Exactly! Since some of the phage undergo the lysogenic cycle in which the bacteria is not killed after immediate infection (the phage lives off of the transcription machinery of the bacterial cell), there will always be some bacteria left alive, which makes it almost impossible to get rid of 100% of the infection.
You might not be able to narrow it down to one specific cluster, but you could hypothesize a couple. This is because looking at the EM images only shows you the phage family (myoviridae, siphoviridae, etc.), and multiple different clusters have phages of the same family. The specificity of each cluster really just comes down to the phage genomes.
curesymposium.org 
Why would a lysogenic phage not kill all bacterial cells in a clinical application? Is a lysogenic phage “too slow” to work effectively?
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Exactly! Since some of the phage undergo the lysogenic cycle in which the bacteria is not killed after immediate infection (the phage lives off of the transcription machinery of the bacterial cell), there will always be some bacteria left alive, which makes it almost impossible to get rid of 100% of the infection.
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Do you think you’ll do any of the further work of classifying this phage into a cluster?
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Not in the near future, but if I end up having time I think it would be good to confirm our phage’s cluster.
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Can you speculate on a cluster based on the electron microscope images?
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You might not be able to narrow it down to one specific cluster, but you could hypothesize a couple. This is because looking at the EM images only shows you the phage family (myoviridae, siphoviridae, etc.), and multiple different clusters have phages of the same family. The specificity of each cluster really just comes down to the phage genomes.
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What were the nutrients you added to enrich the soil sample?
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We used LB media, which is a mixture of tryptone, yeast extract, and table salt, which all promote protein synthesis.
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