In Formation: Confined bacteria communities strengthened by spontaneous ordering

In case you missed it, gut health is trending. In recent years, consumers have been mixing up meal plans and looking for all manner of gut-happy products, tending to their internal ‘gardens’ with gusto in hopes of improving their mental and physical health.  

There are many species of bacteria that coexist in our bodies, and these are fundamental to our well-being; they keep us healthy, digest food and fight off disease. And they sure are competitive little guys.  

“Bacteria competition is common,” explains Dr. Tianyi Ma, a recent graduate of the Department of Physics at U of T. She’s worked with the Milstein Lab, led by Professor Josh Milstein in UTM's Department of Chemical & Physical Sciences, for the past six years. “In the human body, for example, we get infections usually because of bacterial invasion. And sometimes some types of bacteria or microbes are hard to kill because they can survive in a small structure in the body.” 

Throughout the body, there are many spaces in which these cells are confined, small cavities in the gut or mouth which can hold hundreds of bacteria. In these tight pockets, bacteria populations compete with one another for space. And as they grow, they push on each other — if you’re a large, fast-growing bacteria cell and you push your competitor out of the cavity, you’ve won. Right?  

Not so fast. 

Scientists have long studied the competition between types of bacteria by growing them in test tubes. You might study the bacteria to see what chemicals they excrete and how they kill or interact with other cells. However, in these studies there is often a lot of space between them. 

But what happens if you mechanically compress the cells? How do they respond?  

Researchers at U of T have been exploring what the competition looks like between bacteria that co-exist in confined areas. The research is a collaboration between the Milstein Lab and the Zilman Lab, based in the Department of Physics downtown and led by the late Professor Anton Zilman.  

This study was headed by their grad students: Ma and Dr. Jeremy Rothschild, now a graduate of the Department of Physics. Earlier this year, Ma and Rothschild shared their finding in “Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities,” which was published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). 

“There are a lot of different ecosystems that we study using their inhabitants. One of those is us — we’re a host for many different bacterial communities,” says Rothschild, who points out that it’s no different than any other ecological system one might study, such as a forest, or a pond.  

“This is the kind of research that you hope can lead to medical interventions,” he adds. “But step one is understanding these communities.” 

A theoretical physicist by training, Rothschild worked with the Zilman Lab on modeling competition and coexistence in ecological communities. They started working with the Milstein Lab on the project in 2020.   

“We asked, what if we start building a bacterial community from scratch? If we try to build the system as opposed to study the system, what sort of things do we start seeing that may have been overlooked?” says Milstein, explaining their 'bottom-up' approach. 

Their research has two components: in one lab, Ma created small artificial structures, where she introduced two different types of bacteria cells — one modified to be fluorescent green and the other red — and ‘tuned’ one of them to make it grow faster than the other. In the other lab, Rothschild developed a series of computer simulations to mimic the experiments, helping to guide them by making predictions that could be tested.  

“These simulations also served as a sanity check on our understanding of the experiments,” Milstein says. “If the simulations did not match our experimental observations, then we were likely missing some mechanism in our simulations, such as a chemical or physical interaction.” 

The researchers found that though the cells start out randomly oriented, when they're squeezed together in a tight space, cells of the same population spontaneously order together.  

They line up, sometimes in single file, and move as a unit in one direction toward the edges of the cavity wall. (Picture a line of marching pills making their way through a crowd.) The spontaneous reordering protects the entire population group; the cells stop pushing on each other and the weaker cells stabilize.  

“This changes the competitive dynamics a lot,” says Milstein. “Generally, if you have a cell that has a big advantage, you think it’s going to take over and conquer this territory and outcompete the other. But we found that because of this spontaneous ordering, you can put cells that grow fast with cells that grow slow.”  

“They never push into the other population, and that slower population, which you would think would be outcompeted, can exist forever. So, you can have a weak species living for extended, stable periods of time with a much stronger, healthier, quickly reproducing species.” 

In this initial experiment, there are only two bacteria — but the real microbiome is made up of many, many different cells. The team points out that by starting with very simple models they can first make sense of small populations. Then, they can add more cells and, step by step, learn how these complex communities can form and coexist. 

“The amazing thing is that the simulations look just like the experimental data,” Milstein says. “It’s a great example of how you can take a difficult question in the life sciences, go to a Physics lab and build an experimental test bed, and then combine it with computational mathematical modelling. You get a real depth of insight that you’d never get independently.” 

It's research that has important implications for how we treat certain diseases. It may help us to understand why some bacteria might be resistant to antibiotics and give us insight into the nature of our own native bacterial strains.  

“We’re making model systems but we’re hoping to find some fundamental reason — like the physical forces affecting those competitions, for example — that can get us closer to understanding real infectious diseases,” says Ma.  

“Then we can hopefully figure out how to combat them.”