Discovery of new phage defense systems in Vibrio cholerae

This body of work describes a coordinated research program examining phage-host interactions and phage defense systems in Vibrio cholerae and related bacteria. The Waters lab has contributed multiple complementary studies that illuminate how V. cholerae senses phage threat and deploys diverse molecular defenses, how phage infection interfaces with bacterial signaling pathways, and how fundamental regulators of bacterial physiology shape susceptibility to phage. Key contributions include characterization of a CBASS (cyclic oligonucleotide-based antiphage signaling system) anti-phage system in V. cholerae and identification of regulatory inputs that activate it; the 2023 mBio paper reports activation of a V. cholerae CBASS anti-phage system by quorum sensing and folate depletion. This work connects community-level signaling (quorum sensing) and metabolic state (folate levels) to deployment of an innate immune-like bacterial defense.

Complementing CBASS-focused studies, Waters and colleagues reported a broadly conserved deoxycytidine deaminase that protects bacteria from phage infection (Nature Microbiology, 2022). That study positions a deaminase-based mechanism as a widespread defense strategy, expanding the catalog of enzymatic defenses bacteria use against phage. Additional work from the group explores how timing of phage replication cycles influences sensitivity to toxin/antitoxin defense modules; a 2023 PLoS Pathogens paper demonstrates that replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system. Together, these findings indicate that both specific enzymatic activities and the temporal dynamics of infection critically determine the outcome of phage-bacteria encounters.

The Waters lab has also explored how phage infection alters bacterial second-messenger signaling. Development of assays and sensors for cyclic di-nucleotides and studies of cGAMP/c-di-GMP signaling reveal that phage infection reduces DncV activity, as indicated by a 2022 Israel Journal of Chemistry contribution reporting a 3'3'-cyclic GMP-AMP enzyme-linked immunoassay. More broadly, the group has a sustained interest in cyclic oligonucleotide second messengers and their roles in bacterial physiology and defense, reflected in reviews and methodological advances on chemiluminescent sensors for cyclic di-GMP quantitation.

Additional publications from the Waters lab document phage-host specificity and phage infection requirements: a 2023 Infect Immun paper reports that Vibrio cholerae phage ICP3 requires the O1 antigen for infection, clarifying an essential receptor requirement for at least one V. cholerae phage. Collectively, these studies integrate molecular genetics, biochemistry, signaling, and ecological perspectives to map how V. cholerae detects phage, what molecular weapons it uses, and how cellular state and community signals regulate defense deployment.

Across the papers highlighted in this portfolio, Waters and collaborators employ genetic libraries, biochemical assays, enzyme-linked immunoassays, and molecular microbiology to dissect defense systems such as CBASS, deoxycytidine deaminases, and toxin/antitoxin modules, and to connect these to cyclic nucleotide signaling and quorum sensing. The work advances understanding of bacterial innate immunity, documents conserved enzymatic defense strategies, and shows how physiological and ecological contexts modulate phage susceptibility. Together, these contributions substantially extend knowledge of V. cholerae phage defense systems and provide new tools and conceptual frameworks for further discovery and exploitation of bacterial anti-phage mechanisms.