Prior to sequencing a restriction digest can be done and then the cuts of each enzyme can be compared to other phages using PET (http://www.phageenzymetools.com) to estimate how similar/unique our phage is to other phages. Additionally we can compare plaque morphologies and EM pictures of other phages to our own with the PhagesDB database (https://phagesdb.org/). Once sequenced the genome can be visualized and compared to others using the Phamerator database (https://phamerator.org/phages), which is the best indicator of uniqueness.
In your future directions section, why would you suggest to run a restriction digest on the Phaker’s DNA, how does that build off of the experiment you performed?
PCR using certain cluster primers can be done after a restriction digest as a way of testing a cluster hypothesis. As the DNA will only amplify if our phage has the same sequence as other phages in the cluster whose primers were used. Essentially it helps us understand what cluster our phage will likely belong to prior to sequencing.
Phage size measurements are used to classify them by their morphology, for example, siphoviridae are characterized as having a larger tail than head. So size has little biological significance (as far as we know).
How do you know that your bacteriophage hasn’t been discovered before? Is there some kind of database or test you can run to confirm this?
Prior to sequencing a restriction digest can be done and then the cuts of each enzyme can be compared to other phages using PET (http://www.phageenzymetools.com) to estimate how similar/unique our phage is to other phages. Additionally we can compare plaque morphologies and EM pictures of other phages to our own with the PhagesDB database (https://phagesdb.org/). Once sequenced the genome can be visualized and compared to others using the Phamerator database (https://phamerator.org/phages), which is the best indicator of uniqueness.
In your future directions section, why would you suggest to run a restriction digest on the Phaker’s DNA, how does that build off of the experiment you performed?
PCR using certain cluster primers can be done after a restriction digest as a way of testing a cluster hypothesis. As the DNA will only amplify if our phage has the same sequence as other phages in the cluster whose primers were used. Essentially it helps us understand what cluster our phage will likely belong to prior to sequencing.
What is the significance of the size of the phage? Do large phages have higher infectivity rate?
Phage size measurements are used to classify them by their morphology, for example, siphoviridae are characterized as having a larger tail than head. So size has little biological significance (as far as we know).
HI Hank! Great work! Can phage still harm bacteria in humans such as those in the gut?
Yes! Phage harming gut bacteria is one of the main concerns regarding phage therapy.