., Gu, J.-Q., et al. (2008) · Microbiology · doi:10.1099/mic.0.2008/020685-0 · Cited by 89 · see citing works
Synthetic biological approaches to natural product biosynthesis
Winter, J. M., & Tang, Y. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.12.016 · Cited by 88 · see citing works
Deciphering Pactamycin Biosynthesis and Engineered Production of New Pactamycin Analogues
Ito, T., Roongsawang, N., Shirasaka, N., et al. (2009) · ChemBioChem · doi:10.1002/cbic.200900339 · Cited by 86 · see citing works
Isolation and Characterization of Metalloproteases with a Novel Domain Structure by Construction and Screening of Metagenomic Libraries
Waschkowitz, T., Rockstroh, S., & Daniel, R. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02136-08 · Cited by 85 · see citing works
Nitrilase Activity Screening on Structurally Diverse Substrates: Providing Biocatalytic Tools for Organic Synthesis
Vergne‐Vaxelaire, C., Bordier, F., Fossey, A., et al. (2013) · Advanced Synthesis & Catalysis · doi:10.1002/adsc.201201098 · Cited by 83 · see citing works
Substrate-induced gene expression (SIGEX) screening of metagenome libraries
Uchiyama, T., & Watanabe, K. (2008) · Nature Protocols · doi:10.1038/nprot.2008.96 · Cited by 83 · see citing works
Antimicrobial Activity of Heterotrophic Bacterial Communities from the Marine Sponge Erylus discophorus (Astrophorida, Geodiidae)
Graça, A. P., Bondoso, J., Gaspar, H., Xavier, J. R., Monteiro, M. C., de la Cruz, M., Oves‐Costales, D., Vicente, F., & Lage, O. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078992 · Cited by 82 · see citing works
Engineered polyketide biosynthesis and biocatalysis in Escherichia coli
Gao, X., Wang, P., & Tang, Y. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2860-4 · Cited by 82 · see citing works
Identification of a new subfamily of salt-tolerant esterases from a metagenomic library of tidal flat sediment
Jeon, J. H., Lee, H. S., Kim, J. T., et al. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3433-x · Cited by 81 · see citing works
Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria
Martínez, A., Ventouras, L.-A., Wilson, S. T., et al. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00340 · Cited by 80 · see citing works
TREX: A Universal Tool for the Transfer and Expression of Biosynthetic Pathways in Bacteria
Loeschcke, A., Markert, A., Wilhelm, S., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb3000657 · Cited by 80 · see citing works
Microbial natural products: molecular blueprints for antitumor drugs
Giddings, L., & Newman, D. J. (2013) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-013-1331-1 · Cited by 78 · see citing works
A Cryptic Polyene Biosynthetic Gene Cluster in Streptomyces calvus Is Expressed upon Complementation with a Functional bldA Gene
Kalan, L., Gessner, A., Thaker, M., et al. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.09.006 · Cited by 78 · see citing works
2-Deoxystreptamine-containing aminoglycoside antibiotics: Recent advances in the characterization and manipulation of their biosynthetic pathways
Park, S. R., Park, J. W., Ban, Y. H., et al. (2012) · Natural Product Reports · doi:10.1039/c2np20092a · Cited by 77 · see citing works
Transcriptional responses of surface water marine microbial assemblages to deep‐sea water amendment
Shi, Y., McCarren, J., & DeLong, E. F. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02598.x · Cited by 76 · see citing works
Marine Sediment-Derived Streptomyces Bacteria from British Columbia, Canada Are a Promising Microbiota Resource for the Discovery of Antimicrobial Natural Products
Dalisay, D. S., Williams, D. E., Wang, X. L., Centko, R. M., Chen, J., & Andersen, R. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077078 · Cited by 76 · see citing works
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
D’haeseleer, P., Gladden, J. M., Allgaier, M., Chain, P., Tringe, S. G., Malfatti, S., Aldrich, J. T., Nicora, C., Robinson, E. W., Paša‐Tolić, L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068465 · Cited by 73 · see citing works
Proteogenomic Approaches for the MolecularCharacterization of Natural Microbial Communities
Banfield, J. F., VerBerkmoes, N. C., Hettich, R. L., et al. (2005) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2005.9.301 · Cited by 72 · see citing works
Genomic Mining for Novel FADH2-Dependent Halogenases in Marine Sponge-Associated Microbial Consortia
Bayer, K., Scheuermayer, M., Fieseler, L., & Hentschel, U. (2012) · Marine Biotechnology · doi:10.1007/s10126-012-9455-2 · Cited by 69 · see citing works
Approaches for novel enzyme discovery from marine environments
Lee, H. S., Kwon, K. K., Kang, S. G., et al. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.01.015 · Cited by 69 · see citing works
Molecular cloning and characterization of a new cold-active esterase from a deep-sea metagenomic library
Fu, C., Hu, Y., Xie, F., et al. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-3079-0 · Cited by 69 · see citing works
Application and validation of DNA microarrays for the 16S rRNA‐based analysis of marine bacterioplankton
Peplies, J., Lau, S. C. K., Pernthaler, J., et al. (2004) · Environmental Microbiology · doi:10.1111/j.1462-2920.2004.00588.x · Cited by 68 · see citing works
Production of xylanase by an alkaline-tolerant marine-derived Streptomyces viridochromogenes strain and improvement by ribosome engineering
Liu, Z., Zhao, X., & Bai, F. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4290-y · Cited by 67 · see citing works
Proteomics-Based Discovery of Koranimine, a Cyclic Imine Natural Product
Evans, B. S., Ntai, I., Chen, Y., et al. (2011) · Journal of the American Chemical Society · doi:10.1021/ja2015795 · Cited by 66 · see citing works
The regulation and biosynthesis of antimycins
Seipke, R. F., & Hutchings, M. I. (2013) · Beilstein Journal of Organic Chemistry · doi:10.3762/bjoc.9.290 · Cited by 65 · see citing works
Heterologous Production of 4-O-Demethylbarbamide, a Marine Cyanobacterial Natural Product
Kim, E. J., Lee, J. H., Choi, H., Pereira, A. R., Ban, Y. H., Yoo, Y. J., Kim, E., Park, J. W., Sherman, D. H., Gerwick, W. H., et al. (2012) · Organic Letters · doi:10.1021/ol302575h · Cited by 65 · see citing works
Detergent compatible alkaline lipase produced by marine Bacillus smithii BTMS 11
Lailaja, V. P., & Chandrasekaran, M. (2013) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-013-1298-0 · Cited by 65 · see citing works
Sequence and Expression Analyses of Cytophaga -Like Hydrolases in a Western Arctic Metagenomic Library and the Sargasso Sea
Cottrell, M. T., Yu, L., & Kirchman, D. L. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8506-8513.2005 · Cited by 64 · see citing works
Characterization of a new oxidant-stable serine protease isolated by functional metagenomics
Biver, S., Portetelle, D., & Vandenbol, M. (2013) · SpringerPlus · doi:10.1186/2193-1801-2-410 · Cited by 62 · see citing works
Indigenous hydrocarbon-utilizing bacterioflora in oil-polluted habitats in Kuwait, two decades after the greatest man-made oil spill
Al-Awadhi, H. A., Al‐Mailem, D. M., Dashti, N., et al. (2012) · Archives of Microbiology · doi:10.1007/s00203-012-0800-7 · Cited by 61 · see citing works
Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with β-glucosidase, β-fucosidase and β-galactosidase activities
Wierzbicka-Woś, A., Bartasun, P., Cieśliński, H., et al. (2013) · BMC Biotechnology · doi:10.1186/1472-6750-13-22 · Cited by 61 · see citing works
A nitrilase from a metagenomic library acts regioselectively on aliphatic dinitriles
Bayer, S., Birkemeyer, C., & Ballschmiter, M. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2831-9 · Cited by 59 · see citing works
Chemical dereplication of marine actinomycetes by liquid chromatography–high resolution mass spectrometry profiling and statistical analysis
Forner, D., Berrué, F., Correa, H., Duncan, K., & Kerr, R. G. (2013) · Analytica Chimica Acta · doi:10.1016/j.aca.2013.10.029 · Cited by 56 · see citing works
Assessment of the Bacteriocinogenic Potential of Marine Bacteria Reveals Lichenicidin Production by Seaweed-Derived Bacillus spp.
Prieto, M. L., O’Sullivan, L., Tan, S. P., et al. (2012) · Marine Drugs · doi:10.3390/md10102280 · Cited by 56 · see citing works
An Orthogonal Active Site Identification System (OASIS) for Proteomic Profiling of Natural Product Biosynthesis
Meier, J. L., Niessen, S., Hoover, H. S., et al. (2009) · ACS Chemical Biology · doi:10.1021/cb9002128 · Cited by 56 · see citing works
Marine Proteomics: A Critical Assessment of an Emerging Technology
Slattery, M., Ankisetty, S., Corrales, J., Marsh-Hunkin, K. E., Gochfeld, D. J., Willett, K. L., & Rimoldi, J. M. (2012) · Journal of Natural Products · doi:10.1021/np300366a · Cited by 55 · see citing works
The Screening of Antimicrobial Bacteria with Diverse Novel Nonribosomal Peptide Synthetase (NRPS) Genes from South China Sea Sponges
Zhang, W., Li, Z., Miao, X., et al. (2008) · Marine Biotechnology · doi:10.1007/s10126-008-9148-z · Cited by 54 · see citing works
Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment
Xu, M., Xiao, X., & Wang, F. (2007) · Extremophiles · doi:10.1007/s00792-007-0122-x · Cited by 52 · see citing works
Systematics-guided bioprospecting for bioactive microbial natural products
Liu, X., Bolla, K., Ashforth, E. J., et al. (2011) · Antonie van Leeuwenhoek · doi:10.1007/s10482-011-9671-1 · Cited by 51 · see citing works
Identification of Elaiophylin Derivatives from the Marine-Derived Actinomycete Streptomyces sp. 7-145 Using PCR-Based Screening
Wu, C., Tan, Y., Gan, M., et al. (2013) · Journal of Natural Products · doi:10.1021/np4006794 · Cited by 51 · see citing works
Culture-dependent and independent approaches for identifying novel halogenases encoded by Crambe crambe (marine sponge) microbiota
Öztürk, B., de Jaeger, L., Smidt, H., et al. (2013) · Scientific Reports · doi:10.1038/srep02780 · Cited by 50 · see citing works
Identification and characterization of novel esterases from a deep-sea sediment metagenome
Jiang, X., Xu, X., Huo, Y., et al. (2011) · Archives of Microbiology · doi:10.1007/s00203-011-0745-2 · Cited by 50 · see citing works
Synthetic Biology of Antimicrobial Discovery
Zakeri, B., & Lu, T. K. (2012) · ACS Synthetic Biology · doi:10.1021/sb300101g · Cited by 46 · see citing works
Integrated Metagenomic and Metatranscriptomic Analyses of Microbial Communities in the Meso- and Bathypelagic Realm of North Pacific Ocean
Wu, J.-Y., Gao, W., Johnson, R. H., et al. (2013) · Marine Drugs · doi:10.3390/md11103777 · Cited by 45 · see citing works
Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli
Yuzawa, S., Kim, W.-C., Katz, L., et al. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.12.029 · Cited by 42 · see citing works
Culturability and Coexistence of Colony-Forming and Single-Cell Marine Bacterioplankton
Simu, K., Holmfeldt, K., Zweifel, U. L., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.8.4793-4800.2005 · Cited by 42 · see citing works
Use of Randomly Amplified Polymorphic DNA as a Means of Developing Genus- and Strain-Specific Streptomyces DNA Probes
Roberts, M. A., & Crawford, D. L. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2555-2564.2000 · Cited by 40 · see citing works
PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes
Wang, H., Chen, Y., Ge, L., et al. (2013) · Journal of Applied Microbiology · doi:10.1111/jam.12217 · Cited by 40 · see citing works
Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)
Alex, A., Silva, V., Vasconcelos, V. M., & Antunes, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080653 · Cited by 38 · see citing works
Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments
Besaury, L., Marty, F., Buquet, S., et al. (2012) · Microbial Ecology · doi:10.1007/s00248-012-0120-0 · Cited by 37 · see citing works

Flagged first, then by citations

Research works printed but not linked: 1

[242]Laatsch H. Antibase Version 4.0 Wiley-VCH Verlag GmbH & Co Weinheim, Germany 2012

Sorted by citations

Marine Natural Products: A Source of Novel Anticancer Drugs
Khalifa, S. A. M., Elias, N., Farag, M. A., Chen, L., Saeed, A., Hegazy, M.-E. F., Moustafa, M. S., Abd El-Wahed, A., Al-Mousawi, S. M., Musharraf, S. G., et al. (2019) · Marine Drugs · doi:10.3390/md17090491 · Cited by 555 · see citing works
“7 × 1030 microorganisms have been discovered in marine environments [29], 99% of all bacteria cannot be cultured but can synthesize many fascinating natural products that are potential drug leads [30].”
Background

Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies
Li, R. W. (2011) · Cited by 465 · see citing works
Simulating metagenomic stable isotope probing datasets with MetaSIPSimPreprint
Barnett, S. E., & Buckley, D. H. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/735787 · Cited by 4 · see citing works
New Application of Metagenomics and Metatranscriptomics in Environmental Microbial Research
Wei, N. (2014) · Environmental Science & Technology
Reference-free resolving of long-read metagenomic dataPreprint
Khachatryan, L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.6084/m9.figshare.c.4218857.v1
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Barnett, S. E., & Buckley, D. H. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-3372-6 · Cited by 17 · see citing works

Authors: Rocha-Martin, J., Harrington, C., Dobson, A., & O'Gara, F.
Affiliations: BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
National University of Ireland (IE)
ORCID: Dobson, Alan
O'Gara, Fergal
Venue: Marine Drugs
Publisher: MDPI AG
Published: 2014-06-10
Volume: 12
Issue: 6
Pages: 3516-3559
ISSN: 1660-3397 (ISSN-L)
DOI: 10.3390/md12063516
PMC: PMC4071589
OpenAlex: W2060522674
Cited by: 84
References: 236
Citations by year: 2026: 4 · 2025: 9 · 2024: 3 · 2023: 10 · 2022: 6 · 2021: 7 · 2020: 7 · 2019: 10 · 2017: 6 · 2016: 11 · 2015: 8 · 2014: 3
FWCI: 1.20
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/3.0/ (vor)
Locations: Marine Drugs (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eSpace (Curtin University) (submittedVersion)
Funders: Health Research Board (HRA/2009/146)
European Commission (312184, 311975, FP7-KBBE-2012-6, FP7-PEOPLE-2013, OCEAN2012, FP7‐PEOPLE‐ 2013‐ITN, FP7-KBBE, 256596, 607786, 287589)
Irish Research Council for Science, Engineering and Technology (RS/2010/2413, PD/2011/2414)
Teagasc
Irish Research Council
Russian Science Foundation
FP7 Food, Agriculture and Fisheries, Biotechnology (287589, 311975, 312184)
FP7 People: Marie-Curie Actions (FP7-PEOPLE-2013-ITN, 607786, FP7-PEOPLE-2013)
Topics: Health Sciences › Medicine › Pharmacology › Microbial Natural Products and Biosynthesis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Marine Sponges and Natural Products
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Synthesis and Biological Activity
Keywords: marine microorganisms, marine bioactive compounds, biodiscovery, dereplication, marine metabolites, halogenated natural products, combinatorial biosynthesis, synthetic biology, metagenomics, biocatalysts, expression systems, bioactivity screening
MeSH terms: Animals, Biological Products, Biotechnology, Humans, Marine Biology, Biocatalysis, Drug Discovery

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Abstract

Integrity signals

Claims the paper makes

Self-check

Cites

Cited by

Related

Record

About these checks