Dominick Faith

All Publications

• A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli. PLoS pathogens Pershing, N. L., Brzozowski, R. S., Schmidt, A. K., Faith, D. R., Joyce, A. C., de Ora, L. O., Kominsky, J. D., Dankwardt, A., Maciver, A., Bell, R., Henriques, W. S., Andersen, S. E., Wiedenheft, B., Casjens, S. R., Duerkop, B. A., Round, J. L., Secor, P. R. 2026; 22 (1): e1013836

  Abstract

  Prophages are prevalent features of bacterial genomes that can reduce susceptibility to infection by competing phages, yet the mechanisms involved are often elusive. Here, we identify a small RNA (svsR) encoded by the lambdoid prophage NC-SV in adherent-invasive Escherichia coli strain NC101 that limits infection by virulent coliphages. Comparative genomics revealed that NC-SV-like prophages and svsR homologs are broadly conserved across Enterobacteriaceae. Transcriptomic analyses show that svsR represses maltodextrin transport genes, including lamB, which encodes the outer membrane maltoporin LamB, a known receptor for numerous coliphages. Deletion of the lamB gene reveals that while LamB is not required for replication of the virulent phages tested, it contributes to plaque expansion, indicating a role in phage spread but not as an essential receptor. Nutrient supplementation experiments further linked maltodextrin and glucose availability to changes in plaque expansion and phage adsorption. In vivo, we compared wild-type NC101 and a prophage-deletion strain (NC101∆NC-SV) in mice to assess the impact of NC-SV on lytic phage susceptibility. Although intestinal E. coli densities remained stable across groups, animals colonized with NC101 exhibited markedly reduced phage burdens in both the intestinal lumen and mucosa compared to mice colonized with NC101∆NC-SV. This reduced phage pressure was associated with increased dissemination of E. coli to extraintestinal tissues, including the spleen and liver. Together, these findings highlight a nutrient-responsive, prophage-encoded mechanism that protects E. coli from phage predation and may promote bacterial persistence in and dissemination from the mammalian gut.

  View details for DOI 10.1371/journal.ppat.1013836

  View details for PubMedID 41481766

  View details for PubMedCentralID PMC12803456

• Phage reprogramming of Pseudomonas aeruginosa amino acid metabolism drives efficient phage replication. mBio Fitzpatrick, A. D., Taylor, V. L., Patel, P. H., Faith, D. R., Secor, P. R., Maxwell, K. L. 2025; 16 (3): e0246624

  Abstract

  Phages have been shown to use diverse strategies to commandeer bacterial host cell metabolism during infection. However, for many of the physiological changes in bacteria during infection, it is often unclear if they are part of a bacterial response to infection or if they are actively driven by the phage itself. Here, we identify two phage proteins that promote efficient phage replication by reprogramming host amino acid metabolism. These proteins, Eht1 and Eht2, are expressed early in the infection cycle and increase the levels of key amino acids and the arginine-derived polyamine putrescine. This provides a fitness advantage as these metabolites are important for phage replication and are often depleted during infection. We provide evidence that Eht1 and Eht2 alter the expression of bacterial host metabolic genes, and their activities may impinge on metabolism-related signaling processes. This work provides new insight into how phages ensure access to essential host resources during infection and the competitive advantage this provides.IMPORTANCEBacterial viruses, known as phages, are abundant in all environments that are inhabited by bacteria. During the infection process, phages exploit bacterial resources, resulting in notable changes to bacterial metabolism. However, precise mechanisms underlying these changes, and if they are driven by the phage or are a generalized bacterial response to infection, remain poorly understood. We characterized two proteins in Pseudomonas aeruginosa phage JBD44 whose activities alter bacterial host metabolism to optimize phage replication. Our work provides insight into how phages control bacterial processes to ensure access to essential host resources during infection.

  View details for DOI 10.1128/mbio.02466-24

  View details for PubMedID 39918338

  View details for PubMedCentralID PMC11898732

• Targeted deletion of Pf prophages from diverse Pseudomonas aeruginosa isolates has differential impacts on quorum sensing and virulence traits. Journal of bacteriology Schmidt, A. K., Schwartzkopf, C. M., Pourtois, J. D., Burgener, E. B., Faith, D. R., Joyce, A., Lamma, T., Kumar, G., Bollyky, P. L., Secor, P. R. 2024: e0040223

  Abstract

  Pseudomonas aeruginosa is an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infect P. aeruginosa impact numerous virulence phenotypes. Most work on Pf phages has focused on Pf4 and its host P. aeruginosa PAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf phages infecting P. aeruginosa clinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene, pflM (PA0718), that enables the effective elimination of Pf prophages from diverse P. aeruginosa hosts. The pflM gene shows diversity among different Pf phage isolates; however, all examined pflM alleles encode the DUF5447 domain. We demonstrate that pflM deletion results in prophage excision but not replication, leading to total prophage loss, indicating a role for lysis/lysogeny decisions for the DUF5447 domain. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, pigment production, and virulence against the bacterivorous nematode Caenorhabditis elegans. We find that Pf phages have strain-specific impacts on quorum sensing and biofilm formation, but nearly all suppress pigment production and increase C. elegans avoidance behavior. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverse P. aeruginosa isolates but also advances our understanding of the complex relationship between P. aeruginosa and filamentous Pf phages.IMPORTANCEPseudomonas aeruginosa is an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. Although prior work has focused on Pf4 and PAO1, this study investigates diverse Pf in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance gene pflM (PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding of P. aeruginosa and filamentous Pf phage interactions.

  View details for DOI 10.1128/jb.00402-23

  View details for PubMedID 38687034

• Characterization and genomic analysis of the Lyme disease spirochete bacteriophage ϕBB-1. PLoS pathogens Faith, D. R., Kinnersley, M., Brooks, D. M., Drecktrah, D., Hall, L. S., Luo, E., Santiago-Frangos, A., Wachter, J., Samuels, D. S., Secor, P. R. 2024; 20 (4): e1012122

  Abstract

  Lyme disease is a tick-borne infection caused by the spirochete Borrelia (Borreliella) burgdorferi. Borrelia species have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids some of which are required throughout the enzootic cycle. Included in this plasmid repertoire by almost all Lyme disease spirochetes are the 32-kb circular plasmid cp32 prophages that are capable of lytic replication to produce infectious virions called ϕBB-1. While the B. burgdorferi genome contains evidence of horizontal transfer, the mechanisms of gene transfer between strains remain unclear. While we know that ϕBB-1 transduces cp32 and shuttle vector DNA during in vitro cultivation, the extent of ϕBB-1 DNA transfer is not clear. Herein, we use proteomics and long-read sequencing to further characterize ϕBB-1 virions. Our studies identified the cp32 pac region and revealed that ϕBB-1 packages linear cp32s via a headful mechanism with preferential packaging of plasmids containing the cp32 pac region. Additionally, we find ϕBB-1 packages fragments of the linear chromosome and full-length plasmids including lp54, cp26, and others. Furthermore, sequencing of ϕBB-1 packaged DNA allowed us to resolve the covalently closed hairpin telomeres for the linear B. burgdorferi chromosome and most linear plasmids in strain CA-11.2A. Collectively, our results shed light on the biology of the ubiquitous ϕBB-1 phage and further implicates ϕBB-1 in the generalized transduction of diverse genes and the maintenance of genetic diversity in Lyme disease spirochetes.

  View details for DOI 10.1371/journal.ppat.1012122

  View details for PubMedID 38558079

  View details for PubMedCentralID PMC11008901

• Inhibition of PQS signaling by the Pf bacteriophage protein PfsE enhances viral replication in Pseudomonas aeruginosa. Molecular microbiology Schwartzkopf, C. M., Taylor, V. L., Groleau, M. C., Faith, D. R., Schmidt, A. K., Lamma, T. L., Brooks, D. M., Déziel, E., Maxwell, K. L., Secor, P. R. 2024; 121 (1): 116-128

  Abstract

  Quorum sensing, a bacterial signaling system that coordinates group behaviors as a function of cell density, plays an important role in regulating viral (phage) defense mechanisms in bacteria. The opportunistic pathogen Pseudomonas aeruginosa is a model system for the study of quorum sensing. P. aeruginosa is also frequently infected by Pf prophages that integrate into the host chromosome. Upon induction, Pf phages suppress host quorum sensing systems; however, the physiological relevance and mechanism of suppression are unknown. Here, we identify the Pf phage protein PfsE as an inhibitor of Pseudomonas Quinolone Signal (PQS) quorum sensing. PfsE binds to the host protein PqsA, which is essential for the biosynthesis of the PQS signaling molecule. Inhibition of PqsA increases the replication efficiency of Pf virions when infecting a new host and when the Pf prophage switches from lysogenic replication to active virion replication. In addition to inhibiting PQS signaling, our prior work demonstrates that PfsE also binds to PilC and inhibits type IV pili extension, protecting P. aeruginosa from infection by type IV pili-dependent phages. Overall, this work suggests that the simultaneous inhibition of PQS signaling and type IV pili by PfsE may be a viral strategy to suppress host defenses to promote Pf replication while at the same time protecting the susceptible host from competing phages.

  View details for DOI 10.1111/mmi.15202

  View details for PubMedID 38038061

  View details for PubMedCentralID PMC10842821

• Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection. Proceedings of the National Academy of Sciences of the United States of America de Mattos, C. D., Faith, D. R., Nemudryi, A. A., Schmidt, A. K., Bublitz, D. C., Hammond, L., Kinnersley, M. A., Schwartzkopf, C. M., Robinson, A. J., Joyce, A., Michaels, L. A., Brzozowski, R. S., Coluccio, A., Xing, D. D., Uchiyama, J., Jennings, L. K., Eswara, P., Wiedenheft, B., Secor, P. R. 2023; 120 (9): e2216430120

  Abstract

  Monitoring the extracellular environment for danger signals is a critical aspect of cellular survival. However, the danger signals released by dying bacteria and the mechanisms bacteria use for threat assessment remain largely unexplored. Here, we show that lysis of Pseudomonas aeruginosa cells releases polyamines that are subsequently taken up by surviving cells via a mechanism that relies on Gac/Rsm signaling. While intracellular polyamines spike in surviving cells, the duration of this spike varies according to the infection status of the cell. In bacteriophage-infected cells, intracellular polyamines are maintained at high levels, which inhibits replication of the bacteriophage genome. Many bacteriophages package linear DNA genomes and linear DNA is sufficient to trigger intracellular polyamine accumulation, suggesting that linear DNA is sensed as a second danger signal. Collectively, these results demonstrate how polyamines released by dying cells together with linear DNA allow P. aeruginosa to make threat assessments of cellular injury.

  View details for DOI 10.1073/pnas.2216430120

  View details for PubMedID 36802441

  View details for PubMedCentralID PMC9992862

• Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes. PLoS pathogens Schwartzkopf, C. M., Robinson, A. J., Ellenbecker, M., Faith, D. R., Schmidt, A. K., Brooks, D. M., Lewerke, L., Voronina, E., Dandekar, A. A., Secor, P. R. 2023; 19 (2): e1010925

  Abstract

  The opportunistic pathogen Pseudomonas aeruginosa PAO1 is infected by the filamentous bacteriophage Pf4. Pf4 virions promote biofilm formation, protect bacteria from antibiotics, and modulate animal immune responses in ways that promote infection. Furthermore, strains cured of their Pf4 infection (ΔPf4) are less virulent in animal models of infection. Consistently, we find that strain ΔPf4 is less virulent in a Caenorhabditis elegans nematode infection model. However, our data indicate that PQS quorum sensing is activated and production of the pigment pyocyanin, a potent virulence factor, is enhanced in strain ΔPf4. The reduced virulence of ΔPf4 despite high levels of pyocyanin production may be explained by our finding that C. elegans mutants unable to sense bacterial pigments through the aryl hydrocarbon receptor are more susceptible to ΔPf4 infection compared to wild-type C. elegans. Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allows P. aeruginosa to evade detection by innate host immune responses.

  View details for DOI 10.1371/journal.ppat.1010925

  View details for PubMedID 36800381

  View details for PubMedCentralID PMC9980816

• PICI thieves: Molecular piracy and cooperation. Cell host & microbe Schmidt, A. K., Faith, D. R., Secor, P. R. 2023; 31 (1): 3-5

  Abstract

  Phage-inducible chromosomal islands (PICIs) steal structural proteins from helper phages. In two related studies, Penadés and coworkers reveal that PICIs are not parasites but mutualists. Some PICIs mobilize defense systems that restrict niche competitors, while other PICIs encode their own capsids and steal helper phage tails without affecting their fitness.

  View details for DOI 10.1016/j.chom.2022.12.008

  View details for PubMedID 36634621

• Complete Genome Sequence of the N4-like Pseudomonas aeruginosa Bacteriophage vB_PaeP_CMS1. Microbiology resource announcements Faith, D., Kinnersley, M., Schwartzkopf, C. M., de Mattos, C. D., Schmidt, A. K., Secor, P. R. 2022; 11 (7): e0023922

  Abstract

  vB_PaeP_CMS1 is a lytic bacteriophage that infects Pseudomonas aeruginosa. Whole-genome sequencing revealed that vB_PaeP_CMS1 has a linear double-stranded DNA (dsDNA) genome composed of 72,673 bp, with a GC content of 54.9%, that harbors 92 predicted open reading frames, with the greatest genome homology to members of the family Podoviridae, genus Litunavirus.

  View details for DOI 10.1128/mra.00239-22

  View details for PubMedID 35638894

  View details for PubMedCentralID PMC9302080

• A Filamentous Bacteriophage Protein Inhibits Type IV Pili To Prevent Superinfection of Pseudomonas aeruginosa. mBio Schmidt, A. K., Fitzpatrick, A. D., Schwartzkopf, C. M., Faith, D. R., Jennings, L. K., Coluccio, A., Hunt, D. J., Michaels, L. A., Hargil, A., Chen, Q., Bollyky, P. L., Dorward, D. W., Wachter, J., Rosa, P. A., Maxwell, K. L., Secor, P. R. 1800: e0244121

  Abstract

  Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in a variety of settings. Many P. aeruginosa isolates are infected by filamentous Pf bacteriophage integrated into the bacterial chromosome as a prophage. Pf virions can be produced without lysing P. aeruginosa. However, cell lysis can occur during superinfection, which occurs when Pf virions successfully infect a host lysogenized by a Pf prophage. Temperate phages typically encode superinfection exclusion mechanisms to prevent host lysis by virions of the same or similar species. In this study, we sought to elucidate the superinfection exclusion mechanism of Pf phage. Initially, we observed that P. aeruginosa that survive Pf superinfection are transiently resistant to Pf-induced plaquing and are deficient in twitching motility, which is mediated by type IV pili (T4P). Pf utilize T4P as a cell surface receptor, suggesting that T4P are suppressed in bacteria that survive superinfection. We tested the hypothesis that a Pf-encoded protein suppresses T4P to mediate superinfection exclusion by expressing Pf proteins in P. aeruginosa and measuring plaquing and twitching motility. We found that the Pf protein PA0721, which we termed Pf superinfection exclusion (PfsE), promoted resistance to Pf infection and suppressed twitching motility by binding the T4P protein PilC. Because T4P play key roles in biofilm formation and virulence, the ability of Pf phage to modulate T4P via PfsE has implications in the ability of P. aeruginosa to persist at sites of infection. IMPORTANCE Pf bacteriophage (phage) are filamentous viruses that infect Pseudomonas aeruginosa and enhance its virulence potential. Pf virions can lyse and kill P. aeruginosa through superinfection, which occurs when an already infected cell is infected by the same or similar phage. Here, we show that a small, highly conserved Pf phage protein (PA0721, PfsE) provides resistance to superinfection by phages that use the type IV pilus as a cell surface receptor. PfsE does this by inhibiting assembly of the type IV pilus via an interaction with PilC. As the type IV pilus plays important roles in virulence, the ability of Pf phage to modulate its assembly has implications for P. aeruginosa pathogenesis.

  View details for DOI 10.1128/mbio.02441-21

  View details for PubMedID 35038902

• Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals. Annual review of virology Kirsch, J. M., Brzozowski, R. S., Faith, D., Round, J. L., Secor, P. R., Duerkop, B. A. 2021; 8 (1): 95-113

  Abstract

  Bacteria and their viruses (bacteriophages or phages) interact antagonistically and beneficially in polymicrobial communities such as the guts of animals. These interactions are multifaceted and are influenced by environmental conditions. In this review, we discuss phage-bacteria interactions as they relate to the complex environment of the gut. Within the mammalian and invertebrate guts, phages and bacteria engage in diverse interactions including genetic coexistence through lysogeny, and phages directly modulate microbiota composition and the immune system with consequences that are becoming recognized as potential drivers of health and disease. With greater depth of understanding of phage-bacteria interactions in the gut and the outcomes, future phage therapies become possible.

  View details for DOI 10.1146/annurev-virology-091919-101238

  View details for PubMedID 34255542

  View details for PubMedCentralID PMC8484061

• Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry. Molecular cell Rollins, M. F., Chowdhury, S., Carter, J., Golden, S. M., Miettinen, H. M., Santiago-Frangos, A., Faith, D., Lawrence, C. M., Lander, G. C., Wiedenheft, B. 2019; 74 (1): 132-142.e5

  Abstract

  Bacteria and archaea have evolved sophisticated adaptive immune systems that rely on CRISPR RNA (crRNA)-guided detection and nuclease-mediated elimination of invading nucleic acids. Here, we present the cryo-electron microscopy (cryo-EM) structure of the type I-F crRNA-guided surveillance complex (Csy complex) from Pseudomonas aeruginosa bound to a double-stranded DNA target. Comparison of this structure to previously determined structures of this complex reveals a ∼180-degree rotation of the C-terminal helical bundle on the "large" Cas8f subunit. We show that the double-stranded DNA (dsDNA)-induced conformational change in Cas8f exposes a Cas2/3 "nuclease recruitment helix" that is structurally homologous to a virally encoded anti-CRISPR protein (AcrIF3). Structural homology between Cas8f and AcrIF3 suggests that AcrIF3 is a mimic of the Cas8f nuclease recruitment helix.

  View details for DOI 10.1016/j.molcel.2019.02.001

  View details for PubMedID 30872121

  View details for PubMedCentralID PMC6521718