The phage from the local lagoon

This post is by MSU postdoc Sarah Doore

Earlier this year, I wrote a blog post about doing some hunting with a graduate class here at Michigan State University. I’m not talking about hunting in the traditional sense though, since what we sought were bacteriophages—or viruses that infect bacteria—in the local environment. We were specifically interested in bacteriophages that infect enteric bacteria, like Escherichia coli, Salmonella enterica, and Shigella flexneri.

We asked the students to come up with a location and methods they wanted to use to check for bacteriophages (“phages” for short), then did some hands-on isolation using non-pathogenic strains of bacteria in our lab. We got to look at some new phages and the students’ creativity helped us find at samples we never would’ve imagined testing before. The project was fun for the students and fun for us!

By spring, we’d already planned to repeat the activity in the same grad course and were trying to bring phage isolation to undergraduate biology labs at MSU. So, when a Nebraska high school teacher heard about the project and seemed interested in doing something similar for his science class, we brought him to our lab over the summer and showed him the ropes.

Fig 1. Jason fishing for some phage in Nebraska.

After taking him through the isolation procedure, we made a plan for how he could have his students isolate their own phages back in his classroom. We also sent Jason, one of the lab’s graduate students, to Nebraska to do a trial run and see what the classroom still needed. You can see Jason collecting a Nebraska water sample for this in Figure 1. Come fall, we sent a box full of supplies to the high school and anxiously waited for the phage hunting module to begin. We were SO curious to see where students would decide to look—and, even better, what types of phages they’d find.

On collection day, each of the 50 students got their own sterile tube and went to a place they thought would most likely have phage, or at least somewhere they thought might have interesting results. They labeled the tube with their sampling location, then brought it back to the classroom to test it for phage.

A few common themes emerged among the sample locations the students picked: pond and river water were popular choices, as were the school’s baseball and football fields. There were also some more creative ideas, like the two students who sampled their dogs’ water bowls and the one who scooped a deer’s footprint in the woods. One of my personal favorites was “pond by frog,” which is just specific enough to make you wonder: what frog? What was the frog up to? Could this frog be an unknown reservoir for enteric phages? (Spoiler: it wasn’t, and I’m oddly disappointed by this result.)

Back in the classroom, the students tested their samples to see if they had found any phage. Out of the 50 samples, 16 of these had phages in them. Most phages—11 out of 16—came from ponds. The rest of the phages came from the baseball field (3), football field (1), and grass outside the classroom (1). The students sent their samples to our lab at MSU so we could also take a closer look at these new phages.

We’re still in the process of characterizing all of them, but so far it looks like some have interesting morphologies (see Figure 2 for an example of what I’d call an interesting plaque morphology). One also has a unique host range that we haven’t seen yet. This phage infects Salmonella enterica, Escherichia coli, and Citrobacter freundii: three types of enteric bacteria that belong to the same family but are otherwise significantly different. This particular phage came from pond water near a cattail. So…maybe cattails make better homes for phages than frogs do?

Fig 2. On an agar plate like this, phages kill their host and leave a clear spot where bacteria would have grown (“the circle of death”), known as a plaque. This one has fuzzy edges and a little belly button in the middle.

Although we’ve only been doing this kind of isolation for about a year, we’ve already discovered a total of 36 new phages, some of which are pretty rare and/or have really unique qualities (like the broad host range mentioned above). We plan to keep challenging students to sample their environment as long as we have the resources to keep up with them.

Although bacteriophages have been studied for over a century, and we’ve known for awhile that they’re abundant, we don’t know as much about the diversity or identity of the phages that are out there in the environment. Hopefully now we’re starting to answer that question too, and in the process we’re beginning to appreciate our own local composition of microbes.

If you’re interested in doing some of your own citizen science, we’ve got some resources for you! Maybe you’re a teacher who wants to try this in your classroom, or you know of someone who might be interested.

The protocols can all be found on the Parent lab’s website here (under “Video Protocols”). There’s a written version for the entire process of phage isolation, with videos for certain steps that are easier to understand and do yourself after seeing someone else do them. You can also follow us and/or ask us questions on Twitter @phage4lyfe.

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