Publications

Wu, C.;  Shang, Z.;  Lemetre, C.;  Ternei, M. A.; Brady, S. F., Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria. Journal of the American Chemical Society 2019, 141 (9), 3910-3919.

A.;  Calle, P. Y.;  Lemetre, C.;  Owen, J. G.; Brady, S. F., Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences. Nat Commun 2019, 10 (1), 3848. 10.1038/s41467-019-11658-z

Kim, S. H.;  Lu, W.;  Ahmadi, M. K.;  Montiel, D.;  Ternei, M. A.; Brady, S. F., Atolypenes, Tricyclic Bacterial Sesterterpenes Discovered Using a Multiplexed In Vitro Cas9-TAR Gene Cluster Refactoring Approach. ACS synthetic biology 2019, 8 (1), 109-118. 10.1021/acssynbio.8b00361

Estrela, A. B.;  Nakashige, T. G.;  Lemetre, C.;  Woodworth, I. D.;  Weisman, J. L.;  Cohen, L. J.; Brady, S. F., Functional Multigenomic Screening of Human-Associated Bacteria for NF-kappaB-Inducing Bioactive Effectors. mBio 2019, 10 (6). 10.1128/mBio.02587-19

Colosimo, D. A.;  Kohn, J. A.;  Luo, P. M.;  Piscotta, F. J.;  Han, S. M.;  Pickard, A. J.;  Rao, A.;  Cross, J. R.; Cohen, L. J.; Brady, S. F., Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors. Cell Host Microbe 2019, 26 (2), 273-282 e7. 10.1016/j.chom.2019.07.002

Chu, J.;  Vila-Farres, X.; Brady, S. F., Bioactive Synthetic-Bioinformatic Natural Product Cyclic Peptides Inspired by Nonribosomal Peptide Synthetase Gene Clusters from the Human Microbiome. Journal of the American Chemical Society 2019, 141 (40), 15737-15741. 10.1021/jacs.9b07317

Vila-Farres, X.;  Chu, J.;  Ternei, M. A.;  Lemetre, C.;  Park, S.;  Perlin, D. S.; Brady, S. F., An Optimized Synthetic-Bioinformatic Natural Product Antibiotic Sterilizes Multidrug-Resistant Acinetobacter baumannii-Infected Wounds. mSphere 2018, 3 (1). 10.1128/mSphere.00528-17

Peek, J.;  Lilic, M.;  Montiel, D.;  Milshteyn, A.;  Woodworth, I.;  Biggins, J. B.;  Ternei, M. A.;  Calle, P. Y.; Danziger, M.;  Warrier, T.;  Saito, K.;  Braffman, N.;  Fay, A.;  Glickman, M. S.;  Darst, S. A.;  Campbell, E. A.; Brady, S. F., Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018, 9 (1), 4147. 10.1038/s41467-018-06587-2

Milshteyn, A.;  Colosimo, D. A.; Brady, S. F., Accessing Bioactive Natural Products from the Human Microbiome. Cell Host Microbe 2018, 23 (6), 725-736. 10.1016/j.chom.2018.05.013

Hover, B. M.;  Kim, S. H.;  Katz, M.;  Charlop-Powers, Z.;  Owen, J. G.;  Ternei, M. A.;  Maniko, J.;  Estrela, A. B.;  Molina, H.;  Park, S.;  Perlin, D. S.; Brady, S. F., Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nat Microbiol 2018. 10.1038/s41564-018-0110-1

Cohen, L. J.;  Han, S.;  Huang, Y. H.; Brady, S. F., Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library. ACS Infect Dis 2018, 4 (1), 27-32. 10.1021/acsinfecdis.7b00081

Cohen, L. J.;  Esterhazy, D.;  Kim, S. H.;  Lemetre, C.;  Aguilar, R. R.;  Gordon, E. A.;  Pickard, A. J.;  Cross, J. R.;  Emiliano, A. B.;  Han, S. M.;  Chu, J.;  Vila-Farres, X.;  Kaplitt, J.;  Rogoz, A.;  Calle, P. Y.;  Hunter, C.;  Bitok, J. K.; Brady, S. F., Corrigendum: Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2018, 556 (7699), 135. 10.1038/nature25997

Chu, J.;  Vila-Farres, X.;  Inoyama, D.;  Gallardo-Macias, R.;  Jaskowski, M.;  Satish, S.;  Freundlich, J. S.; Brady, S. F., Human Microbiome Inspired Antibiotics with Improved beta-Lactam Synergy against MDR Staphylococcus aureus. ACS Infect Dis 2018, 4 (1), 33-38. 10.1021/acsinfecdis.7b00056

Vila-Farres, X.;  Chu, J.;  Inoyama, D.;  Ternei, M. A.;  Lemetre, C.;  Cohen, L. J.;  Cho, W.;  Reddy, B. V.;  Zebroski, H. A.;  Freundlich, J. S.;  Perlin, D. S.; Brady, S. F., Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters. Journal of the American Chemical Society 2017, 139 (4), 1404-1407. 10.1021/jacs.6b11861

Lemetre, C.;  Maniko, J.;  Charlop-Powers, Z.;  Sparrow, B.;  Lowe, A. J.; Brady, S. F., Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale. Proceedings of the National Academy of Sciences of the United States of America 2017, 114 (44), 11615-11620. 10.1073/pnas.1710262114

Cohen, L. J.;  Esterhazy, D.;  Kim, S. H.;  Lemetre, C.;  Aguilar, R. R.;  Gordon, E. A.;  Pickard, A. J.;  Cross, J. R.;  Emiliano, A. B.;  Han, S. M.;  Chu, J.;  Vila-Farres, X.;  Kaplitt, J.;  Rogoz, A.;  Calle, P. Y.;  Hunter, C.;  Bitok, J. K.; Brady, S. F., Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2017,549 (7670), 48-53. 10.1038/nature23874

Bitok, J. K.;  Lemetre, C.;  Ternei, M. A.; Brady, S. F., Identification of biosynthetic gene clusters from metagenomic libraries using PPTase complementation in a Streptomyces host. FEMS microbiology letters 2017,364 (16). 10.1093/femsle/fnx155

Valentic, T. R.;  Jackson, D. R.;  Brady, S. F.; Tsai, S. C., Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis. ACS chemical biology 2016, 11 (12), 3421-3430. 10.1021/acschembio.6b00658

Katz, M.;  Hover, B. M.; Brady, S. F., Culture-independent discovery of natural products from soil metagenomes. Journal of industrial microbiology & biotechnology 2016, 43 (2-3), 129-41. 10.1007/s10295-015-1706-6

Kang, H. S.;  Charlop-Powers, Z.; Brady, S. F., Multiplexed CRISPR/Cas9- and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast. ACS synthetic biology 2016, 5 (9), 1002-10. 10.1021/acssynbio.6b00080

Iqbal, H. A.;  Low-Beinart, L.;  Obiajulu, J. U.; Brady, S. F., Natural Product Discovery through Improved Functional Metagenomics in Streptomyces. Journal of the American Chemical Society 2016, 138 (30), 9341-4. 10.1021/jacs.6b02921

Chu, J.;  Vila-Farres, X.;  Inoyama, D.;  Ternei, M.;  Cohen, L. J.;  Gordon, E. A.;  Reddy, B. V.;  Charlop-Powers, Z.;  Zebroski, H. A.;  Gallardo-Macias, R.;  Jaskowski, M.;  Satish, S.;  Park, S.;  Perlin, D. S.;  Freundlich, J. S.; Brady, S. F., Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nature chemical biology 2016, 12 (12), 1004-1006. 10.1038/nchembio.2207

Charlop-Powers, Z.;  Pregitzer, C. C.;  Lemetre, C.;  Ternei, M. A.;  Maniko, J.;  Hover, B. M.;  Calle, P. Y.;  McGuire, K. L.;  Garbarino, J.;  Forgione, H. M.;  Charlop-Powers, S.; Brady, S. F., Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity. Proceedings of the National Academy of Sciences of the United States of America 2016, 113 (51), 14811-14816. 10.1073/pnas.1615581113

Owen, J. G.;  Charlop-Powers, Z.;  Smith, A. G.;  Ternei, M. A.;  Calle, P. Y.;  Reddy, B. V.;  Montiel, D.; Brady, S. F., Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proceedings of the National Academy of Sciences of the United States of America 2015, 112 (14), 4221-6. 10.1073/pnas.1501124112

Montiel, D.;  Kang, H. S.;  Chang, F. Y.;  Charlop-Powers, Z.; Brady, S. F., Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters. Proceedings of the National Academy of Sciences of the United States of America 2015, 112 (29), 8953-8. 10.1073/pnas.1507606112

Medema, M. H.;  Kottmann, R.;  Yilmaz, P.;  Cummings, M.;  Biggins, J. B.;  Blin, K.;  de Bruijn, I.;  Chooi, Y. H.;  Claesen, J.;  Coates, R. C.;  et al. Minimum Information about a Biosynthetic Gene cluster. Nature chemical biology 2015, 11 (9), 625-31. 10.1038/nchembio.1890

Katz, M.;  Hover, B. M.; Brady, S. F., Culture-independent discovery of natural products from soil metagenomes. Journal of industrial microbiology & biotechnology 2015. 10.1007/s10295-015-1706-6

Cohen, L. J.;  Kang, H. S.;  Chu, J.;  Huang, Y. H.;  Gordon, E. A.;  Reddy, B. V.;  Ternei, M. A.;  Craig, J. W.; Brady, S. F., Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proceedings of the National Academy of Sciences of the United States of America 2015, 112 (35), E4825-34. 10.1073/pnas.1508737112

Charlop-Powers, Z.;  Owen, J. G.;  Reddy, B. V.;  Ternei, M. A.;  Guimaraes, D. O.;  de Frias, U. A.;  Pupo, M. T.;  Seepe, P.;  Feng, Z.; Brady, S. F., Global biogeographic sampling of bacterial secondary metabolism. eLife 2015, 4, e05048. 10.7554/eLife.05048

Charlop-Powers, Z.; Brady, S. F., phylogeo: an R package for geographic analysis and visualization of microbiome data. Bioinformatics 2015, 31 (17), 2909-11. 10.1093/bioinformatics/btv269

Chang, F. Y.;  Ternei, M. A.;  Calle, P. Y.; Brady, S. F., Targeted metagenomics: finding rare tryptophan dimer natural products in the environment. Journal of the American Chemical Society 2015, 137 (18), 6044-52. 10.1021/jacs.5b01968

Reddy, B. V.;  Milshteyn, A.;  Charlop-Powers, Z.; Brady, S. F., eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes. Chemistry & biology 2014, 21 (8), 1023-33. 10.1016/j.chembiol.2014.06.007

Milshteyn, A.;  Schneider, J. S.; Brady, S. F., Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities. Chemistry & biology 2014, 21 (9), 1211-1223. 10.1016/j.chembiol.2014.08.006

Kang, H. S.; Brady, S. F., Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols. ACS chemical biology 2014, 9 (6), 1267-72. 10.1021/cb500141b

Iqbal, H. A.;  Craig, J. W.; Brady, S. F., Antibacterial enzymes from the functional screening of metagenomic libraries hosted in Ralstonia metallidurans. FEMS microbiology letters 2014, 354 (1), 19-26. 10.1111/1574-6968.12431

Charlop-Powers, Z.;  Owen, J. G.;  Reddy, B. V.;  Ternei, M. A.; Brady, S. F., Chemical-biogeographic survey of secondary metabolism in soil. Proceedings of the National Academy of Sciences of the United States of America 2014, 111 (10), 3757-62. 10.1073/pnas.1318021111

Charlop-Powers, Z.;  Milshteyn, A.; Brady, S. F., Metagenomic small molecule discovery methods. Current opinion in microbiology 2014, 19, 70-5. 10.1016/j.mib.2014.05.021

Chang, F. Y.;  Kawashima, S. A.; Brady, S. F., Mutations in the proteolipid subunits of the vacuolar H+-ATPase provide resistance to indolotryptoline natural products. Biochemistry 2014. 10.1021/bi501078j

Chang, F. Y.; Brady, S. F., Characterization of an environmental DNA-derived gene cluster that encodes the bisindolylmaleimide methylarcyriarubin. Chembiochem : a European journal of chemical biology 2014, 15 (6), 815-21. 10.1002/cbic.201300756

Biggins, J. B.;  Kang, H. S.;  Ternei, M. A.;  DeShazer, D.; Brady, S. F., The chemical arsenal of Burkholderia pseudomallei is essential for pathogenicity. Journal of the American Chemical Society 2014, 136 (26), 9484-90. 10.1021/ja504617n

Qaisar, U.;  Luo, L.;  Haley, C. L.;  Brady, S. F.;  Carty, N. L.;  Colmer-Hamood, J. A.; Hamood, A. N., The pvc operon regulates the expression of the Pseudomonas aeruginosa fimbrial chaperone/usher pathway (cup) genes. PloS one 2013, 8 (4), e62735. 10.1371/journal.pone.0062735

Owen, J. G.;  Reddy, B. V.;  Ternei, M. A.;  Charlop-Powers, Z.;  Calle, P. Y.;  Kim, J. H.; Brady, S. F., Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. Proceedings of the National Academy of Sciences of the United States of America 2013, 110 (29), 11797-802. 10.1073/pnas.1222159110

Kang, H. S.; Brady, S. F., Arimetamycin A: improving clinically relevant families of natural products through sequence-guided screening of soil metagenomes. Angewandte Chemie 2013, 52 (42), 11063-7. 10.1002/anie.201305109

Engel, K.;  Ashby, D.;  Brady, S. F.;  Cowan, D. A.;  Doemer, J.;  Edwards, E. A.;  Fiebig, K.;  Martens, E. C.;  McCormac, D.;  Mead, D. A.;  Miyazaki, K.;  Moreno-Hagelsieb, G.;  O’Gara, F.;  Reid, A.;  Rose, D. R.;  Simonet, P.;  Sjoling, S.;  Smalla, K.;  Streit, W. R.;  Tedman-Jones, J.;  Valla, S.;  Wellington, E. M.;  Wu, C. C.;  Liles, M. R.; Neufeld, J. D.;  Sessitsch, A.; Charles, T. C., Meeting report: 1st international functional metagenomics workshop may 7-8, 2012, st. Jacobs, Ontario, Canada. Standards in genomic sciences 2013, 8 (1), 106-11. 10.4056/sigs.3406845

Charlop-Powers, Z.;  Banik, J. J.;  Owen, J. G.;  Craig, J. W.; Brady, S. F., Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis. ACS chemical biology 2013, 8 (1), 138-43. 10.1021/cb3004918

Chang, F. Y.;  Ternei, M. A.;  Calle, P. Y.; Brady, S. F., Discovery and synthetic refactoring of tryptophan dimer gene clusters from the environment. Journal of the American Chemical Society 2013, 135 (47), 17906-12. 10.1021/ja408683p

Chang, F. Y.; Brady, S. F., Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening. Proceedings of the National Academy of Sciences of the United States of America 2013,110 (7), 2478-83. 10.1073/pnas.1218073110

Reddy, B. V.;  Kallifidas, D.;  Kim, J. H.;  Charlop-Powers, Z.;  Feng, Z.; Brady, S. F., Natural product biosynthetic gene diversity in geographically distinct soil microbiomes. Applied and environmental microbiology 2012, 78 (10), 3744-52. 10.1128/AEM.00102-12

Kallifidas, D.;  Kang, H. S.; Brady, S. F., Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. Journal of the American Chemical Society 2012, 134 (48), 19552-5. 10.1021/ja3093828

Kallifidas, D.; Brady, S. F., Reassembly of functionally intact environmental DNA-derived biosynthetic gene clusters. Methods in enzymology 2012, 517, 225-39. 10.1016/B978-0-12-404634-4.00011-5

Iqbal, H. A.;  Feng, Z.; Brady, S. F., Biocatalysts and small molecule products from metagenomic studies. Current opinion in chemical biology 2012, 16 (1-2), 109-16. 10.1016/j.cbpa.2012.02.015

Feng, Z.;  Chakraborty, D.;  Dewell, S. B.;  Reddy, B. V.; Brady, S. F., Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis. Journal of the American Chemical Society 2012, 134 (6), 2981-7. 10.1021/ja207662w

Biggins, J. B.;  Ternei, M. A.; Brady, S. F., Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. Journal of the American Chemical Society 2012, 134 (32), 13192-5. 10.1021/ja3052156

Feng, Z.;  Kallifidas, D.; Brady, S. F., Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites. Proceedings of the National Academy of Sciences of the United States of America 2011, 108 (31), 12629-34. 10.1073/pnas.1103921108

Craig, J. W.;  Cherry, M. A.; Brady, S. F., Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria. Journal of bacteriology 2011, 193 (20), 5707-15. 10.1128/JB.05426-11

Craig, J. W.; Brady, S. F., Discovery of a metagenome-derived enzyme that produces branched-chain acyl-(acyl-carrier-protein)s from branched-chain alpha-keto acids. Chembiochem : a European journal of chemical biology 2011, 12 (12), 1849-53. 10.1002/cbic.201100215

Chang, F. Y.; Brady, S. F., Cloning and characterization of an environmental DNA-derived gene cluster that encodes the biosynthesis of the antitumor substance BE-54017. Journal of the American Chemical Society 2011,133 (26), 9996-9. 10.1021/ja2022653

Biggins, J. B.;  Liu, X.;  Feng, Z.; Brady, S. F., Metabolites from the induced expression of cryptic single operons found in the genome of Burkholderia pseudomallei. Journal of the American Chemical Society 2011, 133(6), 1638-41. 10.1021/ja1087369

Biggins, J. B.;  Gleber, C. D.; Brady, S. F., Acyldepsipeptide HDAC inhibitor production induced in Burkholderia thailandensis. Organic letters 2011, 13 (6), 1536-9. 10.1021/ol200225v

Kim, J. H.;  Feng, Z.;  Bauer, J. D.;  Kallifidas, D.;  Calle, P. Y.; Brady, S. F., Cloning large natural product gene clusters from the environment: piecing environmental DNA gene clusters back together with TAR. Biopolymers 2010, 93 (9), 833-44. 10.1002/bip.21450

Feng, Z.;  Kim, J. H.; Brady, S. F., Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster. Journal of the American Chemical Society 2010, 132 (34), 11902-3. 10.1021/ja104550p

Craig, J. W.;  Chang, F. Y.;  Kim, J. H.;  Obiajulu, S. C.; Brady, S. F., Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Applied and environmental microbiology 2010, 76 (5), 1633-41. 10.1128/AEM.02169-09

Bick, M. J.;  Banik, J. J.;  Darst, S. A.; Brady, S. F., Crystal structures of the glycopeptide sulfotransferase Teg12 in a complex with the teicoplanin aglycone. Biochemistry 2010, 49 (19), 4159-68. 10.1021/bi100150v

Bick, M. J.;  Banik, J. J.;  Darst, S. A.; Brady, S. F., The 2.7 A resolution structure of the glycopeptide sulfotransferase Teg14. Acta crystallographica. Section D, Biological crystallography 2010, 66 (Pt 12), 1278-86. 10.1107/S0907444910036681

Bauer, J. D.;  King, R. W.; Brady, S. F., Utahmycins a and B, azaquinones produced by an environmental DNA clone. Journal of natural products 2010, 73 (5), 976-9. 10.1021/np900786s

Banik, J. J.;  Craig, J. W.;  Calle, P. Y.; Brady, S. F., Tailoring enzyme-rich environmental DNA clones: a source of enzymes for generating libraries of unnatural natural products. Journal of the American Chemical Society 2010, 132 (44), 15661-70. 10.1021/ja105825a

Banik, J. J.; Brady, S. F., Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Current opinion in microbiology 2010, 13 (5), 603-9. 10.1016/j.mib.2010.08.012