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Volumn 113, Issue 51, 2016, Pages 14811-14816

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity

Author keywords

Biosynthesis; Metagenomics; Natural products

Indexed keywords

ANTIBIOTIC AGENT; ANTIFUNGAL AGENT; ANTINEOPLASTIC AGENT; BACTERIAL DNA; NATURAL PRODUCT; BIOLOGICAL PRODUCT;

EID: 85006445969     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1615581113     Document Type: Article
Times cited : (79)

References (44)
  • 1
    • 84962367258 scopus 로고    scopus 로고
    • Natural products as sources of new drugs from 1981 to 2014
    • Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79(3):629-661.
    • (2016) J Nat Prod , vol.79 , Issue.3 , pp. 629-661
    • Newman, D.J.1    Cragg, G.M.2
  • 2
    • 14544294545 scopus 로고    scopus 로고
    • Bioactive microbial metabolites
    • Bérdy J (2005) Bioactive microbial metabolites. J Antibiot (Tokyo) 58(1):1-26.
    • (2005) J Antibiot (Tokyo) , vol.58 , Issue.1 , pp. 1-26
    • Bérdy, J.1
  • 3
    • 84865683314 scopus 로고    scopus 로고
    • Thoughts and facts about antibiotics: Where we are now and where we are heading
    • Bérdy J (2012) Thoughts and facts about antibiotics: Where we are now and where we are heading. J Antibiot (Tokyo) 65(8):441.
    • (2012) J Antibiot (Tokyo) , vol.65 , Issue.8 , pp. 441
    • Bérdy, J.1
  • 4
    • 0024470551 scopus 로고
    • The macrolactins, a novel class of antiviral and cytotoxic macrolides from a deep-sea marine bacterium
    • Gustafson K, Roman M, Fenical W (1989) The macrolactins, a novel class of antiviral and cytotoxic macrolides from a deep-sea marine bacterium. J Am Chem Soc 111:7519-7524.
    • (1989) J Am Chem Soc , vol.111 , pp. 7519-7524
    • Gustafson, K.1    Roman, M.2    Fenical, W.3
  • 5
    • 34548404485 scopus 로고    scopus 로고
    • Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42
    • Chen XH, et al. (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25(9):1007-1014.
    • (2007) Nat Biotechnol , vol.25 , Issue.9 , pp. 1007-1014
    • Chen, X.H.1
  • 6
    • 85006456501 scopus 로고    scopus 로고
    • (US Census Bureau, Washington, DC). Accessed August 1, 2016
    • United States Census Bureau (2016) Quick Facts: New York City, New York, (US Census Bureau, Washington, DC). Available at www.census.gov/quickfacts/table/PST045215/3651000. Accessed August 1, 2016.
    • (2016) Quick Facts: New York City, New York
  • 9
    • 84908132133 scopus 로고    scopus 로고
    • Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally
    • Ramirez KS, et al. (2014) Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. Proc Biol Sci 281(1795):20141988.
    • (2014) Proc Biol Sci , vol.281 , Issue.1795
    • Ramirez, K.S.1
  • 10
    • 84874568157 scopus 로고    scopus 로고
    • Digging the New York City Skyline: Soil fungal communities in green roofs and city parks
    • McGuire KL, et al. (2013) Digging the New York City Skyline: Soil fungal communities in green roofs and city parks. PLoS One 8(3):e58020.
    • (2013) PLoS One , vol.8 , Issue.3
    • McGuire, K.L.1
  • 11
    • 84876002671 scopus 로고    scopus 로고
    • Natural products: A continuing source of novel drug leads
    • Cragg GM, Newman DJ (2013) Natural products: A continuing source of novel drug leads. Biochim Biophys Acta 1830(6):3670-3695.
    • (2013) Biochim Biophys Acta , vol.1830 , Issue.6 , pp. 3670-3695
    • Cragg, G.M.1    Newman, D.J.2
  • 12
    • 19944362206 scopus 로고    scopus 로고
    • New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: Detection and distribution of these biosynthetic gene sequences in major taxonomic groups
    • Ayuso-Sacido A, Genilloud O (2005) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: Detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49(1):10-24.
    • (2005) Microb Ecol , vol.49 , Issue.1 , pp. 10-24
    • Ayuso-Sacido, A.1    Genilloud, O.2
  • 13
    • 23744472955 scopus 로고    scopus 로고
    • Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta
    • Schirmer A, et al. (2005) Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl Environ Microbiol 71(8):4840-4849.
    • (2005) Appl Environ Microbiol , vol.71 , Issue.8 , pp. 4840-4849
    • Schirmer, A.1
  • 15
    • 84976630564 scopus 로고    scopus 로고
    • Dispersal similarly shapes both population genetics and community patterns in the marine realm
    • Chust G, et al. (2016) Dispersal similarly shapes both population genetics and community patterns in the marine realm. Sci Rep 6:28730.
    • (2016) Sci Rep , vol.6 , pp. 28730
    • Chust, G.1
  • 17
    • 84996993134 scopus 로고    scopus 로고
    • Global biogeographic sampling of bacterial secondary metabolism
    • Charlop-Powers Z, et al. (2015) Global biogeographic sampling of bacterial secondary metabolism. eLife 4:e05048.
    • (2015) eLife , vol.4
    • Charlop-Powers, Z.1
  • 18
    • 84920263575 scopus 로고    scopus 로고
    • eSNaPD: A versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes
    • Reddy BV, Milshteyn A, Charlop-Powers Z, Brady SF (2014) eSNaPD: A versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes. Chem Biol 21(8):1023-1033.
    • (2014) Chem Biol , vol.21 , Issue.8 , pp. 1023-1033
    • Reddy, B.V.1    Milshteyn, A.2    Charlop-Powers, Z.3    Brady, S.F.4
  • 19
    • 84880370987 scopus 로고    scopus 로고
    • Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products
    • Owen JG, et al. (2013) Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. Proc Natl Acad Sci USA 110(29):11797-11802.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.29 , pp. 11797-11802
    • Owen, J.G.1
  • 20
    • 84903218940 scopus 로고    scopus 로고
    • Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols
    • Kang HS, Brady SF (2014) Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols. ACS Chem Biol 9(6):1267-1272.
    • (2014) ACS Chem Biol , vol.9 , Issue.6 , pp. 1267-1272
    • Kang, H.S.1    Brady, S.F.2
  • 21
    • 84929493030 scopus 로고    scopus 로고
    • Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors
    • Owen JG, et al. (2015) Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proc Natl Acad Sci USA 112(14):4221-4226.
    • (2015) Proc Natl Acad Sci USA , vol.112 , Issue.14 , pp. 4221-4226
    • Owen, J.G.1
  • 22
    • 84929353102 scopus 로고    scopus 로고
    • Targeted metagenomics: Finding rare tryptophan dimer natural products in the environment
    • Chang FY, Ternei MA, Calle PY, Brady SF (2015) Targeted metagenomics: Finding rare tryptophan dimer natural products in the environment. J Am Chem Soc 137(18):6044-6052.
    • (2015) J Am Chem Soc , vol.137 , Issue.18 , pp. 6044-6052
    • Chang, F.Y.1    Ternei, M.A.2    Calle, P.Y.3    Brady, S.F.4
  • 23
    • 84870714378 scopus 로고    scopus 로고
    • Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters
    • Kallifidas D, Kang HS, Brady SF (2012) Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. J Am Chem Soc 134(48):19552-19555.
    • (2012) J Am Chem Soc , vol.134 , Issue.48 , pp. 19552-19555
    • Kallifidas, D.1    Kang, H.S.2    Brady, S.F.3
  • 24
    • 85006370581 scopus 로고    scopus 로고
    • National Center for Biotechnology Information (Nat Cent Biotechnol Info, Bethesda, MD)
    • National Center for Biotechnology Information (2016) PubChem Compound Summary for CID 6445540 (Nat Cent Biotechnol Info, Bethesda, MD).
    • (2016) PubChem Compound Summary for CID 6445540
  • 26
    • 84959238034 scopus 로고    scopus 로고
    • Advancing urban ecosystem governance in New York City: Shifting towards a unified perspective for conservation management
    • Forgione HM, Pregitzer CC, Charlop-Powers S, Gunthier B (2016) Advancing urban ecosystem governance in New York City: Shifting towards a unified perspective for conservation management. Environ Sci Policy 62:127-132.
    • (2016) Environ Sci Policy , vol.62 , pp. 127-132
    • Forgione, H.M.1    Pregitzer, C.C.2    Charlop-Powers, S.3    Gunthier, B.4
  • 27
    • 23744472955 scopus 로고    scopus 로고
    • Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta
    • Schirmer A, et al. (2005) Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl Environ Microbiol 71(8):4840-4849.
    • (2005) Appl Environ Microbiol , vol.71 , Issue.8 , pp. 4840-4849
    • Schirmer, A.1
  • 28
    • 84917735497 scopus 로고    scopus 로고
    • An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
    • Fadrosh DW, et al. (2014) An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2(1):6.
    • (2014) Microbiome , vol.2 , Issue.1 , pp. 6
    • Fadrosh, D.W.1
  • 30
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate OTU sequences from microbial amplicon reads
    • Edgar RC (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10(10):996-998.
    • (2013) Nat Methods , vol.10 , Issue.10 , pp. 996-998
    • Edgar, R.C.1
  • 31
    • 84876427223 scopus 로고    scopus 로고
    • phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
    • McMurdie PJ, Holmes S (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8(4):e61217.
    • (2013) PLoS One , vol.8 , Issue.4
    • McMurdie, P.J.1    Holmes, S.2
  • 32
    • 0030018666 scopus 로고    scopus 로고
    • Epothilons A and B: Antifungal and cytotoxic compounds from Sorangium cellulosum (Myxobacteria). Production, physico-chemical and biological properties
    • Gerth K, Bedorf N, Höfle G, Irschik H, Reichenbach H (1996) Epothilons A and B: Antifungal and cytotoxic compounds from Sorangium cellulosum (Myxobacteria). Production, physico-chemical and biological properties. J Antibiot (Tokyo) 49(6):560-563.
    • (1996) J Antibiot (Tokyo) , vol.49 , Issue.6 , pp. 560-563
    • Gerth, K.1    Bedorf, N.2    Höfle, G.3    Irschik, H.4    Reichenbach, H.5
  • 33
    • 0016724057 scopus 로고
    • Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle
    • Vézina C, Kudelski A, Sehgal SN (1975) Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle. J Antibiot (Tokyo) 28(10):721-726.
    • (1975) J Antibiot (Tokyo) , vol.28 , Issue.10 , pp. 721-726
    • Vézina, C.1    Kudelski, A.2    Sehgal, S.N.3
  • 34
    • 0017802396 scopus 로고
    • Teichomycins, new antibiotics from Actinoplanes teichomyceticus nov. sp. II. Extraction and chemical characterization
    • Bardone MR, Paternoster M, Coronelli C (1978) Teichomycins, new antibiotics from Actinoplanes teichomyceticus nov. sp. II. Extraction and chemical characterization. J Antibiot (Tokyo) 31(3):170-177.
    • (1978) J Antibiot (Tokyo) , vol.31 , Issue.3 , pp. 170-177
    • Bardone, M.R.1    Paternoster, M.2    Coronelli, C.3
  • 37
    • 0032879027 scopus 로고    scopus 로고
    • Forty years of genetics with Streptomyces: From in vivo through in vitro to in silico
    • Hopwood DA (1999) Forty years of genetics with Streptomyces: From in vivo through in vitro to in silico. Microbiology 145(Pt 9):2183-2202.
    • (1999) Microbiology , vol.145 , pp. 2183-2202
    • Hopwood, D.A.1
  • 38
    • 0023250466 scopus 로고
    • Tiacumicins, a novel complex of 18-membered macrolide antibiotics. I. Taxonomy, fermentation and antibacterial activity
    • Theriault RJ, et al. (1987) Tiacumicins, a novel complex of 18-membered macrolide antibiotics. I. Taxonomy, fermentation and antibacterial activity. J Antibiot (Tokyo) 40(5):567-574.
    • (1987) J Antibiot (Tokyo) , vol.40 , Issue.5 , pp. 567-574
    • Theriault, R.J.1
  • 39
    • 0030461311 scopus 로고    scopus 로고
    • New antitumor substances, FR901463, FR901464 and FR901465. I. Taxonomy, fermentation, isolation, physico-chemical properties and biological activities
    • Nakajima H, et al. (1996) New antitumor substances, FR901463, FR901464 and FR901465. I. Taxonomy, fermentation, isolation, physico-chemical properties and biological activities. J Antibiot (Tokyo) 49(12):1196-1203.
    • (1996) J Antibiot (Tokyo) , vol.49 , Issue.12 , pp. 1196-1203
    • Nakajima, H.1
  • 40
    • 0023708531 scopus 로고
    • FR-900520 and FR-900523, novel immunosuppressants isolated from a Streptomyces. I. Taxonomy of the producing strain
    • Hatanaka H, Iwami M, Kino T, Goto T, Okuhara M (1988) FR-900520 and FR-900523, novel immunosuppressants isolated from a Streptomyces. I. Taxonomy of the producing strain. J Antibiot (Tokyo) 41(11):1586-1591.
    • (1988) J Antibiot (Tokyo) , vol.41 , Issue.11 , pp. 1586-1591
    • Hatanaka, H.1    Iwami, M.2    Kino, T.3    Goto, T.4    Okuhara, M.5
  • 41
    • 70449178721 scopus 로고
    • Pimaricin, a new antifungal antibiotic
    • Struyk AP, et al. (1957-1958) Pimaricin, a new antifungal antibiotic. Antibiot Annu 5: 878-885.
    • (1957) Antibiot Annu , vol.5 , pp. 878-885
    • Struyk, A.P.1
  • 42
    • 0017035974 scopus 로고
    • The description and antibiotic production of Streptomyces hygroscopicus var. Geldanus
    • BeBoer C, Dietz A (1976) The description and antibiotic production of Streptomyces hygroscopicus var. Geldanus. J Antibiot (Tokyo) 29(11):1182-1188.
    • (1976) J Antibiot (Tokyo) , vol.29 , Issue.11 , pp. 1182-1188
    • BeBoer, C.1    Dietz, A.2
  • 43
    • 0023886117 scopus 로고
    • LL-F28249 antibiotic complex: A new family of antiparasitic macrocyclic lactones. Isolation, characterization and structures of LL-F28249 alpha, beta, gamma, lambda
    • Carter GT, et al. (1988) LL-F28249 antibiotic complex: A new family of antiparasitic macrocyclic lactones. Isolation, characterization and structures of LL-F28249 alpha, beta, gamma, lambda. J Antibiot (Tokyo) 41(4):519-529.
    • (1988) J Antibiot (Tokyo) , vol.41 , Issue.4 , pp. 519-529
    • Carter, G.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.