Phage Identification Services

Background

Phage identification is a critical process for understanding the interactions between bacteriophages and their bacterial hosts, and it plays a significant role in microbiology, epidemiology, and the development of phage-based therapies.

Phage identification and characterization involve a combination of microbiological, molecular, and bioinformatic approaches to determine phage identity, host range, morphology, and genetic features. Initial isolation is typically achieved through enrichment cultures using target bacterial hosts, followed by plaque assays to detect lytic activity. Phage typing, based on the pattern of bacterial strain lysis, provides insight into the host range and can help differentiate phages with similar morphology. Electron microscopy (e.g., TEM) offers morphological classification by visualizing capsid structure and tail type. For genetic analysis, whole-genome sequencing is the gold standard, enabling annotation of structural and functional genes and identification of virulence or lysogeny-associated elements. Complementary methods such as host range assays, qPCR, restriction enzyme profiling, and protein analysis (e.g., SDS-PAGE, mass spectrometry) further support comprehensive phage characterization.

Figure 1. Overview of the steps in phage isolation and characterization. A, Experimental methods. B, Bioinformatics methods. Abbreviations: LYS, lysine; MET, methionine. (Grigson et al., 2023)

At Creative BioMart Microbe, we offer comprehensive phage identification services designed to support research, clinical, and industrial applications. Our capabilities enable the isolation, genomic characterization, and classification of bacteriophages from a wide range of sample types. Our service integrates classical virology techniques with state-of-the-art sequencing and bioinformatics to ensure precise, reliable, and actionable identification of phages relevant to your specific needs. Please contact us for more information.

Service Procedure

Service Details

Phage Isolation & Purification	From complex environmental or clinical samples, we enrich, isolate, and purify lytic or temperate phages using target host strains and optimized plaque assays.
Host Range Determination / Phage Typing	We assess phage infectivity across a broad panel of bacterial strains to define host range and lytic profiles, supporting phage typing and therapeutic targeting.
Morphological Characterization	Using Transmission Electron Microscopy (TEM), we classify phages based on head shape, tail structure, and overall virion architecture.
Genome Sequencing & Annotation	Full genome sequencing and bioinformatic analysis provide insights into gene content, functional elements, lifestyle prediction (lytic vs. lysogenic), and potential virulence factors.
Molecular & Protein Profiling	Additional techniques such as qPCR, restriction fragment analysis, SDS-PAGE, and mass spectrometry are available for detailed molecular and protein-level characterization.

Deliverables

• Detailed report including phage identity, host range matrix, morphological classification, and genomic features
• Electron micrographs (if TEM selected)
• Annotated genome files (FASTA/GenBank) and raw sequencing data
• Technical consultation to interpret results and discuss next steps

Our Advantages

• Rapid Turnaround Time: Standard project timelines range from 10 to 15 business days. Expedited services are available upon request.
• Host-Specific Enrichment: Enrichment is conducted using either client-supplied or selected host strains, increasing the likelihood of isolating functional, application-specific phages.
• High-Quality Genome Assemblies: We deliver complete or near-complete phage genomes with high fidelity and detailed annotations for downstream research or regulatory submissions.
• Safety Screening: All genomes are screened for lysogeny markers, virulence factors, and antibiotic resistance genes to ensure compliance with safety standards.
• Global Sample Support: We are equipped to handle international sample submissions, with experience in navigating relevant import and biosafety regulations.

Case Study

Case Study 1: Identification and characterization of new bacteriophages to control multidrug-resistant Pseudomonas aeruginosa biofilm on endotracheal tubes.

This study explored alternatives to antimicrobial-coated endotracheal tubes by isolating five new lytic bacteriophages (vB_PaeM_USP_1, _2, _3, _18, and _25) from domestic sewage, all targeting multidrug-resistant Pseudomonas aeruginosa. The phages, members of the Myoviridae family, exhibited broad lytic activity, infecting nearly 70% of tested strains. They were pH- and heat-stable, produced 27–46 particles per cycle, and had genomes of ~62–65 kb encoding 65–89 proteins.

The phages significantly reduced both planktonic growth and biofilm viability of P. aeruginosa, especially in endotracheal tube biofilm models. Electron microscopy confirmed disrupted biofilm structures, indicating strong lytic effects. These findings support the potential of these phages as candidates for therapeutic development or as sources of phage-derived antibiofilm agents.

Figure 2. (A–E) Representative image of phage isolates depicting different plaque morphologies of vB_PaeM_USP_1, vB_PaeM_USP_2, vB_PaeM_USP_3, vB_PaeM_USP_18, and vB_PaeM_USP_25. (F–J) Transmission electron micrographs of individual bacteriophages. (K) Panel of plaque characteristics, phage morphology, latent period, and burst size. (Oliveira et al., 2020)

Case Study 2: Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates.

This study reports the discovery and characterization of a novel temperate bacteriophage, CSP1, that targets multidrug-resistant Corynebacterium striatum (MDR-C. striatum)—an emerging pathogen in healthcare settings. Three genetically identical phages were isolated from environmental samples and determined to have circular double-stranded DNA genomes (39,752 bp) with 61 predicted ORFs and 1 tRNA gene. These phages showed broad lytic activity, infecting 21 out of 54 clinical isolates.

Figure 3. Genomic characteristics of bacteriophages. (A) Genomic extraction and enzyme digestion profiles of phage strains. (B) Nucleotide comparison (left) and homology analysis (right) of the three phage strains. SNP sites in the sequencing results of phage strains 1/3/7 (pg1/3/7) are highlighted in yellow and magenta; the color-coded ribbon diagram displays regions of high homology. (Wang et al., 2024)

FAQs

References:

1. Ács N, Gambino M, Brøndsted L. Bacteriophage enumeration and detection methods. Front Microbiol. 2020;11. doi:10.3389/fmicb.2020.594868
2. Grigson SR, Giles SK, Edwards RA, Papudeshi B. Knowing and naming: phage annotation and nomenclature for phage therapy. Clinical Infectious Diseases. 2023;77(Supplement_5):S352-S359. doi:10.1093/cid/ciad539
3. Oliveira VC, Bim FL, Monteiro RM, et al. Identification and characterization of new bacteriophages to control multidrug-resistant Pseudomonas aeruginosa biofilm on endotracheal tubes. Front Microbiol. 2020;11:580779. doi:10.3389/fmicb.2020.580779
4. Van Der Merwe RG, Van Helden PD, Warren RM, Sampson SL, Gey Van Pittius NC. Phage-based detection of bacterial pathogens. Analyst. 2014;139(11):2617-2626. doi:10.1039/C4AN00208C
5. Wang J, Zhang M, Pei J, et al. Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates. Front Cell Infect Microbiol. 2024;14:1361045. doi:10.3389/fcimb.2024.1361045