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1. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

   https://doi.org/10.1073/pnas.2105739118  

   Staquicini, Daniela I.; Tang, Fenny H.; Markosian, Christopher; Yao, Virginia J.; Staquicini, Fernanda I.; Dodero-Rojas, Esteban; Contessoto, Vinícius G.; Davis, Deodate; O’Brien, Paul; Habib, Nazia; et al (July 2021, Proceedings of the National Academy of Sciences)

   Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the development and initial evaluation of two targeted phage-based vaccination approaches against SARS-CoV-2: dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. For peptide-targeted phage, we performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein. One of these epitopes displayed on the major capsid protein pVIII of phage induced a specific and sustained humoral response when injected in mice. These phage were further engineered to simultaneously display the peptide CAKSMGDIVC on the minor capsid protein pIII to enable their transport from the lung epithelium into the systemic circulation. Aerosolization of these “dual-display” phage into the lungs of mice generated a systemic and specific antibody response. In the second approach, targeted AAVP particles were engineered to deliver the entire S protein gene under the control of a constitutive CMV promoter. This induced tissue-specific transgene expression, stimulating a systemic S protein-specific antibody response in mice. With these proof-of-concept preclinical experiments, we show that both targeted phage- and AAVP-based particles serve as robust yet versatile platforms that can promptly yield COVID-19 vaccine prototypes for translational development. 

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2. Plasmid-Mediated Stabilization of Prophages

   https://doi.org/10.1128/msphere.00930-21  

   Tuttle, Matthew J.; May, Frank S.; Basso, Jonelle T.; Gann, Eric R.; Xu, Julie; Buchan, Alison (April 2022, mSphere)

   McMahon, Katherine (Ed.)

   ABSTRACT Mobile genetic elements (MGEs) drive bacterial evolution, alter gene availability within microbial communities, and facilitate adaptation to ecological niches. In natural systems, bacteria simultaneously possess or encounter multiple MGEs, yet their combined influences on microbial communities are poorly understood. Here, we investigate interactions among MGEs in the marine bacterium Sulfitobacter pontiacus . Two related strains, CB-D and CB-A, each harbor a single prophage. These prophages share high sequence identity with one another and an integration site within the host genome, yet these strains exhibit differences in “spontaneous” prophage induction (SPI) and consequent fitness. To better understand mechanisms underlying variation in SPI between these lysogens, we closed their genomes, which revealed that in addition to harboring different prophage genotypes, CB-A lacks two of the four large, low-copy-number plasmids possessed by CB-D. To assess the relative roles of plasmid content versus prophage genotype on host physiology, a panel of derivative strains varying in MGE content were generated. Characterization of these derivatives revealed a robust link between plasmid content and SPI, regardless of prophage genotype. Strains possessing all four plasmids had undetectable phage in cell-free lysates, while strains lacking either one plasmid (pSpoCB-1) or a combination of two plasmids (pSpoCB-2 and pSpoCB-4) produced high (>10 5 PFU/mL) phage titers. Homologous plasmid sequences were identified in related bacteria, and plasmid and phage genes were found to be widespread in Tara Oceans metagenomic data sets. This suggests that plasmid-dependent stabilization of prophages may be commonplace throughout the oceans. IMPORTANCE The consequences of prophage induction on the physiology of microbial populations are varied and include enhanced biofilm formation, conferral of virulence, and increased opportunity for horizontal gene transfer. These traits lead to competitive advantages for lysogenized bacteria and influence bacterial lifestyles in a variety of niches. However, biological controls of “spontaneous” prophage induction, the initiation of phage replication and phage-mediated cell lysis without an overt stressor, are not well understood. In this study, we observed a novel interaction between plasmids and prophages in the marine bacterium Sulfitobacter pontiacus . We found that loss of one or more distinct plasmids—which we show carry genes ubiquitous in the world’s oceans—resulted in a marked increase in prophage induction within lysogenized strains. These results demonstrate cross talk between different mobile genetic elements and have implications for our understanding of the lysogenic-lytic switches of prophages found not only in marine environments, but throughout all ecosystems. 

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3. CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes

   https://doi.org/10.1128/mBio.02651-18  

   Nasko, Daniel J.; Ferrell, Barbra D.; Moore, Ryan M.; Bhavsar, Jaysheel D.; Polson, Shawn W.; Wommack, K. Eric; Martiny, Jennifer (April 2019, mBio)

   ABSTRACT Viral infection exerts selection pressure on marine microbes, as virus-induced cell lysis causes 20 to 50% of cell mortality, resulting in fluxes of biomass into oceanic dissolved organic matter. Archaeal and bacterial populations can defend against viral infection using the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system, which relies on specific matching between a spacer sequence and a viral gene. If a CRISPR spacer match to any gene within a viral genome is equally effective in preventing lysis, no viral genes should be preferentially matched by CRISPR spacers. However, if there are differences in effectiveness, certain viral genes may demonstrate a greater frequency of CRISPR spacer matches. Indeed, homology search analyses of bacterioplankton CRISPR spacer sequences against virioplankton sequences revealed preferential matching of replication proteins, nucleic acid binding proteins, and viral structural proteins. Positive selection pressure for effective viral defense is one parsimonious explanation for these observations. CRISPR spacers from virioplankton metagenomes preferentially matched methyltransferase and phage integrase genes within virioplankton sequences. These virioplankton CRISPR spacers may assist infected host cells in defending against competing phage. Analyses also revealed that half of the spacer-matched viral genes were unknown, some genes matched several spacers, and some spacers matched multiple genes, a many-to-many relationship. Thus, CRISPR spacer matching may be an evolutionary algorithm, agnostically identifying those genes under stringent selection pressure for sustaining viral infection and lysis. Investigating this subset of viral genes could reveal those genetic mechanisms essential to virus-host interactions and provide new technologies for optimizing CRISPR defense in beneficial microbes. IMPORTANCE The CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset of viral genes with high match frequencies to CRISPR spacers. Moreover, we observed a many-to-many relationship of spacers and viral genes. These high-match viral genes were involved in nucleotide metabolism, DNA methylation, and viral structure. It is possible that CRISPR spacer matching is an evolutionary algorithm pointing to those viral genes most important to sustaining infection and lysis. Studying these genes may advance the understanding of virus-host interactions in nature and provide new technologies for leveraging CRISPR-Cas systems in beneficial microbes. 

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4. Translation Efficiency Impacts Phage Lysis Timing and Its Precision in Single Cells

   https://doi.org/10.1101/2025.05.14.654169  

   Kannoly, Sherin; Singh, Kevin; Juman, Naseerah; Islam, Zubaida Marufee; Quiroga, Iñigo Caballero; Singh, Abhyudai; Dennehy, John J (May 2025, bioRxiv)

   Abstract The timing of host cell lysis is a fundamental life history parameter in bacteriophages as it presents an evolutionary trade-off between maximizing intracellular phage replication and optimizing transmission to new host cells, ultimately determining viral fitness in dynamic bacterial populations. In the bacteriophage λ, lysis time is dependent on the expression of a timekeeper protein, holin, which accumulates in theEscherichia coliinner membrane. Cell lysis is triggered when the membrane concentration of holin crosses a critical threshold level. In the present study, we investigated the effects of the rate of holin translation on lysis timing and its precision. We show that modulating holin translation efficiency through genetic modifications and antibiotic treatment alters bacteriophage lysis timing and its precision, providing insight into how phages optimize the evolutionary trade-off between replication and transmission. Reducing ribosomal binding affinity decreased holin expression and delayed lysis, while optimizing the Shine-Dalgarno sequence enhanced translation and accelerated lysis. Surprisingly, very low tetracycline concentrations may have improved translation efficiency and hastened lysis, whereas higher doses predictably delayed it. In all cases, longer lysis times corresponded with decreased timing variability. A model that incorporates stochastic gene expression with additional stochasticity in the initiation of holin expression was sufficient to explain the data. Thus, we demonstrated that modifying the rate of holin translation can be used as an evolutionary strategy to achieve optimum lysis timing. ImportanceOur prior work demonstrated that phage lysis timing is calibrated to optimize fitness based on environmental conditions affecting host availability and phage replication. We identified an optimal threshold—the critical holin concentration—that minimizes lysis time variability. Genetic manipulation of the holin gene altered the lysis threshold and generated phages with non-optimal early and late lysis times. The current study reveals that adjusting holin translation rates offers another mechanism for modifying lysis timing. Phages therefore have multiple means to adjust the timing of host lysis in order to maximize fitness under different selective pressures. 

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5. Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats

   https://doi.org/10.1038/s41467-025-57276-w  

   Biller, Steven J; Ryan, M Gray; Li, Jasmine; Burger, Andrew; Eppley, John M; Hackl, Thomas; DeLong, Edward F (March 2025, Nature Communications)

   Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats. 

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