Selected Publications / 2019 – Present


101. Altshuller, Maria; He, Xu; MacKrell, Elliot J.; Wernke, Kevin M.; Wong, Joel W.H.; Sellés-Baiget, Selene; Wang, Ting-Yu; Chou, Tsui-Fen; Duxin, Julien P.; Balskus, Emily P.; Herzon, Seth B.; Semlow, Daniel. “The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links” bioRxiv 2024, preprint.

bioRxiv: doi.org/10.1101/2024.01.30.576698


 
 

100. Crooke, Anne Marie; Chand, Anika K.; Balskus, Emily P. “Elucidation of chalkophomycin biosynthesis reveals N-hydroxypyrrole-forming enzymes” bioRxiv 2024, preprint.

bioRxiv: doi.org/10.1101/2024.01.24.577118


 
 

99. Glasser, Nathaniel R.; Cui, Dongtao; Risser, Douglas D.; Okafor, C. Denise; Balskus, Emily P. “Accelerating the discovery of alkyl halide-derived natural products using halide depletion”. Nature Chemistry 2024, online ahead of print. doi.org/10.1038/s41557-023-01390-z


98. Pelayo, Paula; Hussain, Fatima A.; Werlang, Caroline A.; Wu, Chloe; Woolston, Benjamin M.; Ribbeck, Katharina; Kwon, Doug S.; Balskus, Emily P. “Prevotella are major contributors of sialidases in the human vaginal microbiome” bioRxiv 2024, preprint.

bioRxiv: doi.org/10.1101/2024.01.09.574895


97. Segui Perez, Celia; De Jongh, Rivka; Jonkergouw, Robin; Pelayo, Paula; Balskus, Emily P.; Zomer, Aldert; Strijbis, Karin. “Prevotella timonensis degrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities” bioRxiv 2024, preprint.

bioRxiv: doi.org/10.1101/2024.01.09.574844


96. Mayers, Jared R .; Varon, Jack; Zhou, Ruixuan R.; Daniel-Ivad, Martin; Beaulieu, Courtney; Bholse, Amrisha; Glasser, Nathaniel R.; Lichtenauer, Franziska M.; Ng, Julie; Pinilla Vera, Mayra; Huttenhower, Curtis; Perrella, Mark A.; Clish, Clary B.; Zhao, Sihai D.; Baron, Rebecca M.; Balskus, Emily P. “Identification and targeting of microbial putrescine acetylation in bloodstream infections” bioRxiv 2023, preprint.

bioRxiv: doi.org/10.1101/2023.09.21.558834


 
 

95. Nagashima, Kazuki; Zhao, Aishan; Atabakhsh, Katayoon; Bae, Minwoo; Blum, Jamie E.; Weakley, Allison; Jain, Sunit; Meng, Xiandong; Cheng, Alice G.; Wang, Min; Higginbottom, Steven; Dimas, Alex; Murugkar, Pallavi; Sattely, Elizabeth S.; Moon, James J.; Balskus, Emily P.; Fischbach, Michael A. “Mapping the T cell repertoire to a complex gut bacterial community” Nature 2023, 621, 162–170. doi.org/10.1038/s41586-023-06431-8


94. Kountz, Duncan J. and Balskus, Emily P. “A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis” bioRxiv 2023, preprint.

bioRxiv: doi.org/10.1101/2023.07.31.551370


 
 

93. Mandelbaum, Noa; Zhang, Lihan; Carasso, Shaqed; Ziv, Tamar; Lifshiz-Simon, Sapir; Davidovich, Irina; Luz, Ishai; Berinstein, Elliot; Gefen, Tal; Cooks, Tomer; Talmon, Yeshayahu; Balskus, Emily P.; Geva-Zatorsky, Naama. “Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects” NPJ Biofilms and Microbiomes 2023, 9, 30. doi.org/10.1038/s41522-023-00400-9


 
 

92. Van Cura, Devon; Ng, Tai L.; Huang, Jing; Hager, Harry; Hartwig, John F.; Keasling, Jay D.; Balskus, Emily P. “Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production” Angewandte Chemie (International ed. in English) 2023, 62 (28), e202304646 doi.org/10.1002/anie.202304646


 
 

91. Huang, Jing; Quest, Andrew; Cruz-Morales, Pablo; Deng, Kai; Pereira, Jose H.; Van Cura, Devon; Kakumanu, Ramu; Baidoo, Edward E. K.; Dan, Qingyun; Chen, Yan; Petzold, Christopher J.; Northen, Trent R.; Adams, Paul D.; Clark, Douglas S.; Balskus, Emily P.; Hartwig, John F.; Mukhopadhyay, Aindrila; Keasling, Jay D. “Complete integration of carbene-transfer chemistry into biosynthesis” Nature 2023, 617, 403–408 doi.org/10.1038/s41586-023-06027-2


 
 

90. Woo, Amelia Y. M.; Aguilar Ramos, Miguel A.; Narayan, Rohan; Richards-Corke, Khyle C.; Wang, Michelle L.; Sandoval-Espinola, Walter J.; Balskus, Emily P. “Targeting the human gut microbiome with small-molecule inhibitors” Nature reviews Chemistry 2023, 7, 319–339. doi.org/10.1038/s41570-023-00471-4


 
 

89. Mehta, Raaj S.; Mayers, Jared R.; Zhang, Yancong; Bhosle, Amrisha; Glasser, Nathaniel R.; Nguyen, Long H.; Ma, Wenjie; Bae, Sena; Branck, Tobyn; Song, Kijun; Sebastian, Luke; Avila Pacheco, Julian; Seo, Hyuk-Soo; Clish, Clary; Dhe-Paganon, Sirano; Ananthakrishnan, Ashwin N.; Franzosa, Eric A.; Balskus, Emily P.; Chan, Andrew T.; Huttenhower, Curtis. “Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease” Nature Medicine 2023, 29, 700–709. doi.org/10.1038/s41591-023-02217-7


88. Balskus Emily P. “Elucidating the Chemistry and Biology of the Human Microbiome” Biochemistry 2022, 61(24):2777-2778. doi:10.1021/acs.biochem.2c00652


 
 

87. Dong, Xueyang; Guthrie, Ben G. H.; Alexander, Margaret; Noecker, Cecilia; Ramirez, Lorenzo; Glasser, Nathaniel R.; Turnbaugh, Peter J.; Balskus, Emily P. “Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators” Nature Communications 2022, 13, 7624. doi.org/10.1038/s41467-022-33576-3


 
 

86. Volpe, Matthew R.; Velilla, José A.; Daniel-Ivad, Martin; Yao, Jenny J.; Stornetta, Alessia; Villalta, Peter W.; Huang, Hsin-Che; Bachovchin, Daniel A.; Balbo, Silvia; Gaudet, Rachelle; Balskus, Emily P. “A small molecule inhibitor prevents gut bacterial genotoxin production” Nature Chemical Biology 2023, 19, 159–167. doi.org/10.1038/s41589-022-01147-8


 
 

85. Velilla, José A.; Vople, Matthew R.; Kenney, Grace E.; Walsh, Richard M.; Balskus, Emily P.; Gaudet, Rachelle “Structural basis of colibactin activation by the ClbP peptidase” Nature Chemical Biology 2023, 19, 151–158. doi.org/10.1038/s41589-022-01142-z


 
 

84. Le, Chip*; Bae, Minwoo*; Kiamehr, Sina; Balskus, Emily P. “Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily” Annual Review of Biochemistry 2022, 91, 475–504 doi.org/10.1146/annurev-biochem-032620-110804


 
 

83. Fu, Beverly; Nazemi, Azadeh; Levin, Benjamin J.; Yang, Zhongyue; Kulik, Heather J.; Balskus, Emily P. “Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer” Journal of the American Chemical Society 2022, 144, 11110–11119. doi.org/10.1021/jacs.1c13580


 
 

82. Reed, Amber D.; Fletcher, Joshua R.; Huang, Yolanda Y.; Thanissery, Rajani; Rivera, Alissa J.; Parsons, Ruth J.; Stewart, Allison K.; Kountz, Duncan J.; Shen, Aimee; Balskus, Emily P.; Theriot, Casey M. “The Stickland Reaction Precursor trans-4-Hydroxy-l-Proline Differentially Impacts the Metabolism of Clostridioides difficile and Commensal ClostridiamSphere 2022, 7(2), e0092621. doi.org/10.1128/msphere.00926-21


 
 

81. Martins, Teresa P.; Glasser, Nathaniel R.; Kountz, Duncan J.; Oliveira, Paulo; Balskus, Emily P.; Leão, Pedro N. “Biosynthesis of the unusual carbon skeleton of nocuolin A” ACS Chemical Biology 2022, 17, 2528–2537. doi.org/10.1021/acschembio.2c00464

chemRxiv: doi:10.26434/chemrxiv-2022-jv5n7


80. Bloom, Seth M.; Mafunda, Nomfuneko A.; Woolston, Benjamin M.; Hayward, Matthew R.; Frempong, Josephine F.; Abai, Aaron B.; Xu, Jiawu; Mitchell, Alissa J.; Westergaard, Xavier; Hussain, Fatima A.; Xulu, Nondumiso; Dong, Mary; Dong, Krista L.; Gumbi, Thandeka; Ceasar, F. Xolisile; Rice, Justin K.; Choksi, Namit; Ismail, Nasreen; Ndung’u, Thumbi; Ghebremichael, Musie S.; Relman, David A.; Balskus, Emily P.; Mitchell, Caroline M.; Kwon, Douglas S. “Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation” Nature Microbiology 2022, 7, 434–450. doi:10.1038/s41564-022-01070-7


79. Braffman, Nathaniel R.; Ruskoski, Terry B.; Davis, Katherine M.; Glasser, Nathaniel R.; Johnson, Cassidy; Okafor, C. Denise; Boal, Amie K.; Balskus, Emily P. “Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis” eLIFE 2022, 11, e75761. doi:10.7554/eLife.75761


 
 

78. Jenkins, Dominick J.; Woolston, Benjamin M.; Hood-Pishchany, M. Indriati; Pelayo, Paula; Konopaski, Alyssa N.; Peters, M. Quinn; France, Michael T.; Ravel, Jacques; Mitchell, Caroline M.; Rakoff-Nahoum, Seth; Whidbey, Christopher; Balskus, Emily P. “Bacterial amylases enable glycogen degradation by the vaginal microbiome” Nature microbiology 2023 8, 1641–1652. doi: 10.1038/s41564-023-01447-2

bioRxiv 2021 preprint: doi:10.1101/2021.07.19.452977


77. Kountz, Duncan J.; Balskus, Emily P. “Leveraging Microbial Genomes and Genomic Context for Chemical Discovery” Accounts of Chemical Research 2021, 54, 2788–2797. doi:10.1021/acs.accounts.1c00100


 
 

76. Silpe, Justin E.*; Wong, Joel W. H.*; Owen, Siân V.; Baym, Michael; Balskus, Emily P. “The bacterial toxin colibactin triggers prophage induction” Nature 2022, 603, 315–320. doi:10.1038/s41586-022-04444-3

bioRxiv: doi:10.1101/2021.05.24.445430


 
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75. Murray, Kevin J.; Carlson, Erik S.; Stornetta, Alessia; Balskus, Emily P.; Villalta, Peter W.; Balbo, Silvia “Extension of Diagnostic Fragmentation Filtering for Automated Discovery in DNA Adductomics” Analytical Chemistry 2021, 93, 5754–5762.
doi:10.1021/acs.analchem.0c04895


 
isIA-graphical abstract_forSubmission.png
 

74. Dawson, Christopher D.*; Irwin, Stephania M.*; Backman, Lindsey R.F.; Le, Chip; Wang, Jennifer X.; Vennelakanti, Vyshnavi; Yang, Zhongyue; Kulik, Heather J.; Drennan, Catherine L.; Balskus, Emily P. “Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase” Cell Chemical Biology 2021, 28 (9), P1333-1346
doi:10.1016/j.chembiol.2021.03.001


73. Rajakovich, Lauren J.; Fu, Beverly; Bollenbach, Maud; Balskus, Emily P. “Elucidation of an anaerobic pathway for metabolism of L-carnitine derived γ-butyrobetaine to trimethylamine in human gut bacteria” Proceedings of the National Academy of Sciences 2021, 118 (32), e2101498118. doi.org/10.1073/pnas.2101498118


 
 

72. McBride, Molly J.; Pope, Sarah R.; Hu, Kai; Okafor, C. Denise; Balskus, Emily P.; Bollinger, J. Martin, Jr.; Boal, Amie K. “Structure and assembly of the diiron cofactor in the heme-oxygenase–like domain of the N-nitrosourea–producing enzyme SznF” Proceedings of the National Academy of Sciences 2021, 118 (4), e2015931118. doi:10.1073/pnas.2015931118


71. Eusebio, Nadia; Rego, Adriana; Glasser, Nathaniel R.; Castelo-Branco, Raquel; Balskus, Emily P.; Leão, Pedro N. “Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria” BMC genomics 2021, 22, 633 doi.org/10.1186/s12864-021-07939-x

bioRxiv: doi:10.1101/2021.01.05.425448


 
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70. Silpe, Justin E.; Balskus, Emily P. “Deciphering Human Microbiota–Host Chemical Interactions” ACS Central Science 2020, 7, 20–29. doi:10.1021/acscentsci.0c01030


 
 

69. Kenny, Douglas J.; Plichta, Damian R.; Shungin, Dmitry; Koppel, Nitzan; Hall, Brantley; Fu, Beverly; Vasan, Ramachandran S.; Shaw, Stanley Y.; Vlamakis, Hera; Balskus, Emily P.; Xavier, Ramnik J. “Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level” Cell Host & Microbe 2020, 28, 245–257. doi:10.1016/j.chom.2020.05.013


 
 

68. McBride, Molly; Sil, Debangsu; Ng, Tai L.; Crooke, Anne Marie; Kenney, Grace E.; Tysoe, Christina R.; Zhang, Bo; Balskus, Emily P.; Boal, Amie K.; Krebs, Carsten; Bollinger, J. Martin, Jr. “A peroxodiiron(III) intermediate mediating both N-hydroxylation steps in biosynthesis of the N-nitrosourea pharmacophore of streptozotocin by SznF” Journal of the American Chemical Society 2020, 142, 11818–11828. doi:10.1021/jacs.0c03431


 
(67) 20200202_Graphical Abstract.png
 

67. Fu, Beverly; Balskus, Emily P. “Discovery of C–C bond-forming and bond-breaking radical enzymes: enabling transformations for metabolic engineering” Current Opinion in Biotechnology 2020, 65, 94–101. doi:10.1016/j.copbio.2020.02.003


 
 

66. Bisanz, Jordan E.; Soto-Perez, Paola; Noecker, Cecilia; Aksenov, Alexander A.; Lam, Kathy N.; Kenney, Grace E.; Bess, Elizabeth N.; Haiser, Henry J.; Kyaw, Than S.; Yu, Feiqiao B.; Rekdal, Vayu M.; Ha, Connie W.Y.; Devkota, Suzanne; Balskus, Emily P.; Dorrestein, Pieter C.; Allen-Vercoe, Emma; Turnbaugh, Peter J. “A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria” Cell Host & Microbe 2020, 27, 1001–1013. doi:10.1016/j.chom.2020.04.006


 
(65) Bollenbach TOC graphic.png
 

65. Bollenbach, Maud; Ortega, Manuel; Orman, Marina; Drennan, Catherine L.; Balskus, Emily P. “Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria” ACS Medicinal Chemistry Letters 2020, 11, 1980–1985. doi:10.1021/acsmedchemlett.0c00005


 
(64) graphical_abstract epb edits.png
 

64. Backman, Lindsey R.F.*; Huang, Yolanda Y.*; Andorfer, Mary C.; Gold, Brian; Raines, Ronald T.; Balskus, Emily P.; Drennan, Catherine L. “Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme” eLIFE 2020, 9, e51420. doi:10.7554/eLife.51420


 
 

63. Rekdal, Vayu Maini; Bernardino, Paola Nol; Luescher, Michael U.; Kiamehr, Sina; Le, Chip; Bisanz, Jordan E.; Turnbaugh, Peter J.; Bess, Elizabeth N.; Balskus, Emily P. “A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols” eLIFE 2020, 9, e50845. doi:10.7554/eLife.50845

bioRxiv: doi:10.1101/725358


 
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62. Ng, Tai L.*; McCallum. Monica E.*; Zheng, Christine R.; Wang, Jennifer X.; Wu, Kelvin J. Y.; Balskus, Emily P. “The L‐Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis” ChemBioChem 2019, 20. doi:10.1002/cbic.201900565

bioRxiv: doi:10.1101/763607


61. Carlson, Erik S.; Balskus, Emily P. “The mysteries of macrocyclic colibactins” Nature Chemistry 2019, 11, 867–869. doi:10.1038/s41557-019-0339-1


 
 

60. Chen, Sifan; Henderson, Ayana; Petriello, Michael; Romano, Kymberleigh A.; Gearing, Mary; Miao, Ji; Schell, Mareike; Sandoval-Espinola, Walter J.; Tao, Jiahui; Sha, Bingdong; Graham, Mark; Crooke, Rosanne; Kleinridders, Andre; Balskus, Emily P.; Rey, Federico E.; Morris, Andrew; Biddinger, Sudha B. “Trimethylamine N-Oxide Binds and Activates PERK to Promote Metabolic Dysfunction” Cell Metabolism 2019, 30, 1141–1151. doi:10.1016/j.cmet.2019.08.021


 
(59) 19-06-06 updated TOC graphic.png
 

59. Jiang, Yindi; Stornetta, Alessia; Villalta, Peter W.; Wilson, Matthew R.; Boudreau, Paul D.; Zha, Li; Balbo, Silvia; Balskus, Emily P. “Reactivity of an unusual amidase may explain colibactin’s DNA cross-linking activity” Journal of the American Chemical Society 2019, 141, 11489–11496. doi:10.1021/jacs.9b02453

bioRxiv: doi:10.1101/567248


 
(58) Rekdal TOC graphic for website.png
 

58. Maini Rekdal, Vayu; Bess, Elizabeth N.; Bisanz, Jordan E.; Turnbaugh, Peter J.; Balskus, Emily P. “Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism” Science 2019, 364, eaau6323. doi:10.1126/science.aau6323


 
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57. Volpe, Matthew R.; Wilson, Matthew R.; Brotherton, Carolyn A.; Winter, Ethan S.; Johnson, Sheila E.; Balskus, Emily P.In vitro characterization of the colibactin-activating peptidase ClbP enables development of a fluorogenic activity probe” ACS Chemical Biology 2019, 14, 1097–1101. doi:10.1021/acschembio.9b00069

bioRxiv: doi:10.1101/559385


 
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56. Wilson, Matthew R.*; Jiang, Yindi*; Villalta, Peter W.; Stornetta, Alessia; Boudreau, Paul D.; Carrá, Andrea; Brennan, Caitlin A.; Chun, Eunyoung; Ngo, Lizzie; Samson, Leona D.; Engelward, Bevin P.; Garrett, Wendy S.; Balbo, Silvia; Balskus, Emily P. “The human gut bacterial genotoxin colibactin alkylates DNA” Science 2019, 363, eaar7785. doi:10.1126/science.aar7785


 
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55. Ng, Tai L.; Rohac, Roman; Mitchell, Andrew J.; Boal, Amie K.; Balskus, Emily P. “An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin” Nature 2019, 566, 94–99. doi:10.1038/s41586-019-0894-z


 
(54) 19-02-15 large TOC graphic.png
 

54. Schultz, Erica E.*; Braffman, Nathaniel R.*; Luescher, Michael U.; Hager, Harry H.; Balskus, Emily P. “Biocatalytic Friedel–Crafts Alkylation Using a Promiscuous Biosynthetic Enzyme” Angewandte Chemie International Edition 2019, 58, 3151–3155. doi:10.1002/anie.201814016


 
(53) PNAS IslA paper graphical abstract.png
 

53. Peck, Spencer C.; Denger, Karin; Burrichter, Anna; Irwin, Stephania M.; Balskus, Emily P.; Schleheck, David “A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthiaProceedings of the National Academy of Sciences 2019, 116, 3171–3176. doi:10.1073/pnas.1815661116


 
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52. Martins, Teresa P.; Rouger, Caroline; Glasser, Nathaniel R.; Freitas, Sara; de Fraissinette, Nelly B.; Balskus, Emily P.; Tasdemir, Deniz; Leão, Pedro N. “Chemistry, bioactivity and biosynthesis of cyanobacterial alkylresorcinols” Natural Product Reports 2019, 36, 1437–1461. doi:10.1039/C8NP00080H


 
(51) Orman TOC graphic.png
 

51. Orman, Marina; Bodea, Smaranda; Funk, Michael A.; Martínez-del Campo, Ana; Bollenbach, Maud; Drennan, Catherine L.; Balskus, Emily P. “Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria” Journal of the American Chemical Society 2019, 141, 33–37. doi:10.1021/jacs.8b04883