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1. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages

   https://doi.org/10.1093/g3journal/jkac244  

   Howell, Abigail A ; Versoza, Cyril J ; Cerna, Gabriella ; Johnston, Tyler ; Kakde, Shriya ; Karuku, Keith ; Kowal, Maria ; Monahan, Jasmine ; Murray, Jillian ; Nguyen, Teresa ; et al ( September 2022 , G3 Genes|Genomes|Genetics)

   Reyes-Lamothe, R (Ed.)

   Abstract Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages—and thus one of the selective pressures acting on complex microbial systems in nature—remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1–P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2–P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles—a temperate characteristic that impedes their usage in antibacterial applications. 

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2. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack

   https://doi.org/10.1128/mSystems.00534-20  

   Mageeney, Catherine M. ; Mohammed, Hamidu T. ; Dies, Marta ; Anbari, Samira ; Cudkevich, Netta ; Chen, Yanyan ; Buceta, Javier ; Ware, Vassie C. ( October 2020 , mSystems)

   Alegado, Rosie (Ed.)

   ABSTRACT A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc 2 155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31 , confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems. IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance. 

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3. Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions

   https://doi.org/10.3390/microorganisms11010170  

   Milhaven, Mark ; Versoza, Cyril J. ; Garg, Aman ; Cai, Lindsey ; Cherian, Sanjana ; Johnson, Kamalei ; Salas Perez, Kevin ; Blanco, Madison ; Lobatos, Jackelyn ; Mitra, Corinne ; et al ( January 2023 , Microorganisms)

   Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital—however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages—including members from 11 sub-clusters (EA1 to EA11)—and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy. 

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4. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages

   https://doi.org/10.3390/v14081647  

   Versoza, Cyril J. ; Howell, Abigail A. ; Aftab, Tanya ; Blanco, Madison ; Brar, Akarshi ; Chaffee, Elaine ; Howell, Nicholas ; Leach, Willow ; Lobatos, Jackelyn ; Luca, Michael ; et al ( August 2022 , Viruses)

   Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies. 

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5. Genome Sequence of Mycobacteriophage Bassalto

   https://doi.org/10.1128/mra.01351-22  

   Barekzi, Nazir ; Wilkins, Meagan N. ; Williams, Aumon L. ; Moore, Afiya J. ; Duckett, Zachary R. ; Tindall, Danielle M. ; Eaddy, Donnetta R. ; Johnson, Mary B. ; Bass, Malcolm ; Mageeney, Catherine M. ( April 2023 , Microbiology Resource Announcements)

   Dennehy, John J. (Ed.)

   ABSTRACT Bassalto is a newly isolated phage of Mycobacterium smegmatis mc 2 155 from the campus grounds of Norfolk State University in Norfolk, VA. Bassalto belongs to the cluster B and subcluster B3 mycobacteriophages, based on the nucleotide composition and comparison to known mycobacteriophages. 

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