Isolation and characterization of vB_XciM_LucasX, a new jumbo phage that infects Xanthomonas citri and Xanthomonas fuscans

Thermal and Chemical Inactivation of Bacillus Phage BM-P1

Bacillus spp. are often used as probiotics; however, they can be infected by phages, leading to significant economic losses. Biocidal and thermal treatments are considered rapid and effective methods for controlling microbial contamination. To prevent viral contamination in industrial dairy production, the impact of temperature and biocides on the viability of Bacillus methylotrophic phage BM-P1 was assessed. The results demonstrated that reconstituted skim milk (RSM) as a medium showed the most effective protective effect on phage BM-P1. Treatment at 90°C for 5 min or 72°C for 10 min inactivated it to nondetectable levels from the initial titer of 7.19 ± 0.11 log, regardless of the culture medium. Sodium hypochlorite exhibited the best inactivating effect, which could reduce the phage titer below the detection level in 4 min at 50 ppm. Additionally, treatment with 75% ethanol for 20 min or 50% isopropanol for 30 min could achieve inactivation to nondetectable levels. The inactivating effect of peracetic acid was limited; even when treated at the highest concentration (0.45%) for 60 min, only a 2.47 ± 0.17 log reduction was observed. This study may provide some theoretical basis and data support for establishing measures against Bacillus spp. phages.

Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.

Biological Characterization of Pseudomonas fluorescens Phage Pf17397_F_PD1 and Its Application in Food Preservation

In order to explore the application prospects of phages for controlling bacterial contamination, a lytic phage Pf17397_F_PD1 (Later abbreviated as PD1) was isolated from fish guts using Pseudomonas fluorescens ATCC 17397 as the host bacterium. The phage displayed short latency (18 min), long lysis period (212 min), and high lysis volume (1.47 × 102 PFU/each cell). It displayed wide temperature (30-70°C) and pH (4-11) tolerance. Genomic comparison revealed a maximum sequence identity of 48.65% between phage PD1 and other identified phages, indicating that PD1 was a new phage. The phage PD1 significantly inhibited the growth of P. fluorescens in milk and grass carp at 4°C and 25°C. Compared to the negative control, bacterial levels in milk stored at 25°C for 48 h were reduced by 2.71 log CFU/mL and 2.84 log CFU/mL at the multiplicity of infection (MOI) of 100 and 1,000, respectively. In contrast, when grass carp were stored at 25°C for 24 h, the bacterial load was reduced by 1.28 log CFU/g and 2.64 log CFU/g compared to the control (MOI of 100 and 1,000). When the phage was applied for preservation of grass carp blocks, total volatile salt nitrogen (TVB-N) values of phage-treated samples increased by 6.8 mg/100 g and 7.5 mg/100 g at MOI of 100 and 1,000, respectively, after 7 days of storage, which was significantly lower than that of the control group (15.83 mg/100 g). This study showed that phage PD1 was a good natural biological antimicrobial agent against P. fluorescens ATCC 17397.

Isolation of bacteriophages infecting Xanthomonas oryzae pv. oryzae and genomic characterization of novel phage vB_XooS_NR08 for biocontrol of bacterial leaf blight of rice

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases worldwide in rice-growing regions. The Ineffectiveness of chemicals in disease management has increased the interest in phage therapy. In this study, we isolated 19 bacteriophages, infecting Xoo, from a rice field, which belonged to phage families Siphoviridae, Myoviridae, and Podoviridae on the basis of electron microscopy. Among 19 phages, Phage vB_XooS_NR08, a member of the Siphoviridae family, expressed antibacterial activity against all Xoo strains tested and did not lyse X. campestris and other unrelated bacterial hosts. Phage NR08 showed more than 80% viability at a temperature range of 4°C–40°C, pH range of 5–9, and direct exposure to sunlight for 2 h, whereas UV light and chemical agents were highly detrimental. In a one-step growth curve, NR08 has a 40-min latent period, followed by a 30-min burst period with a burst size of 250 particle/bacterium. The genome of NR08 is double-stranded DNA, linear having a size of 98,812 bp with a G + C content of 52.9%. Annotation of the whole-genome sequence indicated that NR08 encodes 142 putative open reading frames (ORFs), including one ORF for tRNA, namely, trna1-GlnTTG. Comparative genome analysis of NR08 showed that it shares maximum similarity with Pseudomonas phage PaMx42 (40% query coverage, 95.39% identity, and acc. Length 43,225) and Xanthomonas phage Samson (40% query coverage, 96.68% identity, and acc. Length 43,314). The average alignment percentage (AP) of NR08 with other Xoophages was only 0.32 to 1.25 since the genome of NR08 (98.8 kb) is almost double of most of the previously reported Xoophages (43–47 kb), thus indicating NR08 a novel Xoophage. In in vitro bacterial challenge assay, NR08 showed bacteriostasis up to 24 h and a 99.95% reduction in bacterial growth in 48 h. In rice pot efficacy trials, single-dose treatment of NR08 showed a significant reduction in disease up to 90.23% and 79.27% on 7 and 21 dpi, respectively. However, treatment using 2% skim milk-supplemented phage preparation was significantly less effective as compared to the neat phage preparation. In summary, this study characterized a novel Xoophage having the potential as a biocontrol agent in the mitigation of BLB in rice.

Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms

As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.

Comparative Analysis of Novel Lytic Phages for Biological Control of Phytopathogenic Xanthomonas spp

Xanthomonas is an important genus of plant-pathogenic bacteria that affects agronomic and economically important crops, causing serious economic losses. In fact, several Xanthomonas species are considered regulated quarantine pests. Due to the lack of effective control measures to treat plant-pathogenic bacteria, innovative control tools are needed to carry out integrated disease management. In this regard, bacteriophages (phages), viruses of bacteria, constitute a promising biocontrol tool. In this work, we report the isolation and characterization of 11 novel Xanthomonas arboricola pv. juglandis phages belonging to different families and genera of the class Caudoviricetes. Infectivity matrix in more than 60 isolates of different xanthomonads and other phytopathogenic bacteria suggests that these phages are specific to the Xanthomonas genus, with different host ranges depending on the isolates tested. Interestingly, some of these phages showed relevant features to be used as biocontrol tools to combat pathogenic Xanthomonas spp. as important as X. oryzae or X. citri. IMPORTANCE Phytopathogenic bacteria represent serious losses worldwide. The lack of current treatments has focused the spotlight on phages, viruses of bacteria, as very promising biocontrol tools. Phages are very specific and can help to control bacterial infections in crops, as is the case of xanthomonads-associated diseases. The discovery of new environmental phages with lytic capacity that can help to combat these pathogens is of special relevance, and it is necessary to implement phage isolation and characterization techniques to determine their host range and their genomic properties. The establishment of phage collections worldwide will allow their use as preventive, diagnostic, or therapeutic tools. Although there is still a long way to go, this work is a step forward in the implementation of new ecofriendly techniques to combat key pathogens in the field.