Publications

Guo CJ, Chang FY, Wyche TP, Backus KM, Acker TM, Funabashi M, Taketani M, Donia MS, Nayfach S, Pollard KS, Craik CS, Cravatt BF, Clardy J, Voigt CA, Fischbach MA: Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell 2017, 168: 517-526.e18.


Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA: Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. Cell Host Microbe 2016, 20: 709-715.


Fischbach MA, Segre JA: Signaling in Host-Associated Microbial Communities. Cell 2016, 164: 1288-300.


Smanski MJ, Zhou H, Claesen J, Shen B, Fischbach MA, Voigt CA: Synthetic biology to access and expand nature's chemical diversity. Nat Rev Microbiol 2016, 14: 135-49.


Scharschmidt TC, Vasquez KS, Truong HA, Gearty SV, Pauli ML, Nosbaum A, Gratz IK, Otto M, Moon JJ, Liese J, Abbas AK, Fischbach MA, Rosenblum MD: A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes. Immunity 2015, 43: 1011-21.


Wilks J, Lien E, Jacobson AN, Fischbach MA, Qureshi N, Chervonsky AV, Golovkina TV: Mammalian Lipopolysaccharide Receptors Incorporated into the Retroviral Envelope Augment Virus Transmission. Cell Host Microbe 2015, 18: 456-62.


Taketani M, Donia MS, Jacobson AN, Lambris JD, Fischbach MA: A Phase-Variable Surface Layer from the Gut Symbiont Bacteroides thetaiotaomicron. MBio 2015, 6: e01339-15.


Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, et al: Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 2015, 11: 625-31.


Schulze CJ, Donia MS, Siqueira-Neto JL, Ray D, Raskatov JA, Green RE, McKerrow JH, Fischbach MA, Linington RG: Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei. ACS Chem Biol 2015, 10: 2373-81.


Devlin AS, Fischbach MA: A biosynthetic pathway for a prominent class of microbiota-derived bile acids. Nat Chem Biol 2015, 11: 685–690.


Medema MH, Fischbach MA: Computational approaches to natural product discovery. Nat Chem Biol 2015, 11: 639–648.


Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, et al: antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015, 43:W237-243.


Nayfach S, Fischbach MA, Pollard KS: MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics 2015, 31: 3368–3370.


Hadjithomas M, Chen IA, Chu K, Ratner A, Palaniappan K, Szeto E, Huang J, Reddy TB, Cimermancic P, Fischbach MA, et al: IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. MBio 2015, 6:e00932-15.


Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA: Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe 2014, 16:495-503.


Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, Fischbach MA: A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell 2014, 158:1402-1414.


Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA: A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PLoS Comput Biol 2014, 10:e1004016.


Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA: Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 2014, 158:412-421.


Lau W, Fischbach MA, Osbourn A, Sattely ES: Key applications of plant metabolic engineering. PLoS Biol 2014, 12:e1001879.


Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M: The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS One 2014, 9:e97279.


Claesen J, Fischbach MA: Synthetic microbes as drug delivery systems. ACS Synth Biol 2015, 4:358-364.


Wollenberg MS, Claesen J, Escapa IF, Aldridge KL, Fischbach MA, Lemon KP: Propionibacterium-produced coproporphyrin III induces Staphylococcus aureus aggregation and biofilm formation. MBio 2014, 5:e01286-01214.


David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ: Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505:559-563.


Wieland Brown LC, Penaranda C, Kashyap PC, Williams BB, Clardy J, Kronenberg M, Sonnenburg JL, Comstock LE, Bluestone JA, Fischbach MA: Production of alpha-galactosylceramide by a prominent member of the human gut microbiota. PLoS Biol 2013, 11:e1001610.


Scharschmidt TC, Fischbach MA: What Lives On Our Skin: Ecology, Genomics and Therapeutic Opportunities Of the Skin Microbiome. Drug Discov Today Dis Mech 2013, 10.


Marcobal A, Kashyap PC, Nelson TA, Aronov PA, Donia MS, Spormann A, Fischbach MA, Sonnenburg JL: A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. Isme j 2013, 7:1933-1943.


Fischbach MA, Bluestone JA, Lim WA: Cell-based therapeutics: the next pillar of medicine. Sci Transl Med 2013, 5:179ps177.


Donia MS, Fischbach MA: Dyeing to learn more about the gut microbiota. Cell Host Microbe 2013, 13:119-120.


Djonovic S, Urbach JM, Drenkard E, Bush J, Feinbaum R, Ausubel JL, Traficante D, Risech M, Kocks C, Fischbach MA, Priebe GP, Ausubel FM: Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants. PLoS Pathog 2013, 9:e1003217.


Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T: antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 2013, 41:W204-212.


Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, et al: Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013, 30:108-160.


Rath CM, Alexandrov T, Higginbottom SK, Song J, Milla ME, Fischbach MA, Sonnenburg JL, Dorrestein PC: Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations. Anal Chem 2012, 84:9259-9267.


Lemon KP, Armitage GC, Relman DA, Fischbach MA: Microbiota-targeted therapies: an ecological perspective. Sci Transl Med 2012, 4:137rv135.


Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Omura S, Khosla C: Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor. J Am Chem Soc 2012, 134:17797-17806.


Sonnenburg JL, Fischbach MA: Community health care: therapeutic opportunities in the human microbiome. Sci Transl Med 2011, 3:78ps12.


Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R: antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011, 39:W339-346.


Kersten RD, Yang YL, Xu Y, Cimermancic P, Nam SJ, Fenical W, Fischbach MA, Moore BS, Dorrestein PC: A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 2011, 7:794-802.


Fischbach MA, Sonnenburg JL: Eating for two: how metabolism establishes interspecies interactions in the gut. Cell Host Microbe 2011, 10:336-347.


Fischbach MA: Combination therapies for combating antimicrobial resistance. Curr Opin Microbiol 2011, 14:519-523.


Zimmermann M, Fischbach MA: A family of pyrazinone natural products from a conserved nonribosomal peptide synthetase in Staphylococcus aureus. Chem Biol 2010, 17:925-930.


Walsh CT, Fischbach MA: Natural products version 2.0: connecting genes to molecules. J Am Chem Soc 2010, 132:2469-2493.


Song JY, Jeong H, Yu DS, Fischbach MA, Park HS, Kim JJ, Seo JS, Jensen SE, Oh TK, Lee KJ, Kim JF: Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites. J Bacteriol 2010, 192:6317-6318.


Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, et al: A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010, 141:69-80.


Fischbach MA, Krogan NJ: The next frontier of systems biology: higher-order and interspecies interactions. Genome Biol 2010, 11:208.


Fischbach M, Voigt CA: Prokaryotic gene clusters: a rich toolbox for synthetic biology. Biotechnol J 2010, 5:1277-1296.


Dawlaty J, Zhang X, Fischbach MA, Clardy J: Dapdiamides, tripeptide antibiotics formed by unconventional amide ligases. J Nat Prod 2010, 73:441-446.


Wieland Brown LC, Acker MG, Clardy J, Walsh CT, Fischbach MA: Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. Proc Natl Acad Sci U S A 2009, 106:2549-2553.


Walsh CT, Fischbach MA: Repurposing libraries of eukaryotic protein kinase inhibitors for antibiotic discovery. Proc Natl Acad Sci U S A 2009, 106:1689-1690.


Walsh CT, Fischbach MA: New ways to squash superbugs. Sci Am 2009, 301:44-51.


Lopez D, Fischbach MA, Chu F, Losick R, Kolter R: Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc Natl Acad Sci U S A 2009, 106:280-285.


Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, et al: Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 2009, 461:393-398.


Fischbach MA, Walsh CT: Antibiotics for emerging pathogens. Science 2009, 325:1089-1093.


Fischbach MA: Antibiotics from microbes: converging to kill. Curr Opin Microbiol 2009, 12:520-527.


Clardy J, Fischbach MA, Currie CR: The natural history of antibiotics. Curr Biol 2009, 19:R437-441.


Walsh CT, Fischbach MA: Inhibitors of sterol biosynthesis as Staphylococcus aureus antibiotics. Angew Chem Int Ed Engl 2008, 47:5700-5702.


Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C, et al: Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res 2008, 18:729-741.


Sattely ES, Fischbach MA, Walsh CT: Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep 2008, 25:757-793.


Fischbach MA, Walsh CT, Clardy J: The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci U S A 2008, 105:4601-4608.


Straight PD, Fischbach MA, Walsh CT, Rudner DZ, Kolter R: A singular enzymatic megacomplex from Bacillus subtilis. Proc Natl Acad Sci U S A 2007, 104:305-310.


Nolan EM, Fischbach MA, Koglin A, Walsh CT: Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate. J Am Chem Soc 2007, 129:14336-14347.


Fischbach MA, Lai JR, Roche ED, Walsh CT, Liu DR: Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes. Proc Natl Acad Sci U S A 2007, 104:11951-11956.


Fischbach MA, Clardy J: One pathway, many products. Nat Chem Biol 2007, 3:353-355.


Butcher RA, Schroeder FC, Fischbach MA, Straight PD, Kolter R, Walsh CT, Clardy J: The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc Natl Acad Sci U S A 2007, 104:1506-1509.


Sharma SV, Fischbach MA, Haber DA, Settleman J: "Oncogenic shock": explaining oncogene addiction through differential signal attenuation. Clin Cancer Res 2006, 12:4392s-4395s.


Luo M, Lin H, Fischbach MA, Liu DR, Walsh CT, Groves JT: Enzymatic tailoring of enterobactin alters membrane partitioning and iron acquisition. ACS Chem Biol 2006, 1:29-32.


Lin H, Fischbach MA, Gatto GJ, Jr., Liu DR, Walsh CT: Bromoenterobactins as potent inhibitors of a pathogen-associated, siderophore-modifying C-glycosyltransferase. J Am Chem Soc 2006, 128:9324-9325.


Larsen NA, Lin H, Wei R, Fischbach MA, Walsh CT: Structural characterization of enterobactin hydrolase IroE. Biochemistry 2006, 45:10184-10190.


Lai JR, Fischbach MA, Liu DR, Walsh CT: A protein interaction surface in nonribosomal peptide synthesis mapped by combinatorial mutagenesis and selection. Proc Natl Acad Sci U S A 2006, 103:5314-5319.


Lai JR, Fischbach MA, Liu DR, Walsh CT: Localized protein interaction surfaces on the EntB carrier protein revealed by combinatorial mutagenesis and selection. J Am Chem Soc 2006, 128:11002-11003.


Jin M, Fischbach MA, Clardy J: A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid. J Am Chem Soc 2006, 128:10660-10661.


Garstecki P, M JF, Fischbach MA, Sia SK, Whitesides GM: Mixing with bubbles: a practical technology for use with portable microfluidic devices. Lab Chip 2006, 6:207-212.


Fischbach MA, Walsh CT: Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 2006, 106:3468-3496.


Fischbach MA, Walsh CT: Biochemistry. Directing biosynthesis. Science 2006, 314:603-605.


Fischbach MA, Settleman J: Regulation of the nucleotide state of oncogenic ras proteins by nucleoside diphosphate kinase. Methods Enzymol 2006, 407:33-45.


Fischbach MA, Lin H, Zhou L, Yu Y, Abergel RJ, Liu DR, Raymond KN, Wanner BL, Strong RK, Walsh CT, et al: The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci U S A 2006, 103:16502-16507.


Fischbach MA, Lin H, Liu DR, Walsh CT: How pathogenic bacteria evade mammalian sabotage in the battle for iron. Nat Chem Biol 2006, 2:132-138.


Dorrestein PC, Blackhall J, Straight PD, Fischbach MA, Garneau-Tsodikova S, Edwards DJ, McLaughlin S, Lin M, Gerwick WH, Kolter R, et al: Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry. Biochemistry 2006, 45:1537-1546.


Clardy J, Fischbach MA, Walsh CT: New antibiotics from bacterial natural products. Nat Biotechnol 2006, 24:1541-1550.


Lin H, Fischbach MA, Liu DR, Walsh CT: In vitro characterization of salmochelin and enterobactin trilactone hydrolases IroD, IroE, and Fes. J Am Chem Soc 2005, 127:11075-11084.


Fischbach MA, Lin H, Liu DR, Walsh CT: In vitro characterization of IroB, a pathogen-associated C-glycosyltransferase. Proc Natl Acad Sci U S A 2005, 102:571-576.


Wolfe DB, Conroy RS, Garstecki P, Mayers BT, Fischbach MA, Paul KE, Prentiss M, Whitesides GM: Dynamic control of liquid-core/liquid-cladding optical waveguides. Proc Natl Acad Sci U S A 2004, 101:12434-12438.


Fischbach MA, Settleman J: Specific biochemical inactivation of oncogenic Ras proteins by nucleoside diphosphate kinase. Cancer Res 2003, 63:4089-4094.