Publications

• Severin, G.B., Ramliden, M.S., Ford, K.C., Van Last, A.J., Sanath-Kumar, R., Decker, K.A., Hsueh, B.Y., Chen, G., Yoon, S.H., Demey, L.M., O'Hara, B.J., Rhoades, C.R., DiRita, V.J., Ng, W.L., and C.M. Waters. 2023. Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion. mBio. e0087523. doi: 10.1128/mbio.00875-23
• Beckman, D.A. and C.M. Waters. 2023. Vibrio cholerae phage ICP3 requires O1 antigen for infection. Infect Immun. 91(9):e0002623. doi: 10.1128/iai.00026-23
• Hsueh, B.Y., Sanath-Kumar, R., Bedore, A.M., and C. M. Waters. 2023. Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system. PLoS Pathog, 19(9):e1011195. doi: 10.1371/journal.ppat.1011195
• Tai, J.S.#, Ferrell, M.J.#, Yan, J.*, and C.M. Waters*. 2023. New Insights into Vibrio cholerae biofilms from molecular biophysics to microbial ecology. In Novel insights on biofilm development in pathogenic Vibrios. Springer Nature, Switzerland AG. Adv Exp Med Biol. 2023;1404:17-39. doi: 10.1007/978-3-031-22997-8_2.
• Gomez, J.B. and C.M. Waters. 2023. Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms. Nature Microbiology. 8(8):1380-1381. doi: 10.1038/s41564-023-01428-5.
• Bedore, A.M. and C.M. Waters. 2023. Plasmid-free cheater cells commonly evolve during laboratory growth. bioRxiv. 2023 May 20:2023.05.19.541508. doi: 10.1101/2023.05.19.541508. Preprint.
• Grant, N.A., Sontz, J.T., and C.M. Waters. 2023. Deployment of a Vibrio cholerae ordered transposon mutant library in a quorum-competent genetic background. bioRxiv. 2023 Nov 1:2023.10.31.564941. doi: 10.1101/2023.10.31.564941. Preprint.

• Rangarajan, A.A. and C.M. Waters. 2022. Double take: A dual-functional Hypr GGDEF synthesizes both cyclic di-GMP and cyclic GMP-AMP to control predation in Bdellovibrio bacteriovorus . PLoS Genetics. 8(7):e1010263. doi: 10.1371/journal.pgen.1010263.
• Hammer, N.D., and C.M. Waters. The 27^th Annual Midwest Microbial Pathogenesis Conference in the Age of COVID, Journal of Bacteriology, e0013622. doi: 10.1128/jb.00136-22. *co-corresponding authors
• Hsueh, B.Y. ^#, Severin, G.B.^#, Elg, C.A., Waldron, E.J., Kant, A., Wessel, A.J., Dover, J.A., Rhoades, C.R., Ridenhour, B.J., Parent, K.N., Neiditch, M.B., Ravi, J., Top, E.M., and C.M. Waters. 2022. A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection. Nature Microbiology. 7(8):1210-1220. doi: 10.1038/s41564-022-01162-4., #contributed equally to this paper
• Hsieh, M.L., Kiel, N., Jenkins, L.M., Ng, W.L., Knipling, L., and C.M. Waters*, and D.M. Hinton*. 2022. The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate. Nucleic Acids Research. 50(8):4484-4499. doi: 10.1093/nar/gkac253, *co-corresponding authors
• Banerjee, B., Zeng, Q., Hsueh, B.Y., Waters, C.M., and M. Yu and C.H. Yang. 2022. Quorum-sensing master regulator VfmE is a c-di-GMP effector that controls pectate lyase production in phytopathogen Dickeya dadantii. mSystems. 10(2):e0180521. doi: 10.1128/spectrum.01805-21
• Wilburn, K.M., Blaylock, J.B., Metcalfe, K.C, Hsueh, B.Y., Tew, D.J., and C.M. Waters. 2022. Development of a 3'3'-cyclic GMP-AMP enzyme linked immunoassay reveals phage infection reduces DncV activity. Israel Journal of Chemistry. In press

• C.M. Waters. 2021. Au naturale: use of biologically derived cyclic di-nucleotides for cancer immunotherapy. Open Biol. 11(12):210277. doi: 10.1098/rsob.210277.
• Silva-Rohwer AR, Held K, Sagawa J, Fernandez NL, Waters CM, Vadyvaloo V. 2021 CsrA Enhances Cyclic-di-GMP Biosynthesis and Yersinia pestis Biofilm Blockage of the Flea Foregut by Alleviating Hfq-Dependent Repression of the hmsT mRNA. mBio.12(4):e0135821. doi: 10.1128/mBio.01358-21
• Robinson, C., Sweeney, E., Ngo J., Ma, E., Perkins, A., Fernandez, N.L., Waters, C.M.,  Remington, S.J., Bohannan, B.J.M., Guillemin, K. 2021. Bacterial chemokinesis regulates host colonization in response to amino acid cues. Cell Host and Microbe. 29(8):1221-1234.e8. doi: 10.1016/j.chom.2021.06.003
• Bruger, E.L., Synder, D.J., Cooper, V.S., and C.M. Waters. 2021. Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation. ISME J. doi: 10.1038/s41396-020-00847-0
• Yoon, S.H., and C.M. Waters. 2021. The ever-expanding world of bacterial cyclic oligonucleotide second messengers. Current Opinions in Microbiology. 60:96-103. doi: 10.1016/j.mib.2021.01.017.
• Cox, A.C., Bogacz, M., El Abbar, F., Browning, D.D., Hsueh, B.Y., Waters, C.M., Lee, V.T., and Thompson, S.A. 2021. The Campylobacter jejuni response regulator and cyclic-di-GMP binding CbrR is a novel regulator of flagellar motility. Microorganisms. 10(1):86. doi: 10.3390/microorganisms10010086

• Maiden, M.M, and C.M. Waters. 2020. Triclosan depletes the membrane potential in Pseudomonas aeruginosa biofilms inhibiting aminoglycoside induced adaptive resistance. PLoS Pathogens, 16(10):e1008529. doi: 10.1371/journal.ppat.1008529
• Fernandez, N.L., Nhu, N.T.Q., Hsueh, B.Y., Franklin, J.L., Dufour, Y.S., and C.M. Waters. 2020. Vibrio cholerae adapts to sessile and motile lifestyles by cyclic di-GMP regulation of cell shape. Proceedings of the National Academy of Sciences. 117(46):29046-29054. doi: 10.1073/pnas.2010199117
• Mhatre, E.L., Snyder, D.J., Sileo1, E., Turner, C.B., Buskirk, S.W., Fernandez, N.L., Neiditch, M.B., Waters, C.M., and V.S. Cooper. 2020. One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity. Proceedings of the National Academy of Sciences. 117(35):21647-21657. doi: 10.1073/pnas.2008540117.
• Martínez-Ortiz IC, Ahumada-Manuel CL, Hsueh BY, Guzmán J, Moreno S, Cocotl-Yañez M, Waters CM, Zamorano-Sánchez D, Espín G, Núñez C. 2020. Cyclic di-GMP-Mediated Regulation of Extracellular Mannuronan C-5 Epimerases Is Essential for Cyst Formation in Azotobacter vinelandii. Journal of Bacteriology. 202(24):e00135-20. doi: 10.1128/JB.00135-20.
• Ahumada-Manuel CL, Martínez-Ortiz IC, Hsueh BY, Guzmán J, Waters CM, Zamorano-Sánchez D, Espín G, Núñez C. 2020. Increased c-di-GMP Levels Lead to the Production of Alginates of High Molecular Mass in Azotobacter vinelandii. Journal of Bacteriology. 202(24):e00134-20. doi: 10.1128/JB.00134-20.
• Hsieh, M.L., Waters, C.M.^#, and Hinton, D.M.^#, 2020. VpsR directly activates transcription of multiple biofilm genes in Vibrio cholerae. Journal of Bacteriology. 202(18):e00234-20. doi: 10.1128/JB.00234-20.
• Snyder, R.A., Ellison, C.K., Severin, G.B., Waters, C.M., and Y.V. Brun. 2020. Surface Sensing Stimulates Cellular Differentiation in Caulobacter crescentus. Proceedings of the National Academy of Sciences. 117(30):17984-17991. doi: 10.1073/pnas.1920291117.
• Yuan, X., Zeng, Q., Xu, J., Severin, G.B., Zhou, X., Waters, C.M., Sundin, G.W., Ibekwe, A.M., Liu, F., Yang, C.H. 2020. Tricarboxylic acid (TCA) cycle enzymes and intermediates modulate intracellular cyclic di-GMP levels and the production of plant-cell-wall degrading enzymes in soft rot pathogen Dickeya dadantii. Molecular Plant-Microbe Interactions, (2):296-307. doi: 10.1094/MPMI-07-19-0203-R.
• Ramliden, M.S., Severin, G.B., O’Hara, B.J., Waters, C.M., and W.L. Ng (2020). Microbial cyclic GMP-AMP signaling pathways. In: RÓ§mling, U. Microbial Cyclic di Nucleotides. Springer Nature Switzerland AG.
• Hsieh, M.L., Hinton, D.M., and C.M. Waters. (2020). Cyclic di-GMP Regulation of Gene Expression. In: RÓ§mling, U. Microbial Cyclic di Nucleotides. Springer Nature Switzerland AG.
• Anderson, W.A., Dippel, A.B., Maiden, M.M., Waters, C.M., and M.C. Hammond. 2020. Chemiluminescent sensors for quantitation of the bacterial second messenger cyclic di-GMP. Methods Enzymol. 2020;640:83-104.

• Jarosova, R., Mcclure, S., Gajda, M., Jovic, M., Girault, H., Lesch, A., Maiden, M.; Waters, C. and G. Swain. 2019. Inkjet Printed Carbon Nanotube Electrodes for Measuring Pyocyanin and Uric Acid in a Wound Fluid Simulant and Culture Media. Analytical Chemistry, in press
• C.M. Waters. 2019. Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint. BioRxiv, doi: https://doi.org/10.1101/644567
• Maiden, M.M., Zachos, M.P., and C.M. Waters. 2019. Hydrogels embedded with melittin and tobramycin are effective against Pseudomonas aeruginosa biofilms in an animal wound model. Frontiers in Microbiology. In press
• Hsueh, B.Y. and C.M. Waters. 2019. Combating Cholera. F1000 Research. In press
• Yoon, S.H., and C.M. Waters. 2019. Vibrio cholerae. Trends in Microbiology. Sep;27(9):806-807. doi: 10.1016/j.tim.2019.03.005
• Severin, G.B., and C.M. Waters. 2019. Pyrimidines and Cyclic Trinucleotides Join the Second Messenger Symphony. Cell Host Microbe. 25(4):471-473.
• Waters, C.M. and Goldberg, J. 2019. Pseudomonas aeruginosa in Cystic Fibrosis: A Chronic Cheater. Proceedings of the National Academies of Sciences, 116(14):6525-6527.
• Yuan, X., Zeng, Q., Khokhani, D., Tian, F., Severin, G. B., Waters, C.M., Xu, J., Zhou, X., Sundin, G.W., Ibekwe, A.M., , Liu, F., Yang, C.H. 2019. A Feed-forward signaling circuit controls bacterial virulence through linking cyclic di-GMP and two mechanistically distinct sRNAs; ArcZ and RsmB. Environmental Microbiology. In press
• Waldron E.J., Snyder, D., Sileo, E., Inoyama, D., Freundlich, J.S., Waters, C.M., Cooper, V.S., Neiditch, M.B. 2019. Structural Basis of DSF Recognition by its Receptor RpfR and its Regulatory Interaction with the DSF Synthase RpfF. PLoS Biology. 17(2):e3000123
• Maiden, M.M., Zachos, M.P., and C.M. Waters. 2019. The ionophore oxyclozanide enhances tobramycin killing of Pseudomonas aeruginosa biofilms by permeabilizing cells and depolarizing the membrane potential. Journal of Antimicrobial Chemotherapy. 74(4):894-906
• Fernandez, N.L. and C.M. Waters. (2019). Cyclic di-GMP Increases Catalase Production and Hydrogen Peroxide Tolerance in Vibrio cholerae. Applied and Environmental Microbiology, Applied and Enviromental Microbiology.01043-19. doi: 10.1128/AEM.01043-19 
• Fernandez, N., C.M. Waters. Analyzing diguanylate cyclase activity in vivo using a heterologous Escherichia coli host. 2019. Current Protocols. 52(1):e74.
• Heindl, J.E., Crosby, D., Brar, S., Pinto, J., Singletary, T., Merenich, D., Eagan, J., Buechlein, A., Bruger, E., Waters, C.; Fuqua, C. 2019. Reciprocal Control of Motility and Biofilm Formation by the PdhS2 Two-Component Sensor Kinase of Agrobacterium tumefaciens. Microbiology. 165(2):146-162.

• Kharadi, R., Castiblanco, L., Waters, C., and G. Sundin. Phosphodiesterase genes regulate amylovoran production, biofilm formation, and virulence in Erwinia amylovora. 2018. Applied and Environmental Microbiology. 85(1). pii: e02233-18
• Orr M, Weiss C, Severin S, Turdiev H, Kim SK, Turdiev A, Liu K, Tu B, Waters C, Winkler W, and Lee V. 2018. A subset of exoribonucleases serve as degradative enzymes for pGpG in c-di-GMP signaling. Journal of Bacteriology. 200(24). pii: e00300-18. 
• Chodur DM, Coulter P, Isaacs J, Pu M, Fernandez N, Waters CM, Rowe-Magnus DA. 2018. Environmental Calcium Initiates a Feed-Forward Signaling Circuit That Regulates Biofilm Formation and Rugosity in Vibrio vulnificus. MBio. 2018 Aug 28;9(4). pii: e01377-18. doi: 10.1128/mBio.01377-18.
• Berne C, Ellison CK, Agarwal R, Severin GB, Fiebig A, Morton RI 3rd, Waters CM, Brun YV. 2018. Feedback regulation of Caulobacter crescentus holdfast synthesis by flagellum assembly via the holdfast inhibitor HfiA. Molecular Microbiology. 2018 110(2):219-238. doi: 10.1111/mmi.14099.
• Hsieh, M.L., Hinton, D.M.#, Waters, C.M.# 2018. VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae. Nucleic Acids Research. 28;46(17):8876-8887. doi: 10.1093/nar/gky606.. #co-corresponding authors
• Severin, G.B.#, Ramliden, M.S.#, Hawver, L.A., Wang, K., Pell, M.E., Kieninger, A.K., Khataokar, A., O’Hara, B.J., Behrmann, L.V., Neiditch, M.B., Benning, C., and C.M. Waters*, and W.L. Ng*. Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae. Proceedings of the National Academy of Sciences. 115(26):E6048-E6055. doi: 10.1073/pnas.1801233115. . # These authors contributed equally, * co-corresponding authors.
• Agostoni, M., Logan-Jackson, A.R., Heinz, E.R., Severin, G., Bruger, E.L., Waters, C.M., and B.L. Montgomery. 2018. Homeostasis of Second Messenger Cyclic-di-AMP is Critical for Cyanobacterial Fitness and Acclimation to Abiotic Stress. Frontiers in Microbiology. 9:1121
• Bruger, E.L. and C.M. Waters. 2018. Maximizing Growth Yield and Dispersal via Quorum Sensing Promotes Cooperation in Vibrio Bacteria. Applied and Environmental Microbiology, 84(14). pii: e00402-18. doi: 10.1128/AEM.00402-18. PMID: 29728393
• Maiden, M.M., Hunt, A.M.A., Zachos, M.P., Gibson, J.A., Hurwitz, M.E., Mulks, M.H., and C.M. Waters. 2018. Triclosan is an aminoglycoside adjuvant for the eradication of Pseudomonas aeruginosa biofilms. Antimicrobial Agents and Chemotherapies.25;62(6). pii: e00146-18. doi: 10.1128/AAC.00146-18.
• Fernandez, N.L., Srivastava, D., Ngouajio, A.L., and C.M. Waters. 2018. Cyclic di-GMP Positively Regulates DNA Repair in Vibrio cholerae. Journal of Bacteriology. 200(15). pii: e00005-18. doi: 10.1128/JB.00005-18.
• Yuan, X., Tian, F., He. C., Severin, G.B., Waters, C.M., Zeng, Q., Liu, F., and C.H. Yang. 2018. The diguanylate cyclase GcpA inhibits the production of pectate lyases via the H-NS protein and RsmB regulatory RNA in Dickey dadantii. Molecular Plant Pathology. in press
• C.M. Waters. 2018. Shining the Light on Cyclic di-GMP Dark Matter. Journal of Bacteriology. pii: JB.00030-18. doi: 10.1128/JB.00030-18
• Pursley, B.R., Maiden, M.M., Hsieh, M.L., Fernandez, N., Severin, G.B., and C.M. Waters. 2018. Cyclic di-GMP regulates TfoY in Vibrio cholerae to control motility by both transcriptional and posttranscriptional mechanisms. Journal of Bacteriology. doi:10.1128/JB.00578-17. 200(7). pii: e00578-17. doi: 10.1128/JB.00578-17. 

• Feirer N., Kim D., Xu J., Fernandez N., Waters C.M., Fuqua C. 2017. The Agrobacterium tumefaciens CheY-like protein ClaR regulates biofilm formation. Microbiology. doi: 10.1099/mic.0.000558. [Epub ahead of print] PMID: 29068284
• Sobe, R.C., Bond, W.G., Wotanis, C.K., Zayner, J.P., Burriss, M.A., Fernandez, N., Bruger, E.L., Waters, C.M., Neufeld, H.S., and E. Karatan. 2017. Spermine inhibits Vibrio cholerae biofilm formation through the NspS-MbaA polyamine signaling system. Journal of Biological Chemistry. In press.
• Sloup R.E., Konal A.E., Severin G.B., Korir M.L., Bagdasarian M.M., Bagdasarian M., and C.M. Waters. Cyclic di-GMP and VpsR Induce the Expression of Type II Secretion in Vibrio cholerae. Journal of Bacteriology. pii: JB.00106-17. doi: 10.1128/JB.00106-17.
• Agostinho Hunt, A.M., Gibson, J.A., Larrivee, C.L., O’Reilly, S., Bozak, S., Busik, J.V., Waters, C.M. 2017. Come to the light side: in vivo monitoring of Pseudomonas aeruginosa biofilm infections in chronic wounds in a diabetic hairless murine model. JoVE. In press
• Agostinho Hunt, A.M., Gibson, J.A., Larrivee, C.L., O’Reilly, S., Bozak, S., Busik, J.V., Waters, C.M. 2017. A bioluminescent Pseudomonas aeruginosa wound model reveals increased mortality of Type 1 diabetic mice to biofilm infection. Journal of Wound Care. in press
• Dalia TN, Yoon SH, Galli E, Barre FX, Waters CM, Dalia AB. Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases. Nucleic Acids Research. 2017 doi: 10.1093/nar/gkx496. PMID: 28575400
• Connelly B.D., Bruger E. L. McKinley P.K., and C. M. Waters. 2016. Resource Abundance and the Critical Transition to Cooperation. Journal of Evolutionary Biology. 30(4):750-761. doi: 10.1111/jeb.13039. Epub 2017 Jan 25. PMID: 28036143
• Chodur D.M., Guo L., Pu M., Bruger E., Fernandez N., Waters C., and D.A. Rowe-Magnus. 2017. The proline variant of the W[F/L/M][T/S]R c-di-GMP binding motif suppresses dependence on signal-association for regulator function.. J Bacteriol. JB.00344-17. doi: 10.1128/JB.00344-17. PMID: 28652300
• Severin, G.B., and C.M. Waters. 2017. “Chapter 7: Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Synthesis”. In Sauer, K. c-di-GMP Signaling: Methods and Protocols. Springer Nature.

• Díaz-Muñoz S.L., Boddy A.M., Dantas G., Waters C.M., Bronstein J.L. 2016. Contextual organismality: Beyond pattern to process in the emergence of organisms. 2016. Evolution. doi: 10.1111/evo.13078. PMID: 27704542.
• Gries C.M., Bruger E.L., Moormeier D.E., Scherr T.D., Waters C.M., Kielian T. 2016. Cyclic di-AMP released from Staphylococcus aureus biofilm induces a macrophage type I interferon response. Infection and Immunity. pii: IAI.00447-16. PMID: 27736778
• Silva I.N., Santos P.M., Santos M.R., Zlosnik J.E., Speert D.P., Buskirk S.W., Bruger E.L., Waters C.M., Cooper V.S., Moreira L.M. 2016. Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection. mSystems. pii: e00029-16. PMID: 27822534.
• Bruger, E.L., and C.M. Waters. 2016. Bacterial quorum sensing stabilizes cooperation by optimizing growth strategies. Applied and Environmental Microbiology. 82(22):6498-6506. PMID: 27565619.
• Wang .Y, Kim S.H., Natarajan R., Heindl J.E., Bruger E.L., Waters C.M., Michael A.J., and C. Fuqua. 2016. Spermidine Inversely Influences Surface Interactions and Planktonic Growth in Agrobacterium tumefaciens. J Bacteriol. 198(19):2682-91. doi: 10.1128/JB.00265-16
• Sloup R.E., Cieza R.J., Needle1 D.B., Abramovitch R.B., Torres A.G., and C.M. Waters. 2016. Polysorbates Prevent Biofilm Formation and Pathogenesis of Escherichia coli O104:H4. Biofouling. 32(9):1131-1140. PMID: 27667095.
• Flynn K.M., Dowell G., Johnson T.M., Koestler B.J, Waters CM, Cooper VS. 2016. Evolution of ecological diversity in biofilms of Pseudomonas aeruginosa by altered cyclic diguanylate signaling. J Bacteriol. 198(19):2608-18. doi: 10.1128/JB.00048-16
• Alyaqoub, F.S., Aldhamen, Y.A., Koestler, B.J., Bruger, E.L., Seregin, S.S., Pereira-Hicks, C., Godbehere, S., and C.M. Waters and A. Amalfitano. 2016. In Vivo Synthesis of Cyclic-di-GMP Using a Recombinant Adenovirus Preferentially Improves Adaptive Immune Responses against Extracellular Antigens. Journal of Immunology. 15;196(4):1741-52, doi: 10.4049/​jimmunol.1501272.

• Yuan, X., Khokhani, D., Wu, X., Yang, F., Biener, G., Koestler, B.J., Raicu, V., He, C., Waters, C.M., Sundin, G.W., Tian, F., and C.H. Yang. 2015. Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviors. Environmental Microbiology. 17(11):4745-63. doi: 10.1111/1462-2920.13029
• Bruger, E and C.M. Waters. 2015. Sharing the sandbox: Evolutionary mechanisms that maintain bacterial cooperation F1000Research 4(F1000 Faculty Rev):1504, doi: 10.12688/f1000research.7363.1
• Orr, M.W., Donaldson, G.P., Severin, G.B., Sintim, H.O., Wang, J., Waters, C.M., and V.T. Lee. 2015. Oligoribonuclease is the primary degradative enzyme for pGpG in Pseudomonas aeruginosa that is required for cyclic-di-GMP turnover. PNAS. 112(36):E5048-57.
• Agostoni, M., Waters, C.M., Montgomery, B.L. 2015. Regulation of biofilm formation and cellular buoyancy through modulationg intracellular cyclic di-GMP levels in engineered cyanobacteria. Biotechnology and Bioengineering.113(2):311-9. doi: 10.1002/bit.25712.
• Pursley, B.R., Hinshaw, K.C., Waters, C.M., Chandler, J.R., Antunes, L.C.M. (2015). Microbial Signaling. In: Bruce, TB and Trindade-Silva, AE (Eds). Molecular Diversity of Environmental Prokaryotes, CRC Press, Taylor & Francis Group. London, GB.
• Feirer, N., Xu, J., Allen, K.D., Koestler, B.J., Bruger, E. Waters, C.M. White, R. H., and C. Fuqua. 2015. A Pterin-Dependent Signaling Pathway Regulates a Dual Function Diguanylate Cyclase-Phosphodiesterase Controlling Surface Attachment in Agrobacterium tumefaciens. mBio.6(4). pii: e00156-15. doi: 10.1128.
• Flores-Valdez M.A., de Jesús Aceves-Sánchez M., Pedroza-Roldán C., Vega-Domínguez P.J., Prado-Montes de Oca E., Bravo-Madrigal J., Laval F., Daffé M., Koestler B., Waters C.M. 2015. IUBMB Life. 67(2):129-38.
• Savage, C.R., Arnold, W.K., Gevre, A., Koestler, B.J., Bruger, E., Barker, J.R., Waters, C.M., and B. Stevenson. 2015. Intracellular concentrations of Borrelia burgdorferi cyclic di-AMP are not changed by altered expression of the CdaA synthase. PLoS One. 10(4):e0125440.
• Srivastava, D., and C.M. Waters. 2015. A Filter Binding Assay to Quantify the Association of Cyclic di-GMP to Proteins. Bio-Protocol.org. Vol 5,Iss 3, Jan 05, 2015

• Koestler, BJ, and C.M. Waters. 2014. Intestinal GPS: bile and bicarbonate control cyclic di-GMP to provide Vibrio cholerae spatial cues within the small intestine. Gut Microbes. 5(6):775-780. PMID: 25621620.
• Koestler BJ, Seregin SS, Rastall DP, Aldhamen YA, Godbehere S, Amalfitano A, Waters CM. 2014. Simulating Innate Immunity by in vivo cyclic di-GMP Synthesis using Adenovirus. Clinical and Vaccine Immunology.  Nov;21(11):1550-9. PMID: 25230938
• Rudlaff, R. and C.M. Waters. 2014. What is the role of cyclic di-GMP signaling in the human gut microbiome? Microbiome Science and Medicine. 1:39-44.
• Wu, X., Zeng, Q., Koestler, B.J., Waters, C.M., Sundin, G.W., Hutching, W., and Yang, C. 2014. Deciphering the components that coordinately regulate virulence factors of the soft rot pathogen Dickeya dadantii. Molecular Plant-Microbe Interactions. 27(10):1119-31.
• Koestler, B.J. and C.M. Waters. 2014. Bile Acids and Bicarbonate Inversely Regulate Intracellular Cyclic di-GMP in Vibrio cholerae. Infection and Immunity. 82(7): 3002-14. PMID: 24799624
• Bobrov, A.G., Kirillina, O., Vadyvaloo, V., Koestler, B.J., Hinz, A.K., Mack D., Waters, C.M., and R.D. Perry. 2014. The Yersinia pestis HmsCDE regulatory system is essential for  blockage of the oriental rat flea (Xenopsylla cheopis), a classic plague vector. Environmental Microbiology.  2014 Feb 15. doi: 10.1111/1462-2920.12419.PMID: 25586342
• Hunter, J.L., Severin, G.B., Koestler, B.J. and C.M. Waters. 2014. The Vibrio cholerae diguanylate cyclase VCA0965 has an AGDEF active site and synthesizes cyclic di-GMP. BMC Microbiology. doi: 10.1186/1471-2180-14-22. PMID: 24490592.

• Srivastava, D., Hsieh, M., Khataokar, A., Neidtich, M. B., and C.M. Waters. 2013. “Cyclic di-GMP inhibits Vibrio cholerae motility by repressing induction of transcription and inducing extracellular polysaccharide production.” Molecular Microbiology. 90(6):1262-76. PMID: 24134710.
• Bai, Y., Yang, J., Eisele, L.E., Underwood, A.J., Koestler, B.J., Waters, C.M., Metzger, D.W., and Bai, G. 2013. “Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess c-di-AMP phosphodiesterase activity and affect bacterial growth and virulence.” Journal of Bacteriology. 195(22):5123-32.
• Sambanthamoorthy, K., Luo, C., Pattabhiraman, N., Feng, X., Koestler, B.J., Waters, C.M., and T. Palys. Identification of Small Molecules Inhibiting Diguanylate Cyclases to Control Bacterial Biofilm Development. Biofouling. 30(1):17-28. PMID: 24117391
• Agostoni, M., Koestler, B.J., Waters, C.M., Williams, B.L., and B.L. Montgomery. Occurence of Cyclic di-GMP-Modulating Output Domains in Cyanobacteria: an Illuminating Perspective.mBio. 13;4(4). Doi:pii: e00451-13.
• Zhao, X., Koestler, B.J., Waters, C.M. and B.K. Hammer. 2013. Post-transcriptional activation of a diguanylate cyclase by quorum sensing small RNAs promotes biofilm formation in Vibrio choelrae. Molecular Microbiology. 89(5):989-1002.
• Xu, J., Koestler, B.J., Choi, J.H., Waters, C.M., and C. Fuqua. 2013. Genetic Analysis of Agrobacterium tumefaciens Unipolar Polysaccharide Production Reveals Complex Integrated Control of the Motile-toSessile Switch. Molecular Microbiology. 89(5):929-48.
• Koestler, B.J. and C.M. Waters. 2013. Exploring environmental control of cyclic di-GMP signaling in Vibrio choelrae using TELCA. Applied and Environmental Microbiology, 79(17):5233-41.
• Barker, J.R., Koestler, B.J., Carpenter, V.K., Burdette, D.L., Waters, C.M., Vance, R.E., and R.H. Valdivia. 2013. STING-Dependent Recognition of Cyclic di-AMP Mediates Type I Interferon Responses during Chlamydia trachomatis Infection. MBio. 4(3):e00018-13.
• Edmunds, A.C.*, Castiblanco, L.F.*, Sundin, G.W., and C.M. Waters. 2013. Cyclic Di-GMP Modulates the Disease Progressin of Erwinia amylovora. Journal of Bacteriology. 195(10):2155-65. *co-first authors
• Amarasinghe, J.J., D'Hondt, R.E., Waters, C.M., and N.J. Mantis. 2013. Exposure of Salmonella enterica serovar Typhimurium to a Protective Monoclonal IgA Triggers Exopolysaccharide Production via a Diguanylate Cyclase-Dependent Pathway. Infection and Immunity. 81(3):653-64.
• C.M. Waters. 2013. Bacterial Wheel Locks: Extracellular Polysaccharide Inhibits Flagellar Rotation. Jounral of Bacteriology. 195(3):409-10.

• Bellows, L.E., Koestler, B.J., Karaba, S.M., Waters, C.M., and W.W. Lathem. 2012. Hfq-dependent co-ordinate control of cyclic diguanylate synthesis and catabolism in the plague pathogen Yersinia pestis. Molecular Microbiology. 86(3):661-74.
• C.M. Waters. The Meteoric Rise of the Signaling Molecule Cyclic di-GMP. 2012. Microbe. August Issue. 353-359.
• Sambanthamoorthy, K., Sloup, R.E., Parashar, V., Smith, J.M., Kim, E. E., , Semmelhack, M.F., Neiditch, M.B., and C.M. Waters. 2012. Identification of Small Molecules that Antagonize Diguanylate Cyclase Enzymes to Inhibit Biofilm Formation. Antimicrobial Agents and Chemotherapy. 56(10):5202-11.
• Massie, J.P., Reynolds, E.L., Koestler, B.K., Cong, J., Agostoni, M., and C.M.Waters. 2012. Quantification of High Specificity Cyclic di-GMP Signaling. PNAS. 109(31):12746-51.
• Al Safadi, R., Galeb, S.A., Sloup, R.E. Rudrik, J.T., Waters, C.M., Eaton, K.A. and S.D. Manning. 2012. Correlation between in vivo biofilm formation and virulence gene expression in Escherichia coli O104:H4.PLOS One. 7(7):e41628
• Srivastava, D. and C.M. Waters. 2012. A Tanlged Web: Regulatory Connections Between Quorum Sensing and Cyclic di-GMP. Journal of Bacteriology. 194(17):4485-93.
• Purcell, E.B., McKee, R.W., McBride, S.M., Waters, C.M., and R. Tamayo. 2012. Cyclic diguanylate inversely regulates motility and aggregation in Clostridium difficile. Journal of Bacteriology. 193(13):3307-16.
• Beckmann, B.E., Knoester, D.B., Connelly, B.D., Waters, C.M., and McKinley, P.K. 2012. Evolution of Resistance to Quorum Quenching in Digital Organisms. Artificial Life. 194(17):4485-93.

• Srivastava, D., Harris, R.C., and Waters, C.M. 2011. Integration of Cyclic di-GMP and Quorum Sensing in the Control of vpsT and aphA in Vibrio choelrae. Journal of Bacteriology. 193(22): 6331-41.
• Sambanthamoorhty, K., Gokhale, A.A., Lao, W. Parashar, Neiditch, M.B., Semmelhack, M.F., and Waters, C.M. 2011. Identification of a Novel Benzimidazole that Inhibits Bacterial Biofilm Formation in a Broad Spectrum Manner. Antimicrobial Agents and Chemotherapy. 55(9):4369-78.
• Bobrov, A.G., Klrillina, O. Ryjenkov, D. A., Waters, C.M., Price, P.A. Fetherston, J.D., Mack, D., Goldman, W.E., Gomelsky, M., and Perry, R.D. 2011. Systematic analysis of cyclic di-GMP signalling enzymes and their role in biofilm formation and virulence in Yersinia pestis. Molecular Microbiology. 79(2):533-51.

• Waters, C.M. 2010, “Chapter 6: Methods for Cyclic di-GMP Detection”. In Visick, K. and Wolfe, A. (Eds). “Second Messenger Cyclic Di-GMP”.  Eds. Wolfe and Visick. ASM Press, Washington, DC. 68-75.
• Waters, C.M., J. Wu, M. Rhamsey, R. Harris, and B.L. Bassler. 2010. Quorum Sensing Represses ExsA to Control Type Three Secretion in Vibrio harveyi. Applied and Environmental Microbiology. 76(15):4996-5004.

• Tu, K.C., C.M. Waters, S.L. Svenningsen, and B.L. Bassler. 2008. A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi. Molecular Microbiology. 70(4): 896-907
• Waters, C.M., W. Lu, J.D. Rabinowitz, and B.L. Bassler. 2008. Quorum Sensing Controls Biofilm Formation in Vibrio cholerae Through Modulation of Cyclic Di-GMP. Journal of Bacteriology. 190:2527-36.
• Svenningsen, S.L., C.M. Waters, and B.L. Bassler. 2008. A negative feedback loop involving small RNAs accelerates Vibrio cholerae’s transition out of quorum-sensing mode. Genes and Development. 22:226-238
• Waters, C.M., and B.L. Bassler. 2006. The Vibrio harveyi Quorum Sensing System Uses Shared Regulatory Components to Discriminate between Multiple Autoinducers. Genes and Development. 20:2754-2767.
• Waters, C.M., and B.L. Bassler. 2005. Cell-cell communication in bacteria. Annual Review of Cell and Developmental Biology. 21:319-346.
• Waters, C.M., H. Hirt, J.K. McCormick, P.M. Schlievert, C.L. Wells, and G.M. Dunny. 2004. An Amino-terminal Domain of Enterococcus faecalis Aggregation Substance is Required for Aggregation, Bacterial Internalization by Epithelial Cells, and Binding to Lipoteichoic Acid. Molecular Microbiology. 52(4):1159-1171.
• Johnson, J.R., C. Clabots, H. Hirt, C. Waters, and G. Dunny. 2004. Enterocococcal Aggregation Substance and Binding Substance Are Not Major Contributors to Urinary Tract Colnization by Enterococcus faecalis in a Mouse Model of Ascending Unobstructed Urinary Tract Infection. Infection and Immunity. 72(4):2445-2448.
• Lee, J.M., P.C. Anderson, J.K. Padgitt, J.M. Hanson, C.M. Waters, and J.A. Johnson. 2003. Nrf2, not the estrogen receptor, mediates catechol estrogen-induced activation of the antioxidant responsive element. Biochimica et Biophysica Acta. 1629(1-3):92-101.
• Waters, C.M., C.L. Wells, and G.M. Dunny. 2003. The Aggregation Domain , but not the RGD Motifs, of Enterococcus faecalis Aggregation Substance is Critical for Efficient Internalization by HT-29 Enterocytes. Infection and Immunity. 71(10):5682-5689.
• Waters, C.M., M.H. Antiporta, B.E. Murray, and G.M. Dunny. 2003. Role of the Enterococcus faecalis GelE Protease in Determination of Cellular Chain Length, Supernatant Pheromone Levels, and the Degradation of Fibrin and Misfolded Surface Proteins. Journal of Bacteriology. 185(12): 3613-3623.
• Weaver,K.E., D.M. Weaver, C.L. Wells, C.M. Waters, M.E. Gardner, and E.A. Ehli.  2003. The Enterococcus faecalis Plasmid pAD1-encoded Fst Toxin Affects Membrane Permeability and Alters Cellular Responses to Lantibiotics. Journal of Bacteriology. 185(7):2169-2177.
• Waters, C.M., and G.M. Dunny. 2001. Analysis of Functional Domains of the Enterococcus faecalis Pheromone-Induced Surface Protein Aggregation Substance. Journal of Bacteriology. 183:5659-5667.
• McCormick, J.K., H. Hirt, C.M. Waters, T. J. Tripp, G. M. Dunny, and P. M. Schlievert. 2001.  Antibodies to a Surface-Exposed, N-terminal Domain of Aggregation Substance Are Not Protective in the Rabbit Model of Enterococcus faecalis Infective Endocarditis. Infection and Immunity. 69:3305-3314.