My research topic is using a lytic bacteriophage cocktail against pathogenic E. coli. However, before we proceed, it is important to identify all the genes present in the bacteriophage and their respective functions. This information will help us determine which genes are responsible for specific functions. I would appreciate any serious insights you may have on this matter. Thank you.
You can try searching for information at NCBI Nucleotide database for a specific or any E. coli specific phage.
You are probably never going to know the function of ALL the genes. The best you can do is sequence all the genomes in the phage cocktail and identify those genes that are already known or are homologous to known genes. It probably also doesn't matter for what you are doing. Either your cocktail is effective or not, and knowing the precise function of each gene won't change that.
To identify and analyse bacteriophage genes, consider the following key functional categories:
- Structural Genes: Encode capsid, tail fibres, and baseplate proteins (e.g., gp23 in T4 phage).
- Lytic Genes: Encode holins and endolysins for bacterial cell lysis (e.g., hol and lyz).
- DNA Replication & Repair Genes: Involved in genome replication (e.g., DNA polymerase, helicase).
- Host Recognition Genes: Encode receptor-binding proteins for host specificity.
- Regulatory Genes: Control phage life cycle and gene expression (e.g., CI repressor in temperate phages).
Whole-genome sequencing and annotation tools like PHASTER, RAST, or BLASTp can help characterise these genes.
how we can culture bordetella pertussis? can anyone give detail information?
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