The Age of Phage

Though you may not have heard of them before, bacteriophage are all around us. They’re in the ground we walk on, the ocean we swim in, even in the rain! These little viruses are thought to be the most numerous organisms on the face of the Earth, with an estimated 10^31 of them all around our planet. Even if you added up every single other life form (so all of the people, blades of grass, bacterial cells, everything), there are still more phage!

So, what are these creatures? They’re viruses that specifically infect bacteria, which they do because they can’t reproduce on their own. This inability to reproduce by themselves spurned a huge debate within the phage community about whether they are living or not. The Delesalle lab likes to give them the benefit of the doubt!! They inject their DNA into a bacterial cell, and then their DNA can integrate into the bacteria’s genome, or they can take over cellular machinery to replicate their own DNA. At some point, phage will typically lyse its host bacteria – once it’s replicated enough, it breaks apart the host so it can get back into the environment and look for more bacterial hosts to infect.

One big reason why researchers are so interested in phage is that they could potentially be more effective at fighting infections than antibiotic drugs are. With a regular antibiotic, a resistant bacteria colony could emerge over time and the antibiotic would no longer be effective. Unlike an antibiotic drug, phage can evolve. Numerous studies have found phage evolving with their bacterial hosts, making it difficult for a completely resistant bacteria strain to emerge. The reason phage are not in your local CVS is twofold.  First, due to phage’s specificity, an effective medication would need to have many different phage. At the current stage of phage research, there are not enough studied phage for such a treatment. Secondly, because one of the major benefits of phage is their ability to evolve with their hosts, it is difficult for the FDA to effectively regulate them. However, the reality is that phage are safe when administered properly, and are already used to prevent infection in food items such as lettuce and cow meat.

While some labs across the nation focus more on the medical applications of phage, we are interested in looking at the evolutionary capabilities of phage! This summer we’re aiming to isolate novel phage from soil samples our lab collected from the American Southwest in previous years. Once we isolate phage, we can get their DNA sequenced, and use comparative genomics to determine why some are able to infect more strains of bacteria than others. Understanding how slight genetic differences impact the host range of a phage is key to understanding how to use the phage. Finding slight genetic differences in otherwise similar phage also lets us perform future evolutionary studies!

 

A Day in the Life of the Lab:

Usually, we start off our day by looking at our petri plates from the day before. Because we need bacteria to grow in order for our phage to replicate, we let our plates sit in the incubator overnight. Because phage kill (or eat, nom nom) the bacteria around them, the little holes (“plaques”) where the light shines through are where phage are present. Different phage make different types of plaques, which can help us to tell them apart!

We also spend most mornings making media that we can use to grow and plate our phage/bacteria combinations.

Madeleine & Sam begin the lengthy process of making agar plates in order to give our phage and bacteria a home.

For current and future experiments, we need to know the specific concentrations of our stock bacteria strains. Most of them we know, but when we grow up more bacteria (like we did this week), we need to do serial dilutions to find the concentration. This is the process of repeatedly diluting the bacteria in order to count colony forming units.  However, this process has a lot of room for inconsistency and contamination, meaning that one strain of bacteria may take many tries to accurately complete.

                                         A cereal dilution

The rest of the day usually consists of working with different concentrations of various strains of phage and bacteria that will eventually be combined so we can observe their interactions on the petri plate the following day.

Aside from wet lab work, our days are also interspersed with bioinformatics work. This can be done after isolating and obtaining a DNA sequence from phage we isolate in lab. With sequence in hand, we can analyze the individual genes that compose each unique phage genome while also comparing each entire phage genome to the genomes of all other phage in online databases (that we try to add to on a regular basis). Each phage we isolate and annotate adds another drop of water to our knowledge of phage (all the phage are like an ocean so we have a ways to go).

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