Genomic Characterization and Annotation of Two Novel Bacteriophages Isolated from a Wastewater Treatment Plant in Qatar.
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ABSTRACT:
SUBMITTER: Ramadoss R
PROVIDER: S-EPMC8759396 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Lysin of bacteriophages isolated from a particular ecosystem could be inducted as a bio-controlling tool against the inhabiting pathogenic bacterial strains. Our study aims at both experimental and computational characterization of the identical lysin gene product inherent in the genomes of two novel Myoviridae bacteriophages, Escherichia Phage C600M2 (GenBank accession number OK040807, Protein ID: UCJ01465) and Escherichia Phage CL1 (GenBank Genome accession number OK040806.1, Protein ID: UCJ01321) isolated from wastewater collected from the main water treatment plant in Qatar. The lysin protein, evinced to be a globular N-acetyl-muramidase with intrinsic "cd00737: endolysin_autolysin" domain, was further expressed and purified to be experimentally validated by turbidimetric assay for its utility as an anti-bacterial agent. Comprehensive computational analysis revealed that the scrutinized lysin protein shared 85-98% sequence identity with 61 bacteriophages, all native to wastewater allied environments. Despite varied Host Recognition Components encoded in their genomes, the similitude of lysins, suggests its apparent significance in host-pathogen interactions endemic to wastewater environment. The present study substantiates the identical lysin from Escherichia Phage C600M2 and Escherichia Phage CL1 as propitious "enzybiotic", a hybrid term to describe enzymes analogous to anti-biotics to combat antibiotic-resistant bacteria by in silico analysis and subsequent experimental validation.
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Project description:Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming.
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Project description:Two lytic double-stranded DNA (dsDNA) bacteriophages, belonging to the family Herelleviridae, were isolated from wastewater in Western Australia. Biyabeda-mokiny 2 appears to belong to the genus Kayvirus, and Koomba-kaat 1 to Silviavirus.
| S-EPMC9753628 | biostudies-literature
Project description:Staphylococcus aureus is one of the most important pathogens, causing various diseases in humans and animals. As methicillin-resistant S. aureus (MRSA) has become increasingly prevalent, controlling this pathogen with standard antibiotic treatment has become challenging. Bacteriophages (phages) have attracted interest as alternative antibacterial agents to control MRSA. In this study, we isolated six S. aureus phages from soils of poultry/livestock farms. Based on the results of host range determination with 150 S. aureus strains and restriction enzyme treatment of phage DNA, two phages, designated SP5 and SP6, were selected for further characterization and genome sequencing. Both SP5 and SP6 were classified as members of the family Siphoviridae. The genome of SP5 comprises 43 305 bp and contains 63 ORFs, while the SP6 genome comprises 42 902 bp and contains 61 ORFs. Although they have different host spectra, the phage genomes exhibit high nucleotide similarity to each other. Adsorption assay results suggested that the host range determinants of the two phages are involved in both adsorption and infection. Comparative genomic analyses of the two phages provided evidence that the lysogenic/lytic control module and tail proteins may be important for host specificity.
| S-EPMC3809110 | biostudies-literature
Project description:A wastewater treatment plant (WWTP) is an environment high in nutrient concentration with diverse bacterial populations and can provide an ideal environment for the proliferation of mobile elements such as plasmids. WWTPs have also been identified as reservoirs for antibiotic resistance genes that are associated with human pathogens. The objectives of this study were to isolate and characterize self-transmissible or mobilizable resistance plasmids associated with effluent from WWTP. An enrichment culture approach designed to capture plasmids conferring resistance to high concentrations of erythromycin was used to capture plasmids from an urban WWTP servicing a population of ca. 210,000. DNA sequencing of the plasmids revealed diversity of plasmids represented by incompatibility groups IncU, col-E, IncFII and IncP-1β. Genes coding resistance to clinically relevant antibiotics (macrolide, tetracycline, beta-lactam, trimethoprim, chloramphenicol, sulphonamide), quaternary ammonium compounds and heavy metals were co-located on these plasmids, often within transposable and integrative mobile elements. Several of the plasmids were self-transmissible or mobilizable and could be maintained in the absence of antibiotic selection. The IncFII plasmid pEFC36a showed the highest degree of sequence identity to plasmid R1 which has been isolated in England more than 50 years ago from a patient suffering from a Salmonella infection. Functional conservation of key regulatory features of this F-like conjugation module were demonstrated by the finding that the conjugation frequency of pEFC36a could be stimulated by the positive regulator of plasmid R1 DNA transfer genes, TraJ.
| S-EPMC4211555 | biostudies-literature
Project description:Somatic coliphages are alternative indicators of fecal pollution and attractive surrogates for viral pathogens. Here, we report the draft genome sequences of three replicate plaques from a novel Myoviridae bacteriophage isolated from raw wastewater. These genomes were similar to felix01virus phage and are predicted to contain up to 148 protein-coding genes.
| S-EPMC6597681 | biostudies-literature
Project description:BackgroundStaphylococcus epidermidis is a commensal bacterium but can colonize the hospital environment due to its ability to form biofilms favouring adhesion to host tissues, medical devices and increasing resistance to antibiotics. In this context, the use of phages to destroy biofilms is an interesting alternative.ResultsThe complete genomes of two Staphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have been analyzed. Their genomes are 43,581 bp and 42,123 bp, and contain 67 and 59 orfs. Bioinformatic analyses enabled the assignment of putative functions to 36 and 29 gene products, respectively, including DNA packaging and morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, regulation, modification and replication. A point mutation in vB_SepiS-phiIPLA5 lysogeny control-associated genes explained its strictly lytic behaviour. Comparative analysis of phi-IPLA5 and phi-IPLA7 genome structure resembled those of S. epidermidis ϕPH15 and ϕCNPH82 phages. A mosaic structure of S. epidermidis prophage genomes was revealed by PCR analysis of three marker genes (integrase, major head protein and holin). Using these genes, high prevalence (73%) of phage DNA in a representative S. epidermidis strain collection consisting of 60 isolates from women with mastitis and healthy women was determined. Putative pectin lyase-like domains detected in virion-associated proteins of both phages could be involved in exopolysaccharide (EPS) depolymerization, as evidenced by both the presence of a clear halo surrounding the phage lysis zone and the phage-mediated biofilm degradation.ConclusionsStaphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have a mosaic structure similar to other widespread S. epidermidis prophages. Virions of these phages are provided of pectin lyase-like domains, which may be regarded as promising anti-biofilm tools.
| S-EPMC3505474 | biostudies-literature
Project description:The microbacteriophages QuadZero and AnnaLie were isolated from soil samples from Charlotte, NC, and were classified into EA and EB clusters, respectively. QuadZero has a 40,140 base-pair double-stranded DNA genome with 62 predicted protein coding genes, whereas AnnaLie has a 41,665-bp genome with 71 predicted protein coding genes.
| S-EPMC9302159 | biostudies-literature
Project description:Background and objectivesIn recent decades, enterococcal resistance to antimicrobials has greatly increased. Furthermore, these chemicals include several side effects on the patients. Since no reports are available of the bacteriophages' effects on eukaryotic cells, they can be good solutions for multidrug-resistant bacterial problems. Therefore, the major aim of this study was to isolate bacteriophages from wastewaters on clinical antibiotic-resistant enterococci.Materials and methodsClinical bacteria were isolated, then enterococcal isolates were identified using different methods. The antibiotic resistance scheme of the enterococcal isolates was assessed. The bacterial isolates were exposed to wastewater samples containing potential bacteriophages. Technically, isolated bacteriophages were studied by electron microscopy.ResultsIsolated bacteria were verified as Enterococcus faecium. Results showed that bacteriophages could easily be isolated from wastewater sources. The isolated bacteriophages were effective on E. faecium as well as Streptococcus dysgalactiae. Furthermore, these bacteriophages were challenged with five other bacteria (ATCC) with no visible effects. In general, the isolated bacteriophages belonged to the Myoviridae, Siphoviridae, and Inoviridae families.ConclusionFurther studies on bacteriophages and their efficacy on enterococcal strains could increase the treatment possibility of enterococcal infections. Due to these bacteriophages' effects on Streptococcus strains, bacteriophages may be used to treat streptococcal infections as well.
| S-EPMC8629828 | biostudies-literature
Project description:Cutibacterium acnes is a pathogen that can cause acne vulgaris, sarcoidosis, endodontic lesions, eye infections, prosthetic joint infections, and prostate cancer. Recently, bacteriophage (phage) therapy has been developed as an alternative to antibiotics. In this study, we attempted to isolate 15 phages specific to C. acnes from 64 clinical samples obtained from patients with acne vulgaris. Furthermore, we sequenced the genomes of these three phages. Bioinformatic analysis revealed that the capsid and tape measure proteins are strongly hydrophobic. To efficiently solubilize the phage particles, we measured the adsorption rate, one-step growth curve, and phage stability using an SMT2 buffer containing Tween 20. Here, we report the genotypic and phenotypic characteristics of the novel C. acnes-specific phages.
| S-EPMC9404880 | biostudies-literature