I've isolated a phage against Staphylococcus aureus, but later discovered that the bacterium hosts a prophage within its genome. Despite this, my phage remains capable of infecting the bacterium. However, I'm curious about the potential impact of the prophage on phage therapy effectiveness and whether my phage's ability to actively infect the bacterium signifies overcoming any replication challenges posed by the prophage.
You can consider the two phages as independent entities that don't have any interference. If the phage you isolated forms plaques on the lysogenic strain, which you say it does, then by definition the lysogen is not interfering. Having natural isolates from the wild be lysognic is very very common. So it is unlikely to impact the effectiveness of your phage therapy.
The only thing that might be of consider is that if you are propagating your phage on this lysogenic host, your phage stock probably is going to have a low level of "contamination" by the lysogenic phage. Lysogenic phages spontaneously are released at some low level. So while this does not really impact what you are doing, it "might" be a regulatory issue for any actual clinical work. So you might want to consider finding a non-lysogenic host to serve as your production host for the bacteriophage.
Thank you for your response. I had my phage sequenced and I'm currently working on the protein of the lytic phage. One strange thing I did notice is that when I set up a PCR reaction in triplicates, the lytic phage protein would get amplified sometimes only. Then in order to really understand the problem I set up a PCR reaction with the bacteria alone and the same LYTIC phage protein was amplified. So I BAST search to check if the same lytic phage protein was present in the lysogenic phage, but there was no similarity found. So could this mean that my bacterial stock was contaminated with the lytic phage protein which is why the amplification was observed.
i think it is unlikely that your bacterial stock is contaminated by the lytic phage because you would see lysis everytime you grow it. I think it more likely that you just have some phage contamination somewhere that got into the PCR, maybe your pipers or a solution. It’s easy to get contaminated by phage.you can do some control PCRs with out adding DNA to check.