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 Biology 2025 doi.org/10.1021/acschembio.3c00556
111. Wong, Joel W. H., & Balskus, Emily P. “Small molecules as modulators of phage–bacteria interactions.” Current Opinion in Chemical Biology2025, 84, 102566. doi.org/10.1016/j.cbpa.2024.102566
110. 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. doi.org/10.1038/s41589-024-01802-2
109. 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 & Microbe 2024, 32, 1–10. doi.org/10.1016/j.chom.2024.10.002
108. 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
107. 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. doi.org/10.1021/jacs.4c10348
106. 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. doi.org/10.1080/19490976.2024.2387877
105. 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. doi.org/10.1016/j.cell.2024.05.005
104. 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 Hepatology 2024, 18, 2, 101350. doi.org/10.1016/j.jcmgh.2024.04.007
103. 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" Cell 2024, 187, 8, 1834-1852.e19. doi.org/10.1016/j.cell.2024.03.014
102. 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” bioRxiv 2024, preprint.
100. 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. doi.org/10.1021/jacs.4c04712
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 Chemistry2024, 16, 173–182. doi.org/10.1038/s41557-023-01390-z
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” PNAS2024, 121 (36) e2400341121. doi.org/10.1073/pnas.240034112
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” Nature2023, 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” bioRxiv2023, preprint.
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” Nature2023, 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 Medicine2023, 29, 700–709.doi.org/10.1038/s41591-023-02217-7
88. Balskus Emily P. “Elucidating the Chemistry and Biology of the Human Microbiome” Biochemistry2022,61(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 Communications2022, 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 Biology2023, 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 Biology2023, 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 Biochemistry2022, 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 Society2022, 144, 11110–11119. doi.org/10.1021/jacs.1c13580
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 Microbiology2022, 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” eLIFE2022, 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 microbiology20238, 1641–1652. doi: 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 Research2021, 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” Nature2022, 603, 315–320. doi: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 Chemistry2021, 93, 5754–5762. doi: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 Biology2021, 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 Sciences2021, 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 Sciences2021, 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 genomics2021, 22, 633 doi.org/10.1186/s12864-021-07939-x
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. 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 & Microbe2020, 27, 1001–1013. doi: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 Letters 2020, 11, 1980–1985. doi: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” 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
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
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
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
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
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. doi: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 Edition 2019, 58, 3151–3155.doi: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 Sciences 2019, 116, 3171–3176. doi: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 Reports 2019, 36, 1437–1461. doi: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. doi:10.1021/jacs.8b04883
