Probiotic bacteria can be engineered to fight antibiotic-resistant superbugs by releasing chemicals that kill them.
In recent years, researchers have been exploring a promising avenue: the use of synthetic biology to engineer new bacteria that may work better than antibiotics. The need continues to grow, as a Lancet study linked antibiotic resistance to over 1.27 million deaths worldwide in 2019, surpassing HIV/AIDS and malaria. The western sub-Saharan Africa region had the highest death rate (27.3 people per 100,000).
Researchers warn that if nothing changes, by 2050, antibiotic resistance could kill 10 million people annually.
To make it worse, our remedy pipelines are drying up. Out of the 18 biggest pharmaceutical companies, 15 abandoned antibiotic development by 2013. According to the AMR Action Fund, venture capital has remained indifferent towards biotech start-ups developing new antibiotics. In 2019, at least two antibiotic start-ups filed for bankruptcy. As of December 2020, there were 43 new antibiotics in clinical development. But because they are based on previously known molecules, scientists say they are inadequate for treating multidrug-resistant bacteria. Researchers warn that if nothing changes, by 2050, antibiotic resistance could kill 10 million people annually.
The rise of synthetic biology
To circumvent this dire future, scientists have been working on alternative solutions using synthetic biology tools, meaning genetically modifying good bacteria to fight the bad ones.
From the time life evolved on earth around 3.8 billion years ago, bacteria have engaged in biological warfare. They constantly strategize new methods to combat each other by synthesizing toxic proteins that kill competition.
For example, Escherichia coli produces bacteriocins or toxins to kill other strains of E.coli that attempt to colonize the same habitat. Microbes like E.coli (which are not all pathogenic) are also naturally present in the human microbiome. The human microbiome harbors up to 100 trillion symbiotic microbial cells. The majority of them are beneficial organisms residing in the gut at different compositions.
The chemicals that these “good bacteria” produce do not pose any health risks to us, but can be toxic to other bacteria, particularly to human pathogens. For the last three decades, scientists have been manipulating bacteria’s biological warfare tactics to our collective advantage.
In the late 1990s, researchers drew inspiration from electrical and computing engineering principles that involve constructing digital circuits to control devices. In certain ways, every cell in living organisms works like a tiny computer. The cell receives messages in the form of biochemical molecules that cling on to its surface. Those messages get processed within the cells through a series of complex molecular interactions.
Synthetic biologists can harness these living cells’ information processing skills and use them to construct genetic circuits that perform specific instructions—for example, secrete a toxin that kills pathogenic bacteria. “Any synthetic genetic circuit is merely a piece of information that hangs around in the bacteria’s cytoplasm,” explains José Rubén Morones-Ramírez, a professor at the Autonomous University of Nuevo León, Mexico. Then the ribosome, which synthesizes proteins in the cell, processes that new information, making the compounds scientists want bacteria to make. “The genetic circuit remains separated from the living cell’s DNA,” Morones-Ramírez explains. When the engineered bacteria replicates, the genetic circuit doesn’t become part of its genome.
Highly intelligent by bacterial standards, some multidrug resistant V. cholerae strains can also “collaborate” with other intestinal bacterial species to gain advantage and take hold of the gut.
In 2000, Boston-based researchers constructed an E.coli with a genetic switch that toggled between turning genes on and off two. Later, they built some safety checks into their bacteria. “To prevent unintentional or deleterious consequences, in 2009, we built a safety switch in the engineered bacteria’s genetic circuit that gets triggered after it gets exposed to a pathogen," says James Collins, a professor of biological engineering at MIT and faculty member at Harvard University’s Wyss Institute. “After getting rid of the pathogen, the engineered bacteria is designed to switch off and leave the patient's body.”
Overuse and misuse of antibiotics causes resistant strains to evolve
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Seek and destroy
As the field of synthetic biology developed, scientists began using engineered bacteria to tackle superbugs. They first focused on Vibrio cholerae, which in the 19th and 20th century caused cholera pandemics in India, China, the Middle East, Europe, and Americas. Like many other bacteria, V. cholerae communicate with each other via quorum sensing, a process in which the microorganisms release different signaling molecules, to convey messages to its brethren. Highly intelligent by bacterial standards, some multidrug resistant V. cholerae strains can also “collaborate” with other intestinal bacterial species to gain advantage and take hold of the gut. When untreated, cholera has a mortality rate of 25 to 50 percent and outbreaks frequently occur in developing countries, especially during floods and droughts.
Sometimes, however, V. cholerae makes mistakes. In 2008, researchers at Cornell University observed that when quorum sensing V. cholerae accidentally released high concentrations of a signaling molecule called CAI-1, it had a counterproductive effect—the pathogen couldn’t colonize the gut.
So the group, led by John March, professor of biological and environmental engineering, developed a novel strategy to combat V. cholerae. They genetically engineered E.coli to eavesdrop on V. cholerae communication networks and equipped it with the ability to release the CAI-1 molecules. That interfered with V. cholerae progress. Two years later, the Cornell team showed that V. cholerae-infected mice treated with engineered E.coli had a 92 percent survival rate.
These findings inspired researchers to sic the good bacteria present in foods like yogurt and kimchi onto the drug-resistant ones.
Three years later in 2011, Singapore-based scientists engineered E.coli to detect and destroy Pseudomonas aeruginosa, an often drug-resistant pathogen that causes pneumonia, urinary tract infections, and sepsis. Once the genetically engineered E.coli found its target through its quorum sensing molecules, it then released a peptide, that could eradicate 99 percent of P. aeruginosa cells in a test-tube experiment. The team outlined their work in a Molecular Systems Biology study.
“At the time, we knew that we were entering new, uncharted territory,” says lead author Matthew Chang, an associate professor and synthetic biologist at the National University of Singapore and lead author of the study. “To date, we are still in the process of trying to understand how long these microbes stay in our bodies and how they might continue to evolve.”
More teams followed the same path. In a 2013 study, MIT researchers also genetically engineered E.coli to detect P. aeruginosa via the pathogen’s quorum-sensing molecules. It then destroyed the pathogen by secreting a lab-made toxin.
Probiotics that fight
A year later in 2014, a Nature study found that the abundance of Ruminococcus obeum, a probiotic bacteria naturally occurring in the human microbiome, interrupts and reduces V.cholerae’s colonization— by detecting the pathogen’s quorum sensing molecules. The natural accumulation of R. obeum in Bangladeshi adults helped them recover from cholera despite living in an area with frequent outbreaks.
The findings from 2008 to 2014 inspired Collins and his team to delve into how good bacteria present in foods like yogurt and kimchi can attack drug-resistant bacteria. In 2018, Collins and his team developed the engineered probiotic strategy. They tweaked a bacteria commonly found in yogurt called Lactococcus lactis to treat cholera.
Engineered bacteria can be trained to target pathogens when they are at their most vulnerable metabolic stage in the human gut. --José Rubén Morones-Ramírez.
More scientists followed with more experiments. So far, researchers have engineered various probiotic organisms to fight pathogenic bacteria like Staphylococcus aureus (leading cause of skin, tissue, bone, joint and blood infections) and Clostridium perfringens (which causes watery diarrhea) in test-tube and animal experiments. In 2020, Russian scientists engineered a probiotic called Pichia pastoris to produce an enzyme called lysostaphin that eradicated S. aureus in vitro. Another 2020 study from China used an engineered probiotic bacteria Lactobacilli casei as a vaccine to prevent C. perfringens infection in rabbits.
In a study last year, Ramírez’s group at the Autonomous University of Nuevo León, engineered E. coli to detect quorum-sensing molecules from Methicillin-resistant Staphylococcus aureus or MRSA, a notorious superbug. The E. coli then releases a bacteriocin that kills MRSA. “An antibiotic is just a molecule that is not intelligent,” says Ramírez. “On the other hand, engineered bacteria can be trained to target pathogens when they are at their most vulnerable metabolic stage in the human gut.”
Collins and Timothy Lu, an associate professor of biological engineering at MIT, found that engineered E. coli can help treat other conditions—such as phenylketonuria, a rare metabolic disorder, that causes the build-up of an amino acid phenylalanine. Their start-up Synlogic aims to commercialize the technology, and has completed a phase 2 clinical trial.
Circumventing the challenges
The bacteria-engineering technique is not without pitfalls. One major challenge is that beneficial gut bacteria produce their own quorum-sensing molecules that can be similar to those that pathogens secrete. If an engineered bacteria’s biosensor is not specific enough, it will be ineffective.
Another concern is whether engineered bacteria might mutate after entering the gut. “As with any technology, there are risks where bad actors could have the capability to engineer a microbe to act quite nastily,” says Collins of MIT. But Collins and Ramírez both insist that the chances of the engineered bacteria mutating on its own are virtually non-existent. “It is extremely unlikely for the engineered bacteria to mutate,” Ramírez says. “Coaxing a living cell to do anything on command is immensely challenging. Usually, the greater risk is that the engineered bacteria entirely lose its functionality.”
However, the biggest challenge is bringing the curative bacteria to consumers. Pharmaceutical companies aren’t interested in antibiotics or their alternatives because it’s less profitable than developing new medicines for non-infectious diseases. Unlike the more chronic conditions like diabetes or cancer that require long-term medications, infectious diseases are usually treated much quicker. Running clinical trials are expensive and antibiotic-alternatives aren’t lucrative enough.
“Unfortunately, new medications for antibiotic resistant infections have been pushed to the bottom of the field,” says Lu of MIT. “It's not because the technology does not work. This is more of a market issue. Because clinical trials cost hundreds of millions of dollars, the only solution is that governments will need to fund them.” Lu stresses that societies must lobby to change how the modern healthcare industry works. “The whole world needs better treatments for antibiotic resistance.”
Stem cells from a fetus can travel to the heart and regenerate the muscle, essentially saving a mother’s life.
If there is a silver lining to peripartum cardiomyopathy, it’s that it is perhaps the most survivable form of heart failure. A remarkable 50% of women recover spontaneously. And there’s an even more remarkable explanation for that glowing statistic: The fetus‘ stem cells migrate to the heart and regenerate the beleaguered muscle. In essence, the developing or recently born child saves its mother’s life.
Saving mama
While this process has not been observed directly in humans, it has been witnessed in mice. In a 2015 study, researchers tracked stem cells from fetal mice as they traveled to mothers’ damaged cardiac cells and integrated themselves into hearts.
Evolutionarily, this function makes sense: It is in the fetus’ best interest that its mother remains healthy.
Scientists also have spotted cells from the fetus within the hearts of human mothers, as well as countless other places inside the body, including the skin, spleen, liver, brain, lung, kidney, thyroid, lymph nodes, salivary glands, gallbladder, and intestine. These cells essentially get everywhere. While most are eliminated by the immune system during pregnancy, some can persist for an incredibly long time — up to three decades after childbirth.
This integration of the fetus’ cells into the mother’s body has been given a name: fetal microchimerism. The process appears to start between the fourth and sixth week of gestation in humans. Scientists are actively trying to suss out its purpose. Fetal stem cells, which can differentiate into all sorts of specialized cells, appear to target areas of injury. So their role in healing seems apparent. Evolutionarily, this function makes sense: It is in the fetus’ best interest that its mother remains healthy.
Sending cells into the mother’s body may also prime her immune system to grow more tolerant of the developing fetus. Successful pregnancy requires that the immune system not see the fetus as an interloper and thus dispatch cells to attack it.
Fetal microchimerism
But fetal microchimerism might not be entirely beneficial. Greater concentrations of the cells have been associated with various autoimmune diseases such as lupus, Sjogren’s syndrome, and even multiple sclerosis. After all, they are foreign cells living in the mother’s body, so it’s possible that they might trigger subtle, yet constant inflammation. Fetal cells also have been linked to cancer, although it isn’t clear whether they abet or hinder the disease.
A team of Spanish scientists summarized the apparent give and take of fetal microchimerism in a 2022 review article. “On the one hand, fetal microchimerism could be a source of progenitor cells with a beneficial effect on the mother’s health by intervening in tissue repair, angiogenesis, or neurogenesis. On the other hand, fetal microchimerism might have a detrimental function by activating the immune response and contributing to autoimmune diseases,” they wrote.
Regardless of a fetus’ cells net effect, their existence alone is intriguing. In a paper published earlier this year, University of London biologist Francisco Úbeda and University of Western Ontario mathematical biologist Geoff Wild noted that these cells might very well persist within mothers for life.
“Therefore, throughout their reproductive lives, mothers accumulate fetal cells from each of their past pregnancies including those resulting in miscarriages. Furthermore, mothers inherit, from their own mothers, a pool of cells contributed by all fetuses carried by their mothers, often referred to as grandmaternal microchimerism.”
So every mother may carry within her literal pieces of her ancestors.
Rodney Gorham, an Australian living with ALS, has reconnected with the world, thanks to a brain-machine interface called the Stentrode.
The brain-computer interface enabling this feat is called the Stentrode. It's the brainchild of Synchron, a company backed by Amazon’s Jeff Bezos and Microsoft cofounder Bill Gates. After Gorham’s neurologist recommended that he try it, he became one of the first volunteers to have an 8mm stent, laced with small electrodes, implanted into his jugular vein and guided by a surgeon into a blood vessel near the part of his brain that controls movement.
After arriving at their destination, these tiny sensors can detect neural activity. They relay these messages through a small receiver implanted under the skin to a computer, which then translates the information into words. This minimally invasive surgery takes a day and is painless, according to Gorham. Recovery time is typically short, about two days.
When a paralyzed patient thinks about trying to move their arms or legs, the motor cortex will fire patterns that are specific to the patient’s thoughts.
When a paralyzed patient such as Gorham thinks about trying to move their arms or legs, the motor cortex will fire patterns that are specific to the patient’s thoughts. This pattern is detected by the Stentrode and relayed to a computer that learns to associate this pattern with the patient’s physical movements. The computer recognizes thoughts about kicking, making a fist and other movements as signals for clicking a mouse or pushing certain letters on a keyboard. An additional eye-tracking device controls the movement of the computer cursor.
The process works on a letter by letter basis. That’s why longer and more nuanced responses often involve some trial and error. “I have been using this for about two years, and I enjoy the sessions,” Gorham typed during our chat session. Zafar Faraz, field clinical engineer at Synchron, sat next to Gorham, providing help when required. Gorham had suffered without internet access, but now he looks forward to surfing the web and playing video games.
Gorham, age 63, has been enjoying Stentrode sessions for about two years.
Rodeny Dekker
The BCI revolution
In the summer of 2021, Synchron became the first company to receive the FDA’s Investigational Device Exemption, which allows research trials on the Stentrode in human patients. This past summer, the company, together with scientists from Icahn School of Medicine at Mount Sinai and the Neurology and Neurosurgery Department at Utrecht University, published a paper offering a framework for how to develop BCIs for patients with severe paralysis – those who can't use their upper limbs to type or use digital devices.
Three months ago, Synchron announced the enrollment of six patients in a study called COMMAND based in the U.S. The company will seek approval next year from the FDA to make the Stentrode available for sale commercially. Meanwhile, other companies are making progress in the field of BCIs. In August, Neuralink announced a $280 million financing round, the biggest fundraiser yet in the field. Last December, Synchron announced a $75 million financing round. “One thing I can promise you, in five years from now, we’re not going to be where we are today. We're going to be in a very different place,” says Elad I. Levy, professor of neurosurgery and radiology at State University of New York in Buffalo.
The risk of hacking exists, always. Cybercriminals, for example, might steal sensitive personal data for financial reasons, blackmailing, or to spread malware to other connected devices while extremist groups could potentially hack BCIs to manipulate individuals into supporting their causes or carrying out actions on their behalf.
“The prospect of bestowing individuals with paralysis a renewed avenue for communication and motor functionality is a step forward in neurotech,” says Hayley Nelson, a neuroscientist and founder of The Academy of Cognitive and Behavioral Neuroscience. “It is an exciting breakthrough in a world of devastating, scary diseases,” says Neil McArthur, a professor of philosophy and director of the Centre for Professional and Applied Ethics at the University of Manitoba. “To connect with the world when you are trapped inside your body is incredible.”
While the benefits for the paraplegic community are promising, the Stentrode’s long-term effectiveness and overall impact needs more research on safety. “Potential risks like inflammation, damage to neural tissue, or unexpected shifts in synaptic transmission due to the implant warrant thorough exploration,” Nelson says.
There are also concens about data privacy concerns and the policies of companies to safeguard information processed through BCIs. “Often, Big Tech is ahead of the regulators because the latter didn’t envisage such a turn of events...and companies take advantage of the lack of legal framework to push forward,” McArthur says. Hacking is another risk. Cybercriminals could steal sensitive personal data for financial reasons, blackmailing, or to spread malware to other connected devices. Extremist groups could potentially hack BCIs to manipulate individuals into supporting their causes or carrying out actions on their behalf.
“We have to protect patient identity, patient safety and patient integrity,” Levy says. “In the same way that we protect our phones or computers from hackers, we have to stay ahead with anti-hacking software.” Even so, Levy thinks the anticipated benefits for the quadriplegic community outweigh the potential risks. “We are on the precipice of an amazing technology. In the future, we would be able to connect patients to peripheral devices that enhance their quality of life.”
In the near future, the Stentrode could enable patients to use the Stentrode to activate their wheelchairs, iPods or voice modulators. Synchron's focus is on using its BCI to help patients with significant mobility restrictions—not to enhance the lives of healthy people without any illnesses. Levy says we are not prepared for the implications of endowing people with superpowers.
I wondered what Gorham thought about that. “Pardon my question, but do you feel like you have sort of transcended human nature, being the first in a big line of cybernetic people doing marvelous things with their mind only?” was my last question to Gorham.
A slight smile formed on his lips. In less than a minute, he typed: “I do a little.”