Bacteria, Can’t Keep Them Down
by Jackie Swift
Forget the stereotype of bacteria as simple life forms, swimming mindlessly in a water droplet or stuck on bathroom door handles, waiting for someone to pick them up. “Bacteria are not simple at all,” says Guillaume Lambert, Applied and Engineering Physics at Cornell University. “They are actually extremely sophisticated. They’ve been around for billions of years; they have all kinds of tricks to survive.”
Lambert studies the tricks that help bacteria resist antibiotics. As the number of useful antibiotics continues to dwindle, this resistance is an increasing problem for humans, but it’s business as usual for bacteria. “Bacteria have been evolving resistance throughout their history — against fungi, against other bacteria,” he says. “There’s always been a war, but we humans have brought this to the forefront now.”
A New Technique for Studying Bacterial Cells in Real Time
A physicist by training, Lambert uses his physicist’s tool kit to pursue biological questions. His inquiry into the mechanisms of antibiotic resistance has led him to create a new technique for studying bacteria. Lambert’s technique relies on microfabrication and microfluidics to study individual cells in real time as they react to their environment.
“We focus on just a few individuals that are part of a larger population,” he explains. “In the case of antibiotic resistance, this means we can identify and observe how antibiotics impact cellular physiology. This is unlike the usual assays where you have a test tube of bacteria and you put in an antibiotic and all the cells die. You know you have a good antibiotic, but you don’t know what it actually does to the cells themselves.”
The Lambert lab uses a device called a mother machine, which allows the researchers to confine cells in microfluidic channels where flowing growth media is controlled at the micro level. As a mother cell grows and divides, its daughter cells migrate up the channel and eventually are washed away in the media, but the original mother cell always remains. With an imaging microscope, Lambert and his colleagues can record in real time the reactions of the cells to changes they induce in the environment, such as the addition of an antibiotic treatment.
A Persistent Survivor, a Dormant Bacterial Cell Called Persister
They are especially interested in a dormant bacterial cell type known as a persister cell. “A bacterium in the persister state can survive all kinds of environmental stressors that would normally kill it: antibiotics, PH changes, the bile salts we have in our guts, viruses called phages that infect the cells,” Lambert explains. “It’s a great survival strategy. If there’s an antibiotic treatment that kills 99.99 percent of bacteria, and you’re that .01 percent that went dormant, then when you wake up a few hours or a few days later, you’ve got the whole field to yourself.”
“Bacteria have been evolving resistance throughout their history — against fungi, against other bacteria. There’s always been a war, but we humans have brought this to the forefront now.”
By perturbing the bacteria, the researchers increase the odds of the formation of persister cells, making them easier to study. Then they treat the bacteria with rounds of an antibiotic that targets the machinery of cell division, giving the bacteria time to recover between each round. “With every treatment, there should be a 50 percent chance of any individual cell dying,” Lambert says. “But we are able to find a few cells that never die. The ancestry of these cells is distinct and special compared to the rest of the population. Because they survived, we know they did something right. By analyzing them, we can see what killed the rest by seeing what made the survivors fitter.”
Sequencing the genomes of persister cells that survive, the researchers discovered that they are identical genetically to the other cells. “Through some network rearrangements we’re beginning to understand, they can enter this dormant state,” Lambert says. “They don’t have a mutation; they just have a different phenotype.” He and his colleagues also found that cell death rate is dependent on age.
“If a cell is older, it’s more likely to divide, and if it divides with the antibiotic present, the cell wall will rupture,” Lambert explains. “But cells that are younger or have just divided will not divide for a while, and so they are protected for a time from the antibiotic effects.”
Creating Synthetic Bacteria for Alerting the Body of Trouble
In another line of research, the Lambert lab also investigates synthetic biology, the engineering of organisms for a specific purpose. “The long-term vision is to take bacteria and give them a brain,” Lambert says. “They can swim like bacteria and sense like bacteria and divide like bacteria, but they can also alert us, for example, when there’s a pathogen present in a patient’s body or a toxic compound in the environment.”
To create the synthetic organisms, the researchers insert into a bacterium pieces of DNA from other organisms such as fungi, phages, or other bacteria. To do this, they use CRISPR-Cas12, a process that employs the CRISPR (clustered regularly interspaced short palindromic repeats) DNA sequence and the nuclease Cas12 from bacteria to edit genes in living models. All the new components together create something like a circuit. “At the basic level, all this looks a lot like physics or electronics,” Lambert says. “The interaction between the different components are similar to the logic gates you have in a computer.”
By combining components in novel ways, Lambert and his colleagues hope to create a new function in bacteria that can be useful to humans. “In the future, you could have probiotics that live in your gut and act as sentries,” Lambert explains. “They could detect imbalances in nutrients or the presence of pathogens and then respond in real time. For instance, they might glow red in the presence of a pathogen, and you would be alerted when you saw that in your stool.”
The synthetic molecules might also one day treat diseases, Lambert suggests. For example, they might produce an antimicrobial compound if they detected infection. They could be used also to monitor the environment, such as lakes, where they might attack algae blooms when they sense them.
Using Physics to Study Biology
Lambert started his university work as a pure physicist with no interest in biology. “As an undergrad, I knew about microfabrication and transistors,” he says. “But in graduate school, one of my professors used physics to study biology. I thought, ‘This is so cool. I want to do this. I want to apply my knowledge to biology.’”
Now, as a professor, he has less time to tinker in the lab, but the hands-on approach still calls to him. “Every once in a while, I go into the lab and do a few quick experiments just to keep me grounded,” he says. “When I go in there, I forget about all the other problems I might have. I don’t get bogged down, and I can have a broader vision.”
Originally published on the Cornell Research website. All rights are reserved in the images. If you’d like to reproduce the text for noncommercial purposes, please contact us.
