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1. Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker

   https://doi.org/10.1128/mra.01251-23  

   Valentin_Caban, Keyshla; Kalesnik, Elizabeth; Green, Kaitlyn A; Negro, Christopher J; Nunez_Rodriguez, Ulises; Peele, Milan C; Nguyen, Casandra T; Cahill, Sydney; Dougherty, Keara; Logue, Melissa; et al (April 2024, Microbiology Resource Announcements)

   Roux, Simon (Ed.)

   ABSTRACT Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the hostMicrobacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK. 

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2. 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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3. Global Composition of the Bacteriophage Community in Honey Bees

   https://doi.org/10.1128/msystems.01195-21  

   Busby, Taylor J.; Miller, Craig R.; Moran, Nancy A.; Van Leuven, James T. (April 2022, mSystems)

   Gambino, Michela (Ed.)

   ABSTRACT The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range. 

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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. Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome

   https://doi.org/10.7717/peerj.15383  

   Bueren, Emma K.; Weinheimer, Alaina R.; Aylward, Frank O.; Hsu, Bryan B.; Haak, David C.; Belden, Lisa K. (January 2023, PeerJ)

   The gut of the European honey bee (Apis mellifera)possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%.Snodgrassella alviandGilliamella apicolahad the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogenPaenibacillus larvaehad a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogenMelissococcus plutoniusor any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularlyS. alviandG. apicola. 

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