114. Dong, Xueyang; Bae, Minwoo; Le, Chi; Aguilar Ramos, Miguel A.; Balskus, Emily P. Enantiocomplementary Gut Bacterial Enzymes Metabolize Dietary Polyphenols Journal of the American Chemical Society, 2025. https://doi.org/10.1021/jacs.4c09892
113. Kountz, Duncan J.; Yu, Ruocheng; Lee, Jessie H.; Maloney, Katherine N.; Balskus, Emily P. Flavoaffinins, elusive cellulose-binding natural products from an anaerobic bacterium. bioRxiv2025, preprint. https://doi.org/10.1101/2025.02.08.637243.
112. Bae, Minwoo; Dong, Xueyang; Avila-Pacheco, Julian; Inyama, Fechi; Hill-Maini, Vayu; Clish, Clary; Balskus, Emily P. Distinct classes of gut bacterial molybdenum-dependent enzymes produce urolithins. bioRxiv2025, preprint. https://doi.org/10.1101/2025.01.17.632430.
112. Richards-Corke, Khyle C.; Jiang, Yindi; Yeliseyev, Vladimir; Zhang, Yancong; Franzosa, Eric A.; Wang, Zhipeng A.; Yapa Abeywardana, Maheeshi; Cole, Phillip A.; Huttenhower, Curtis; Bry, Lynn; Balskus, Emily P. A small-molecule inhibitor of gut bacterial urease protects the host from liver injury. ACS Chemical Biology2025. https://doi.org/10.1021/acschembio.3c00556.
110. Wong, Joel W. H.; Balskus, Emily P. Small molecules as modulators of phage–bacteria interactions. Current Opinion in Chemical Biology2025, 84, 102566. https://doi.org/10.1016/j.cbpa.2024.102566.
109. Alkhalaf, Lona M.; Arrowsmith, Cheryl; Balskus, Emily P.; Bergamini, Giovanna; Bhandari, Rashna; Chang, Christopher J.; Chen, Peng; Chen, Xing; Ciulli, Alessio; Cricco, Julia A.; Davis, Benjamin G.; Delbianco, Martina; Dudareva, Natalia; Dueber, Erin; Ferguson, Fleur; de Giuseppe, Priscila Oliveira; Hamachi, Itaru; Hammond, Ming Chen; Hatzios, Stavroula K.; … Winter, Georg. Thoughts for the future. Nature Chemical Biology2025, 21 (1), 6–15. https://doi.org/10.1038/s41589-024-01802-2.
108. Bae, Minwoo; Le, Chi (Chip); Mehta, Raaj S.; Dong, Xueyang; Pieper, Lindsey M.; Ramirez, Lorenzo; Alexander, Margaret; Kiamehr, Sina; Turnbaugh, Peter J.; Huttenhower, Curtis; Chan, Andrew T.; Balskus, Emily P.Metatranscriptomics-Guided Discovery and Characterization of a Polyphenol-Metabolizing Gut Microbial Enzyme. Cell Host & Microbe2024, 32, 1–10. https://doi.org/10.1016/j.chom.2024.10.002.
107. Woo, Amelia Y. M.; Sandoval–Espinola, Walter J.; Bollenbach, Maud; Wong, Alison; Sakanaka–Yokoyama, Mariko; Zhang, Qijun; Nieto, Vincent; Rey, Federico E.; Balskus, Emily P.Phenotypic High-Throughput Screening Identifies Modulators of Gut Microbial Choline Metabolism. bioRxiv2024, preprint. https://doi.org/10.1101/2024.11.08.621386.
106. Fu, Beverly; Yang, Hao; Kountz, Duncan J.; Lundahl, Maike N.; Beller, Harry R.; Broderick, William E.; Broderick, Joan B.; Hoffman, Brian H.; Balskus, Emily P.Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature’s Known Radical Chemistry. Journal of the American Chemical Society2024. https://doi.org/10.1021/jacs.4c10348.
105. Mandarino Alves, Amanda; Lecchi, Chiara; Lopez, Sharon; Stornetta, Alessia; Mathai, Prince P.; Villalta, Peter W.; Ishii, Satoshi; Balskus, Emily P.; Balbo, Silvia; Khoruts, Alexander. Dysfunctional mucus structure in cystic fibrosis increases vulnerability to colibactin-mediated DNA adducts in the colon mucosa. Gut Microbes2024, 6 (1), 2387877. https://doi.org/10.1080/19490976.2024.2387877.
104. McCurry, Megan D.; D'Agostino, Gabriel D.; Walsh, Jasmine T.; Bisanz, Jordan E.; Zalosnik, Ines; Dong, Xueyang; Morris, David J.; Korzenik, Joshua R.; Edlow, Andrea G.; Balskus, Emily P.; Turnbaugh, Peter J.; Huh, Jun R.; Devlin, A. Sloan. Gut Bacteria Convert Glucocorticoids into Progestins in the Presence of Hydrogen Gas. Cell2024, 187, (12), 2952–2968.e13. https://doi.org/10.1016/j.cell.2024.05.005.
103. Bao, Bin; Wang, Youyuan; Boudreau, Paul; Song, Xinyang; Wu, Meng; Chen, Xi; Patik, Izabel; Tang, Ying; Ouahed, Jodie; Ringel, Amit; Barends, Jared; Wu, Chuan; Balskus, Emily P.; Thiagarajah, Jay; Liu, Jian; Wessels, Michael R.; Lencer, Wayne; Kasper, Dennis L.; An, Dingding; Horwitz, Bruce; Snapper, Scott B. Bacterial Sphingolipids Exacerbate Colitis by Inhibiting ILC3-Derived IL-22 Production. Cellular and Molecular Gastroenterology and Hepatology2024, 18, (2), 101350. https://doi.org/10.1016/j.jcmgh.2024.04.007. BioRxiv: https://www.biorxiv.org/content/10.1101/2023.09.05.555400v1.
102. Li, Chenhao; Stražar, Martin; Mohamed, Ahmed M. T.; Pacheco, Julian A.; Walker, Rebecca L.; Lebar, Tina; Zhao, Shijie; Lockart, Julia; Dame, Andrea; Thurimella, Kumar; Jeanfavre, Sarah; Brown, Eric M.; Yan Ang, Qi; Berdy, Brittany; Sergio, Dallis; Invernizzi, Rachele; Tinoco, Antonio; Pishchany, Gleb; Vasan, Ramachandran S.; Balskus, Emily P.; Huttenhower, Curtis; Vlamakis, Hera; Clish, Clary; Shaw, Stanley Y.; Plichta, Damian R.; Xavier, Ramnik J. Gut Microbiome and Metabolome Profiling in Framingham Heart Study Reveals Cholesterol-Metabolizing Bacteria. Cell2024, 187 (8), 1834–1852.e19. https://doi.org/10.1016/j.cell.2024.03.014.
101. Wong, Derek A.; Cabezas, Maria D.; Daniel-Ivad, Martin; Prasanna, Deepali V.; Fernandez, Regina; Nicol, Robert; Balskus, Emily P.; Karim, Ashty S.; Jewett, Michael C. A Cell-Free Workflow for Detecting and Characterizing RiPP Recognition Element-Precursor Peptide Interactions. bioRxiv2024, Preprint. https://doi.org/10.1101/2024.03.25.586624.
100. 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. bioRxiv2024, Preprint. https://doi.org/10.1101/2024.01.30.576698.
99. Crooke, Anne Marie; Chand, Anika K.; Cui, Zheng; Balskus, Emily P. Elucidation of Chalkophomycin Biosynthesis Reveals N-Hydroxypyrrole-Forming Enzymes. Journal of the American Chemical Society2024, 146 (23), 16268–16280. https://doi.org/10.1021/jacs.4c04712.
98. Pelayo, Paula; Hussain, Fatima A.; Werlang, Caroline A.; Wu, Chloe; Woolston, Benjamin M.; Xiang, Claire M.; Rutt, Lindsay; France, Michael T.; Ravel, Jacques; Ribbeck, Katharina; Kwon, Douglas S.; Balskus, Emily P. Prevotella Are Major Contributors of Sialidases in the Human Vaginal Microbiome. Proceedings of the National Academy of Sciences2024, 121 (36), e2400341121. https://doi.org/10.1073/pnas.2400341121 .
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. https://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. Nature2023, 617, 403–408. https://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 Chemistry2023, 7, 319–339. https://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 Medicine2023, 29, 700–709. https://doi.org/10.1038/s41591-023-02217-7.
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 Communications2022, 13, 7624. https://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 Biology2023, 19, 159–167. https://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 Biology2023, 19, 151–158. https://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 Biochemistry2022, 91, 475–504. https://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 Society2022, 144, 11110–11119. https://doi.org/10.1021/jacs.1c13580.
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. https://doi.org/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. https://doi.org/10.1038/s41564-023-01447-2
77. Kountz, Duncan J.; Balskus, Emily P. Leveraging Microbial Genomes and Genomic Context for Chemical Discovery. Accounts of Chemical Research 2021, 54, 2788–2797. https://doi.org/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. https://doi.org/10.1038/s41586-022-04444-3.
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. https://doi.org/10.1021/acs.analchem.0c04895.
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. https://doi.org/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 Sciences2021, 118 (32), e2101498118. https://doi.org/10.1073/pnas.2101498118. BioRxiv: https://www.biorxiv.org/content/10.1101/2021.01.25.428109v1.
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 Sciences2021, 118 (4), e2015931118. https://doi.org/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 Genomics2021, 22, 633. https://doi.org/10.1186/s12864-021-07939-x.
70. Silpe, Justin E.; Balskus, Emily P. Deciphering Human Microbiota–Host Chemical Interactions. ACS Central Science2020,7, 20–29. https://doi.org/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 & Microbe2020,28, 245–257. https://doi.org/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 Society2020,142, 11818–11828. https://doi.org/10.1021/jacs.0c03431.
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 Biotechnology2020,65, 94–101. https://doi.org/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 & Microbe2020,27, 1001–1013. https://doi.org/10.1016/j.chom.2020.04.006.
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 Letters2020,11, 1980–1985. https://doi.org/10.1021/acsmedchemlett.0c00005.
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. eLife2020,9, e51420. https://doi.org/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. eLife2020,9, e50845. https://doi.org/10.7554/eLife.50845 bioRxiv: https://doi.org/10.1101/725358.
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. ChemBioChem2019,20. https://doi.org/10.1002/cbic.201900565. bioRxiv: https://doi.org/10.1101/763607.
61. Carlson, Erik S.; Balskus, Emily P. “The mysteries of macrocyclic colibactins” Nature Chemistry2019, 11, 867–869. doi:10.1038/s41557-019-0339-1
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 Society2019,141, 11489–11496. https://doi.org/10.1021/jacs.9b02453. bioRxiv: https://doi.org/10.1101/567248.
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. Science2019,364, eaau6323. https://doi.org/10.1126/science.aau6323.
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 Biology2019,14, 1097–1101. https://doi.org/10.1021/acschembio.9b00069. bioRxiv: https://doi.org/10.1101/559385.
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” Science2019, 363, eaar7785. doi:10.1126/science.aar7785
55. Ng, Tai L.; Rohac, Roman; Mitchell, Andrew J.; Boal, Amie K.; Balskus, Emily P. An N-nitrosating Metalloenzyme Constructs the Pharmacophore of Streptozotocin. Nature2019,566, 94–99. https://doi.org/10.1038/s41586-019-0894-z.
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 Edition2019,58, 3151–3155. https://doi.org/10.1002/anie.201814016.
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 wadsworthia. Proceedings of the National Academy of Sciences2019,116, 3171–3176. https://doi.org/10.1073/pnas.1815661116.
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 Reports2019,36, 1437–1461. https://doi.org/10.1039/C8NP00080H.
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 Society2019,141, 33–37. https://doi.org/10.1021/jacs.8b04883.