Could Your Probiotic Be Making You Sicker?
Mindy D. had suffered from constipation for years when her gastroenterologist advised her, at 38, to take a popular over-the-counter probiotic. Over the next two years, she experimented with different dosages, sometimes taking it three times a day. But she kept getting sicker—sometimes so ill she couldn't work.
"We shouldn't just presume probiotics are safe."
Her symptoms improved only after she traveled from Long Island to Georgia to see Satish S. C. Rao, a gastroenterologist at Augusta University. "The key thing was taking her off probiotics and treating her with antibiotics," he says.
That solution sounds bizarre, if, like many, you believe that antibiotics are bad and probiotics good. Millions of Americans take probiotics—live bacteria deemed useful—assuming there can be only positive effects. The truth is that you really don't know how any probiotic will affect you. To quote the American Gastroenterological Association Center for Gut Microbiome Research and Education, "It remains unclear what strains of bacteria at what dose by what route of administration are safe and effective for which patients."
"We shouldn't just presume probiotics are safe," says Purna Kashyap, a gastroenterologist from the Mayo Clinic, in Rochester, Minnesota, and a member of the Center's scientific advisory board. Neither the U.S. Food and Drug Administration or the European Food Safety Authority have approved probiotics as a medical treatment. Things can go very wrong in the ill: Among patients with severe acute pancreatitis, one study found that a dose of probiotics increased the chance of death. Even randomized controlled trials of probiotics rarely report harms adequately and the effect over the long-term has not been studied.
Many people pick up a product at a drug store or health store without ever telling a doctor. Doctors are fans, too: in a 2017 survey of healthcare providers at Stanford, more than 60 percent of the respondents said they prescribed probiotics. Many did so inconsistently, leaving the choice of which probiotic up to the patient. Healthy people take them for a range of unproven benefits, including protection from infections or heart disease or to sharpen their brains.
It's fine—unless it isn't. "Probiotics are capable of altering the microbiome in unpredictable ways," explains Leo Galland, an internist in New York who specializes in difficult digestions. "I've had patients who got gas and bloating, constipation or diarrhea from probiotics."
Your Microbiome Is Unique
The booming probiotic market has fed on excitement about the new science of the microbiome, the genetic material of all the microbes that live in our bodies and on our skin. Microbes make up 1 to 3 percent of every human being's body mass—you carry trillions of them, including more than a hundred species and thousands of strains. To identify a microbe, you need to know the genus, species and strain. For example, in Lactobacillus rhamnosus GG, the ingredient in the OTC probiotic Culturelle, Lactobacillus is the genus, rhamnosus is the species and GG is the strain designation.
Variations in your microbiome could help explain why you put on weight or suffer from Crohn's or depression. Each of us has our own unique mix.
A decade ago, the U.S. National Institute of Health (NIH) launched the Microbiome Project to establish a baseline description of health. Scientists sequenced the DNA in more than 2,200 strains, still a small fraction of the whole.
Within a couple of years, we had evidence that our microbiomes are distinctive. Another team used the NIH data set to look into the idea of microbial "fingerprints." A classic computer science algorithm allowed it to assign individuals "codes" defined by DNA sequences of their microbes—no human DNA required. Using information solely from the guts, "Eighty percent of individuals could still be uniquely identified up to a year later," they wrote.
That distinctiveness makes a difference when we try to change our mix by swallowing bacteria considered "pro." Even in healthy people, the reactions to probiotics vary widely, according to a study in Cell in September. The team examined the intestines of healthy volunteers who had taken a cocktail of eleven strains of probiotics for the experiment. Which took up residence in the intestinal lining? The answer depended on the person. Led by Eran Segal and colleagues at the Weizmann Institute of Science, in Rehovot, Israel, the authors concluded that effective supplements would have to be personalized.
Patients with "brain fog" improved dramatically when they were taken off their probiotics and given antibiotics as well.
To truly customize a probiotic, however, we'd have to know the state of an individual's gut microbiome, identify danger signs and link them to symptoms, isolate relevant strains of probiotics that might be needed, and get them into the gut lining effectively. Commercial tests are still at step one. Several companies claim to assess your microbiome based on a stool sample—but the Weizmann team has also shown that the differences between our gut linings aren't apparent from our stool. Galland has explored testing his patients looking for ways to help. "I've concluded that uBiome, American Gut Project, and others don't yield useful information," he observes.
Can A Probiotic Make Your Brain Foggy?
Besides taking her probiotic, Mindy D. had cut out gluten and upped her vegetables and fruits. But soon after she ate her seemingly healthy meals, she would begin to feel dizzy and sometimes even slurred her words, as if she were drunk. "It was such an intense feeling," she said.
A slender 5 ft. 2 inches, she dropped 20 pounds, becoming unhealthily thin. She traveled to see specialists in Minnesota and Connecticut and took two month-long medical leaves before she found Rao in Georgia.
In June, Rao created a stir when he and his coauthors reported that a cluster of his patients with "brain fog"—the "intense feeling" Mindy D. described—improved dramatically when they were taken off their probiotics and given antibiotics as well.
His idea was that lactobacilli and other bacteria colonized their small intestines, rather than making it to the colon as intended—a condition known as "small intestinal bacteria overgrowth" (SIB0) that some gastroenterologists treat with antibiotics. In this group, he argues, the small intestine produced the brain fog symptoms as a consequence of D-lactic acidosis, a phenomenon usually associated with damaged intestines. "If you have brain fogginess along with gas and bloating, please don't take probiotics," Rao says.
The paper prompted a rebuttal at the end of September from Eamonn Quigley, a gastroenterologist at Houston Methodist, who criticized the methodology in detail. Kashyap, of the Mayo Clinic, is skeptical as well. "People were picked for their brain fogginess and they were taking probiotics. Probiotics could be an innocent bystander," he says.
"It's hard for me to imagine the mechanism of say, Culturelle, causing SIB0," says Shira Doron, a specialist in infectious diseases and associate professor at Tufts University School of Medicine who studies probiotics. "The vast majority of people will never suffer a side effect from a probiotic. But probiotics are a live organism so they have a unique set of potential risks that other supplements don't have. They can give you a severe infection in very rare circumstances."
The larger point is that probiotics should be used under a doctor's care. In April, a panel of 14 experts on behalf of the European Society for Primary Care Gastroenterology concluded that "specific probiotics are beneficial in certain lower GI problems." That does not mean any over-the-counter probiotic is likely to help you because it helped your cousin.
"Even your doctor may be going by anecdotal experience, rather than hard science."
Both Galland and Rao use probiotics in their practice, but carefully. "We advise caution against excessive and indiscriminate use of probiotics especially without a well-defined medical indication, and particularly in patients with gastrointestinal dysmotility," when the muscles of the digestive system don't work normally, Rao's team wrote.
"Because there are so many studies out there that are poorly done, that aren't looking at side effects, the science is murky. Even your doctor may be going by anecdotal experience, rather than hard science," Doron adds. Your doctor may tell you that many of his patients report a great experience with probiotics. As Doron points out, however, with disorders like irritable bowel syndrome, the most common gastrointestinal diagnosis, the placebo effect is very strong. Many patients could "respond to anything if they believe it works," she says.
Scientists redesign bacteria to tackle the antibiotic resistance crisis
In 1945, almost two decades after Alexander Fleming discovered penicillin, he warned that as antibiotics use grows, they may lose their efficiency. He was prescient—the first case of penicillin resistance was reported two years later. Back then, not many people paid attention to Fleming’s warning. After all, the “golden era” of the antibiotics age had just began. By the 1950s, three new antibiotics derived from soil bacteria — streptomycin, chloramphenicol, and tetracycline — could cure infectious diseases like tuberculosis, cholera, meningitis and typhoid fever, among others.
Today, these antibiotics and many of their successors developed through the 1980s are gradually losing their effectiveness. The extensive overuse and misuse of antibiotics led to the rise of drug resistance. The livestock sector buys around 80 percent of all antibiotics sold in the U.S. every year. Farmers feed cows and chickens low doses of antibiotics to prevent infections and fatten up the animals, which eventually causes resistant bacterial strains to evolve. If manure from cattle is used on fields, the soil and vegetables can get contaminated with antibiotic-resistant bacteria. Another major factor is doctors overprescribing antibiotics to humans, particularly in low-income countries. Between 2000 to 2018, the global rates of human antibiotic consumption shot up by 46 percent.
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 Lancetstudy 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
Seek and destroy
As the field of synthetic biology developed, scientists began using engineered bacteria to tackle superbugs. They first focused on Vibrio cholerae, whichin 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. choleraestrains 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 byJohn March, professor of biological and environmental engineering, developed a novel strategy to combat V. cholerae. They genetically engineered E.coli toeavesdrop 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 oftendrug-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. obeumin 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 commonly found bacteria in yogurt called Lactococcus lactis.
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.”
Meet Dr. Renee Wegrzyn, the first Director of President Biden's new health agency, ARPA-H
In today’s podcast episode, I talk with Renee Wegrzyn, appointed by President Biden as the first director of a health agency created last year, the Advanced Research Projects Agency for Health, or ARPA-H. It’s inspired by DARPA, the agency that develops innovations for the Defense department and has been credited with hatching world-changing technologies such as ARPANET, which became the internet.
Time will tell if ARPA-H will lead to similar achievements in the realm of health. That’s what President Biden and Congress expect in return for funding ARPA-H at 2.5 billion dollars over three years.
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How will the agency figure out which projects to take on, especially with so many patient advocates for different diseases demanding moonshot funding for rapid progress?
I talked with Dr. Wegrzyn about the opportunities and challenges, what lessons ARPA-H is borrowing from Operation Warp Speed, how she decided on the first ARPA-H project that was announced recently, why a separate agency was needed instead of reforming HHS and the National Institutes of Health to be better at innovation, and how ARPA-H will make progress on disease prevention in addition to treatments for cancer, Alzheimer’s and diabetes, among many other health priorities.
Dr. Wegrzyn’s resume leaves no doubt of her suitability for this role. She was a program manager at DARPA where she focused on applying gene editing and synthetic biology to the goal of improving biosecurity. For her work there, she received the Superior Public Service Medal and, in case that wasn’t enough ARPA experience, she also worked at another ARPA that leads advanced projects in intelligence, called I-ARPA. Before that, she ran technical teams in the private sector working on gene therapies and disease diagnostics, among other areas. She has been a vice president of business development at Gingko Bioworks and headed innovation at Concentric by Gingko. Her training and education includes a PhD and undergraduate degree in applied biology from the Georgia Institute of Technology and she did her postdoc as an Alexander von Humboldt Fellow in Heidelberg, Germany.
Dr. Wegrzyn told me that she’s “in the hot seat.” The pressure is on for ARPA-H especially after the need and potential for health innovation was spot lit by the pandemic and the unprecedented speed of vaccine development. We'll soon find out if ARPA-H can produce gamechangers in health that are equivalent to DARPA’s creation of the internet.
ARPA-H - https://arpa-h.gov/
Dr. Wegrzyn profile - https://arpa-h.gov/people/renee-wegrzyn/
Dr. Wegrzyn Twitter - https://twitter.com/rwegrzyn?lang=en
President Biden Announces Dr. Wegrzyn's appointment - https://www.whitehouse.gov/briefing-room/statement...
Leaps.org coverage of ARPA-H - https://leaps.org/arpa/
ARPA-H program for joints to heal themselves - https://arpa-h.gov/news/nitro/ -
ARPA-H virtual talent search - https://arpa-h.gov/news/aco-talent-search/
Dr. Renee Wegrzyn was appointed director of ARPA-H last October.
Matt Fuchs is the editor-in-chief of Leaps.org and Making Sense of Science. He is also a contributing reporter to the Washington Post and has written for the New York Times, Time Magazine, WIRED and the Washington Post Magazine, among other outlets. Follow him @fuchswriter.