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We report two EK1 cluster bacteriophages isolated from soil samples using the host Microbacterium foliorum. EM imaging showed that both exhibit the podovirus morphology. Genome sequencing and annotation showed similarity with many EK1 phage genomes. Our phages contain a putative PAP gene, also expressed in plants.
Toxoplasma gondii infection is associated with intestinal microbiome disruption, but its effects on genome-resolved bacterial populations, the gut virome, and bacteriome-virome relationships remain poorly understood. Using previously generated shotgun metagenomic datasets from 36 intestinal samples collected from 18 Sprague-Dawley rats across control, acute, and chronic infection groups, we reconstructed 294 quality-filtered, non-redundant bacterial metagenome-assembled genomes (MAGs) and identified 899 medium-to-high-quality viral operational taxonomic units (vOTUs) from assembled metagenomic contigs. Infection was associated with reduced bacterial richness in the small intestine during both acute and chronic stages and lower Shannon diversity during chronic infection. In contrast, large-intestinal α-diversity remained stable despite significant compositional reorganization. Taxonomic changes included increased Lactobacillus intestinalis, Limosilactobacillus reuteri, and Prevotella sp900547005, together with decreased Rothia sp002492045 and Akkermansia muciniphila. Functional profiling revealed region- and stage-specific changes in predicted bacterial metabolic potential, including reduced energy-related pathways and carbohydrate-active enzyme abundance. The virome also showed significant compositional changes in both intestinal regions. Quimbyviridae and Podoviridae_crAss-like viruses decreased in the small intestine during chronic infection, while Quimbyviridae, Flandersviridae, and Podoviridae_crAss-like viruses showed stage-specific decreases in the large intestine. Predicted bacterial hosts were assigned to 48.39% of vOTUs, with Lachnospiraceae and Ruminococcaceae being the most frequently linked families. Trans-kingdom networks further revealed region-specific positive and negative abundance correlations between bacterial and viral taxa. These findings extend previous microbiota-metabolome observations by integrating genome-resolved bacteriome analysis with contig-based virome profiling, providing a foundation for future mechanistic studies of toxoplasmosis-associated microbiome remodeling.
The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.
Vancomycin resistance in bacteria has been classified under high priority category by World Health Organization (WHO) and its presence in hospital effluent is reported to be increasing owing to excess antibiotics use. Among various strategies, bacteriophage has been recently considered as a promising biological agent for combating such antimicrobial resistant bacteria (ARB). However, the influence of effluent's properties on phage-ARB interaction in actual hospital effluent is not completely understood. The present works intends to study this influence of hospital effluent and its parameters on the interaction between vancomycin resistant E. coli (VRE) and its host specific bacteriophage. The isolated VRE was identified by 16S rRNA sequencing, matrix-assisted laser desorption/ionization-time of flight (MALDI - TOF) and whole genome sequencing. The infectivity of phage onto host bacteria was investigated using electron microscopic techniques, dynamic light scattering (DLS), spectrofluorophotometer and confirmed using double agar overlay method. The monovalency and polyvalency of isolated phage against various bacterial species were determined. The phage morphology was identical to T7 phage belonging to Podoviridae. The phage lysis was maximum at pH 7 (90.2%), 37 °C (91.6%) and vancomycin concentration of 50 μg/mL in both synthetic media (89.13%) and effluent (100%). At a maximum vancomycin concentration of 100 μg/mL, decrease in Ca, K, Mg and P (up to 19.70, 14.18, 28, and 15.82% respectively) concentration in effluent was observed due to phage infectivity when compared to control. The whole genome sequencing was performed and the bioinformatics analysis presented the role of mdfA gene encoding the efflux pump in causing vancomycin resistance in E. coli. It also depicted the presence of multiple genes responsible for mercury, cobalt, zinc and cadmium resistance in VRE. These results clearly indicate that bacteriophage mediated combating of VRE is possible in actual hospital effluent and can be used as one of the treatment methods.
Staphylococcus spp., other than S. aureus (SOSA, formerly CoNS), are opportunistic pathogens often linked to biofilm infections on indwelling devices. Their rising antibiotic resistance highlights the need for novel therapies. Bacteriophages are promising due to their specificity and ability to inhibit cell growth and biofilm formation. In this study, lytic phages isolated from swab pools were characterized against six clinical S. epidermidis and S. warneri isolates. Two distinct groups were identified via their host range, transmission electron microscopy, and genome sequencing. Group 1 phage ΘBRJ9 belongs to genus Sepunavirus (Myoviridae), while Group 2 phage ΘBRJ18 belongs to genus Andhravirus (Podoviridae). Both showed rapid adsorption, short latent periods (20 min), and high burst sizes (79 and 60 PFU/cell). They strongly inhibited planktonic SOSA growth at MOI 10, with efficacy comparable to or better than vancomycin, and their genomes lacked lysogeny, virulence, or resistance genes. These phages display a lytic lifestyle and are candidates for targeted SOSA therapies. Future work will assess biofilm efficacy, antibiotic synergies, and in vivo performance.
Pseudomonas syringae pv. actinidiae (Psa) is the causative agent of bacterial canker in kiwifruit (Actinidia spp.). Psa biovar 3 is the most prevalent and virulent, causing frequent and severe outbreaks worldwide. While current treatments have low efficacy, bacteriophages emerge as possible environmentally safe alternative biocontrol agents. In this study, bacteriophage Brt_Psa3 was isolated from the soil of a kiwifruit orchard in Portugal. Morphologically, Brt_Psa3 forms clear plaques and has a Podoviral morphotype. The bacteriophage exhibited broad lytic activity against several plant-pathogenic Pseudomonas strains, including Psa isolates. The isolated bacteriophage has a latent period of 100 min, a burst size of 143 particles/cell, and demonstrates stability at different temperatures and pH values found in kiwifruit orchards. In addition, Brt_Psa3 exhibited tolerance to UVA irradiation during 120 min of incubation. Brt_Psa3 belongs to the Autographiviridae family and Ghunavirus genus, based on full-genome nucleotide alignment and supported by phylogenetic analysis of structural proteins. The phage contains 51 open reading frames with no antibiotic resistance genes identified, within a genome of 40.509 base pairs. In vitro experiments with kiwifruit leaves demonstrated significant reduction of Psa levels (40%) on leaf surfaces, highlighting the bacteriophage's therapeutic potential in managing bacterial canker in kiwifruits.
In recent years, various bacteriophages that infect Vibrio spp. have been isolated and characterized. However, many characteristics concerning their infection mechanisms remain unknown. Here, we isolated and characterized a novel phage, VipHU7, that infects Vibrio parahaemolyticus. The morphology of VipHU7 was examined using transmission electron microscopy, which demonstrated that it has a short, noncontractile tail characteristic of podoviruses. VipHU7 formed clear plaques with halo zones on a bacterial lawn of V. parahaemolyticus MFS 1101, and host range analysis revealed that it had a limited host range. Analysis of the propagation and one-step growth curve of VipHU7 in liquid medium indicated that its replication rate increases in the presence of divalent cations, which did not affect its adsorption. Genome sequencing revealed that the VipHU7 genome is 76,454 bp long, with a 38.48% GC content and 112 predicted open reading frames. VipHU7 has a genomic structure similar to that of other Varunavirus phages that infect Vibrio spp. VIRIDIC analysis showed that the intergenomic similarity between VipHU7 and Vibrio phage BUCT194 was 83.7%, indicating that VipHU7 is a novel species belonging to the family Schitoviridae and genus Varunavirus.