Targeting the human gut microbiome with small-molecule inhibitors

Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicity

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Micrometeorological Methods for Measuring Methane Emission Reduction at Beef Cattle Feedlots: Evaluation of 3‐Nitrooxypropanol Feed Additive

McGinn, S. M., Flesch, T. K., Beauchemin, K. A., Shreck, A. L., & Kindermann, M. (2019) · Journal of Environmental Quality · doi:10.2134/jeq2018.11.0412 · Cited by 48

Characterization of bromoethanesulfonate-resistant mutants of Methanococcus voltae: evidence of a coenzyme M transport system

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Tungstate Antagonism of Molybdate in Aspergillus niger.

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Challenges & opportunities for phage-based in situ microbiome engineering in the gut

Voorhees, P. J., Cruz-Teran, C. A., Edelstein, J., & Lai, S. K. (2020) · Journal of Controlled Release · doi:10.1016/j.jconrel.2020.06.016 · Cited by 45

Potential Repurposing of Known Drugs as Potent Bacterial β-Glucuronidase Inhibitors

Ahmad, S., Hughes, M. A., Yeh, L.-A., & Scott, J. E. (2012) · SLAS Discovery · doi:10.1177/1087057112444927 · Cited by 44

Could AlphaFold revolutionize chemical therapeutics?

Tong, A., Burch, J. D., McKay, D. B., Bustamante, C., Crackower, M. A., & Wu, H. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00670-x · Cited by 43

Specific Inhibition of Bacterial β-Glucuronidase by Pyrazolo[4,3- c ]quinoline Derivatives via a pH-Dependent Manner To Suppress Chemotherapy-Induced Intestinal Toxicity

Cheng, K.-W., Tseng, C.-H., Yang, C., Tzeng, C., Cheng, T.-C., Leu, Y.-L., Chuang, Y.-C., Wang, J., Lu, Y., Chen, Y.-L., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00963 · Cited by 42

Nitrification

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Acarbose, a Pseudooligosaccharide, Is Transported but Not Metabolized by the Maltose-Maltodextrin System of Escherichia coli

Brunkhorst, C., Andersen, C., & Schneider, E. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.8.2612-2619.1999 · Cited by 40

Butyrolactone‐I, an efficient α‐glucosidase inhibitor, improves type 2 diabetes with potent TNF‐α–lowering properties through modulating gut microbiota in db/db mice

Wu, W. D., Liu, L., Zhu, H., Sun, Y., Wu, Y., Liao, H., Gui, Y., Li, L., Liu, L., Sun, F., et al. (2019) · The FASEB Journal · doi:10.1096/fj.201901061r · Cited by 37

Microbial sulfate reduction measured by an automated electrical impedance technique

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Nitrogen fixation by Azotobacter vinelandii in tungsten-containing medium.

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Effect of miglitol on the suppression of nonalcoholic steatohepatitis development and improvement of the gut environment in a rodent model

Kishida, Y., Okubo, H., Ohno, H., Oki, K., & Yoneda, M. (2017) · Journal of Gastroenterology · doi:10.1007/s00535-017-1331-4 · Cited by 34

Comparison of Peritoneal Macrophages from Germfree and Conventional Mice

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Nitrocompounds as potential methanogenic inhibitors in ruminant animals: A review

Zhang, Z., Cao, Z., Wang, Y.-L., Wang, Y., Yang, H., & Li, S. (2017) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2017.12.010 · Cited by 31

Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome

Pellock, S. J., Walton, W. G., Ervin, S. M., Torres-Rivera, D., Creekmore, B. C., Bergan, G., Dunn, Z. D., Ли, Б., Tripathy, A., & Redinbo, M. R. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.01.013 · Cited by 31

A High Throughput Assay for Discovery of Bacterial β-Glucuronidase Inhibitors

Ahmad, S., Hughes, M. A., Lane, K. T., Redinbo, M. R., Yeh, L.-A., & Scott, J. E. (2011) · Current Chemical Genomics · doi:10.2174/1875397301105010013 · Cited by 29

Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria

Bollenbach, M., Ortega, M. A., Orman, M., Drennan, C. L., & Balskus, E. P. (2020) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.0c00005 · Cited by 29

Current clinical translation of microbiome medicines

McCoubrey, L. E., Elbadawi, M., & Basit, A. W. (2022) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.02.001 · Cited by 28

wild-type choline TMA lyase in complex with betaine aldehyde

Funk, M. A., & Drennan, C. L. (2018) · Worldwide Protein Data Bank · doi:10.2210/pdb6nd3/pdb · Cited by 27

Manipulating the soil microbiome for improved nitrogen management

Hu, H., & He, J. (2018) · Microbiology Australia · doi:10.1071/ma18007 · Cited by 26

Inhibition of the Class II HMG–CoA reductase of Pseudomonas mevalonii

Hedl, M., & Rodwell, V. W. (2004) · Protein Science · doi:10.1110/ps.03597504 · Cited by 25

Nonmicrobicidal Small Molecule Inhibition of Polysaccharide Metabolism in Human Gut Microbes: A Potential Therapeutic Avenue

Santilli, A. D., Dawson, E. M., Whitehead, K. J., & Whitehead, D. C. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00309 · Cited by 25

Analysis of the Impact of Rosuvastatin on Bacterial Mevalonate Production Using a UPLC-Mass Spectrometry Approach

Nolan, J. A., Kinsella, M., Hill, C., Joyce, S. A., & Gahan, C. G. M. (2016) · Current Microbiology · doi:10.1007/s00284-016-1014-z · Cited by 24

Sulphate Transport and Metabolism Desulphovibrio Desulphuricans

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Dietary Fatty Acids Control the Species of N-Acyl-Phosphatidylethanolamines Synthesized by Therapeutically Modified Bacteria in the Intestinal Tract

Dosoky, N. S., Guo, L., Chen, Z., Feigley, A. V., & Davies, S. S. (2017) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.7b00127 · Cited by 22

Nitrogen fixation system of tungsten-resistant mutants of Azotobacter vinelandii

Riddle, G. D., Simonson, J. G., Hales, B. J., & Braymer, H. D. (1982) · Journal of Bacteriology · doi:10.1128/jb.152.1.72-80.1982 · Cited by 21

Connecting the dots: Targeting the microbiome in drug toxicity

Luo, Y., & Zhou, T. (2021) · Medicinal Research Reviews · doi:10.1002/med.21805 · Cited by 20

Chemical Derivatization Enables MALDI-TOF-Based High-Throughput Screening for Microbial Trimethylamine (TMA)-Lyase Inhibitors

Winter, M., Bretschneider, T., Thamm, S., Kleiner, C., Grabowski, D., Chandler, S., Ries, R., Kley, J. T., Fowler, D., Bartlett, C., et al. (2019) · SLAS DISCOVERY · doi:10.1177/2472555219838216 · Cited by 19

Transport of coenzyme M (2-mercaptoethanesulfonic acid) and methylcoenzyme M [(2-methylthio)ethanesulfonic acid] in Methanococcus voltae: identification of specific and general uptake systems

Dybas, M. J., & Konisky, J. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.11.5866-5871.1989 · Cited by 16

Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists

Jean-Pierre, F., Henson, M. A., & O’Toole, G. A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.634479 · Cited by 16

Chemoproteomic Analysis of Microbiota Metabolite–Protein Targets and Mechanisms

Zhao, X., Yang, X., & Hang, H. C. (2022) · Biochemistry · doi:10.1021/acs.biochem.1c00758 · Cited by 16

A benzoxazole derivative as an inhibitor of anaerobic choline metabolism by human gut microbiota

Gabr, M. T., Machalz, D., Pach, S., & Wolber, G. (2020) · RSC Medicinal Chemistry · doi:10.1039/d0md00218f · Cited by 15

Discovery of a Histidine‐Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine‐Lyase

Gabr, M. T., & Świderek, K. (2020) · ChemMedChem · doi:10.1002/cmdc.202000571 · Cited by 14

Difficulties in the analysis of acid-labile sulfide in Mo-S and Mo-Fe-S systems

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Some Historical Elements of Microbial Ecology

Caumette, P., Bertrand, J.-C., & Normand, P. (2014) · Springer eBooks · doi:10.1007/978-94-017-9118-2_2 · Cited by 12

The Microbiome Factor in Drug Discovery and Development

Nuzzo, A., & Brown, J. R. (2019) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.9b00333 · Cited by 11

Peptidomimetic‐based approach toward inhibitors of microbial trimethylamine lyases

Gabr, M. T., Deganutti, G., & Reynolds, C. A. (2020) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13775 · Cited by 10

Non-lethal growth inhibition by arresting the starch utilization system of clinically relevant human isolates of Bacteroides dorei

Santilli, A. D., Russell, J. T., Triplett, E. W., Whitehead, K. J., & Whitehead, D. C. (2019) · MedChemComm · doi:10.1039/c9md00301k · Cited by 10

Anion transport as a target of adaption to perchlorate in sulfate-reducing communities

Stoeva, M. K., Kuehl, J. V., Kazakov, A. E., Wang, O., Rushton-Green, R., & Coates, J. D. (2019) · The ISME Journal · doi:10.1038/s41396-019-0540-7 · Cited by 9

Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases

Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193

Another renaissance for bile acid gastrointestinal microbiology

Ridlon, J. M., & Gaskins, H. R. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00896-2 · Cited by 205

Hydrogen sulfide produced by the gut microbiota impairs host metabolism via reducing GLP-1 levels in male mice

Qi, Q., Zhang, H., Jin, Z., Wang, C., Xia, M., Chen, B., Lv, B., Diaz, L. P., Li, X., Feng, R., et al. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01068-x · Cited by 129

Horizon scanning the application of probiotics for wildlife

Garcías-Bonet, N., Roik, A., Tierney, B. T., García, F. C., Villela, H., Dungan, A. M., Quigley, K. M., Sweet, M. J., Berg, G., Gram, L., et al. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.08.012 · Cited by 81

Pharmacomicrobiomics: The Role of the Gut Microbiome in Immunomodulation and Cancer Therapy

Bolte, L. A., Björk, J. R., Gaćeša, R., & Weersma, R. K. (2025) · Gastroenterology · doi:10.1053/j.gastro.2025.04.025 · Cited by 39

Drugging the gut microbiota: toward rational modulation of bacterial composition in the gut

Altamura, F., Maurice, C. F., & Castagner, B. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.09.005 · Cited by 17

Drugging the microbiome: targeting small microbiome molecules

Sharma, S., Hegde, P. V., Panda, S., Orimoloye, M. O., & Aldrich, C. C. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102234 · Cited by 2

Probing and manipulating the gut microbiome with chemistry and chemical tools

Mantravadi, P. K., Kovi, B. S., Reddy, S. R., Pandian, G. N., Kalesh, K., & Parthasarathy, A. (2025) · Gut Microbiome · doi:10.1017/gmb.2025.4 · Cited by 4

Discovery of small molecule enzyme inhibitors from gut microbes as potential antiinflammatory and anticancer agents

Stierle, A. A. (2013) · Journal of Postgenomics Drug & Biomarker Development

Deciphering Human Microbiota–Host Chemical Interactions

Silpe, J. E., & Balskus, E. P. (2020) · ACS Central Science · doi:10.1021/acscentsci.0c01030 · Cited by 43