Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family

Chitosan-encapsulated bacteriophage cocktail as promising oral delivery system to surpass gastrointestinal infection caused by Klebsiella aerogenes

Bacteriophages hold promise for combating pathogenic bacteria in the human intestinal tract, but their therapeutic potential is limited by harsh stomach conditions, including low pH and digestive enzymes. This study aimed to develop a natural protective mechanism for orally administering phages to treat gastric infections caused by Klebsiella aerogenes. Results revealed that free phages became inactive at pH 3 without protective measures. Encapsulation within sodium alginate (SA) alone (Bead 1) enabled phage survival at pH 2.5. More notably, Bead 2, consisting of a phage cocktail encapsulated in a chitosan-SA matrix supplemented with honey, casein, and gelatin, demonstrated enhanced survival even at pH 1.5. Phage titers in Bead 2 exhibited a controlled release, with near-complete discharge over 5 h in a simulated intestinal solution at 37 °C, ensuring effective delivery to the intestinal environment. Exposure of K. aerogenes to Bead 2 under these conditions resulted in a maximum reduction of 6.2 log10 CFU/mL, compared to maximal reductions of 2.8 log10 CFU/mL for Bead 1 and free phages. This optimized bead-encapsulation method provides a viable, efficient, and cost-effective strategy for delivering functional phages to specifically target intestinal bacteria.

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.

Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome

Bacteriophages ("phage") play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.

Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University

Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.

Diverse Durham collection phages demonstrate complex BREX defense responses

Bacteriophages (phages) outnumber bacteria ten-to-one and cause infections at a rate of 1025 per second. The ability of phages to reduce bacterial populations makes them attractive alternative antibacterials for use in combating the rise in antimicrobial resistance. This effort may be hindered due to bacterial defenses such as Bacteriophage Exclusion (BREX) that have arisen from the constant evolutionary battle between bacteria and phages. For phages to be widely accepted as therapeutics in Western medicine, more must be understood about bacteria-phage interactions and the outcomes of bacterial phage defense. Here, we present the annotated genomes of 12 novel bacteriophage species isolated from water sources in Durham, UK, during undergraduate practical classes. The collection includes diverse species from across known phylogenetic groups. Comparative analyses of two novel phages from the collection suggest they may be founding members of a new genus. Using this Durham phage collection, we determined that particular BREX defense systems were likely to confer a varied degree of resistance against an invading phage. We concluded that the number of BREX target motifs encoded in the phage genome was not proportional to the degree of susceptibility. IMPORTANCE Bacteriophages have long been the source of tools for biotechnology that are in everyday use in molecular biology research laboratories worldwide. Phages make attractive new targets for the development of novel antimicrobials. While the number of phage genome depositions has increased in recent years, the expected bacteriophage diversity remains underrepresented. Here we demonstrate how undergraduates can contribute to the identification of novel phages and that a single City in England can provide ample phage diversity and the opportunity to find novel technologies. Moreover, we demonstrate that the interactions and intricacies of the interplay between bacterial phage defense systems such as Bacteriophage Exclusion (BREX) and phages are more complex than originally thought. Further work will be required in the field before the dynamic interactions between phages and bacterial defense systems are fully understood and integrated with novel phage therapies.

A Novel Aeromonas popoffii Phage AerP_220 Proposed to Be a Member of a New Tolavirus Genus in the Autographiviridae Family

Aeromonas popoffii is one of the environmental Aeromonas species. A number of factors of virulence have been described for this species and it has been reported as a causative agent of urinary tract infection. The first A. popoffii bacteriophage AerP_220 along with its host strain A. popoffii CEMTC 4062 were isolated from river water. The phage has a podovirus morphotype, shows a narrow host range and is lytic against the host strain. The AerP_220 genome comprises 45,207 bp and does not contain genes responsible for antibiotic resistance and toxin production. Fifty-nine co-directional putative ORFs were found in the AerP_220 genome. Thirty-three ORFs encoded proteins with predicted functions; the products of 26 ORFs were hypothetical proteins. AerP_220 genome analysis revealed that this phage can be considered a novel species within the Autographiviridae family. Comparative genomic and proteomic analysis revealed that AerP_220 along with the Aeromonas phage vB_AspA_Tola (OM913599) are members of a new putative Tolavirus genus in the family Autographiviridae. The Gajwadongvirus and proposed Tolavirus genera along with Pantoea phage Nufs112 and phage Reminis could form a new Tolavirinae subfamily within the Autographiviridae family.