CONSIDERING HOW WELL STUDIED THEY ARE, SOME LARGE GAPS remain in our scientific understanding of bacteria. For instance, we don’t yet know how bacterial chromosomes are separated into daughter cells during cell division or how their complicated chemical language really works. Using techniques from a broad spectrum of fields—including biochemistry, genetics, materials science and engineering—biochemistry professor Doug Weibel is designing advanced microtools and novel experimental setups to answer, for the first time, persisting questions about these surprisingly complex microorganisms. Through this basic work, he’s finding novel antibiotics and other interesting drug candidates.
Why are there still so many major unknowns about bacteria? How can that be?
The issue with bacteria is they are so small. By comparison, eukaryotic cells are enormous! For a calibration point, a human hair is about 100 microns in diameter. That’s about the thickness of a piece of scotch tape. And a eukaryote—when it’s spread on a surface—is maybe 40 microns in diameter. But the bacteria we look at are about one micron long, and their short axis is just several hundred nanometers. Until recently it was very difficult to look at them under a microscope and see anything useful going on inside the cell. Fortunately, there’s been a revolution in optical microscopy techniques over the last five years, and now we can see inside them with pretty good resolution.
How has our understanding about these microorganisms grown in recent years?
Historically, bacteria have always been thought of in the context of the way that we studied them: as individuals. They were always freely suspended in liquid nutrients and were dilute enough so that they never made physical contact with each other. But it’s pretty clear now that many bacteria in the ecosystem exist in tight-knit communities.
And during certain developmental stages, bacterial cells will display collective dynamics, where they are no longer acting as individual cells—as little one-bit processors—but are actually making collective decisions. In these cases, they are communicating and acting more like a multicellular organism—as something a lot more sophisticated than we’ve ever really appreciated.
Tell me more about this collective behavior.
A lot of people know that bacteria swim in solution, but they also swim in groups on surfaces. This collective movement on surfaces is called swarming.
As the bacterial community moves across a surface, the cells mix—and this mixing ensures that all of the cells get nutrients and growth factors to continue replicating. Swarming allows the cells to grow explosively and to colonize whatever niche they’re provided with.
What are you trying to learn about swarming in your lab?
We’re trying to figure out two things. One has to do with behavior: How does the motion of individual cells on a small scale lead to the pattern formation—the continuous mixing—of the swarm on a large scale? The other question is really the biochemistry of how it works. How do cells sense the surface and then change their morphology to interact with it?
This work should tell us some basic rules about how cells sense things outside of themselves—from fluids to surfaces to other cells. I think this is super interesting.
Can you describe one of the microtools you’ve developed to study bacteria?
Sure, but let me give you some more context first. In addition to studying the physical interactions between bacteria during swarming, we’re also interested in the role that chemical communication plays in the development of swarms. And swarming is just an early stage of biofilm development, so we are also interested in biofilms, which are basically bacterial communities that are firmly attached to surfaces.
One question that’s been in the field for a long time is, what is the length scale over which these chemical signals can be propagated? That is, if you have a swarm or a small early-stage biofilm that’s secreting signals, how far away does another biofilm have to be before it can no longer eavesdrop? To answer this question we created a microtool that we call the waffle.
You know how waffles have those little squares, right? Well, instead of the waffle being bread, the waffle in our case is made out of a special gel, and we can control the size of the cubes in the waffle and the thickness of the walls between them.
Using this tool we can grow biofilms that are spatially confined from each other. So you can take an organism that’s engineered to send a signal and then another organism that’s engineered to produce green fluorescent protein or some other measurable reporter protein when it receives that signal. You put these bacteria into various regions of the waffle and let them grow into biofilms. The walls physically constrain the cells, but they permit the free diffusion of small molecules. So the chemicals just diffuse through the waffle and then we measure and quantify the level of activation of the signal-receiving biofilm at different length scales away from the signal-sending biofilm.
We’ve used this waffle tool to determine that biofilms can eavesdrop on each other when they’re within about one centimeter. One interesting thing we found is that the chemical signals from one biofilm really don’t seem to have a substantial effect on nearby biofilms. That was a little bit surprising to us! The signal had a slight effect on growth rates, but it really had no obvious effect on community structure.
So what does that tell us? Mainly that we have a really incomplete understanding of chemical signaling in bacteria. There’s a lot left to learn.
Are there long-term applications for this work?
Eventually we want to look for small molecules that can disrupt the ability of bacteria to differentiate into the swarming phenotype, as well as molecules that promote this behavior. We’ll use these as research tools to study swarming in more depth in the lab, but you can imagine that small molecules that can disrupt bacterial swarming could have a biomedical use. They could be new antibiotics.
And, actually, we already have some really cool compounds, and we’re working with the Wisconsin Alumni Research Foundation to patent some of them. We found most of them through high-throughput screening, using the UW-Madison Keck Laboratory for Biological Imaging’s library of approximately 80,000 unique small molecules. Big pharma does this kind of stuff all of the time. They screen huge libraries of millions of compounds against a target, usually a well-validated target. The difference is we’re studying targets that nobody has worked with before. There just aren’t that many people in academia screening small molecules against certain classes of cell biological proteins. And we’ve found quite a few promising antibiotic compounds this way.