Building a Better Microbiome Stephanie Culler is using genetically engineered, synthetic probiotics to overhaul treatments for a host of ailments.

Microbiome experts have bad news for all you health nuts: Drugstore probiotic supplements don’t have much evidence behind them. Early research has shown that shifting the bacterial makeup of the human microbiome is linked to a host of potential health improvements, from curing infection to improving the effectiveness of cancer treatment. That’s the good news. 

The bad news? 

For the most part, we don’t know which bacteria are beneficial for which diseases—or how to make them stick inside your gut. You might introduce some new bacteria to your body, briefly, by popping a pill or swallowing some yogurt or kombucha. But this is more akin to treating a headache by grabbing the first pill you see in your medicine cabinet than a targeted therapy.

“I wouldn’t mess with a microbiome that is functioning and is part of a healthy environment the same way I wouldn’t mess with the microbiome of a cancer patient who is responding to therapy,” says Nadim Ajami, an expert in the interplay of microbes and disease at the University of Texas MD Anderson Cancer Center in Houston. But he admits that when defining healthy versus unhealthy, “there’s not a real clear line.” 

Researchers like Ajami are now asking what roles various bacteria play in the microbiome, what makes a probiotic or microbiome-based therapy effective, and how slight variations within strains of bacteria could impact these outcomes. But as they are beginning to explore the complex workings of the human microbiome in the context of diseases like cancer, even the field’s most basic questions and premises, such as the idea that a particular bacteria can be linked to a specific illness, can be controversial. 

“Unfortunately, we are not very good at finding what’s a healthy or diseased microbiome, except in the very extreme cases where we can see extremely low diversity or high abundance of a pathogen or an opportunistic bug,” Ajami says. 

Microbiomes also vary by geography, race, and genetic makeup, he says. “It’s really not a one-size-fits-all type of approach.” 

In late 2022, the FDA approved Rebyota, from the New Jersey-based company Ferring Pharmaceuticals. This microbiome product became the first therapy on the market that uses fecal microbiomes to prevent recurrent infections of the bad-and-difficult intestinal bacteria Clostridioides difficile in adults. But even this trailblazing therapy still relies on human donors. Startups like Persephone Biosciences in San Diego hope that other microbiome-based therapies will soon be made synthetically, a scalable option.

The ick factor

In the same way that automated DNA sequencing allowed DNA profiling to evolve from single gene analysis to complex sequencing of multiple genes and whole genomes, advances in machine learning have made personalized microbiome mapping cheaper and faster. This glut of data has allowed scientists to draw rough links between some bacterial strains, the roles they play in the microbiome, and ailments like Clostridioides difficile, which causes a pernicious, painful, and diarrhea-inducing digestive tract infection and is commonly known by its diminutive C. diff.

“We found out—very concerning—that over half of U.S. infants do not have the right microbes.”

Samples of human poop are one way to feed a hungry machine-learning model, and a small Dutch study showed that people with inflammatory bowel disease were generally willing to provide them. But the same cannot be said for healthy people. The same study showed they are eager to collect these stinky samples, citing a general “ick” factor from participants who were asked to preserve small amounts of their own feces in the freezer.  

There’s one group of people who aren’t shy about poop: babies. They’re the focus of a new initiative from Persephone Biosciences, where scientists have collected hundreds of infant stool samples with the intention of mapping their microbiomes. The startup’s founder, Stephanie Culler, launched the company with an eye to oncology, where scientists had already unlocked links between certain microbiome makeups and the success of therapies for specific breast, pancreatic, lung, and colorectal cancers. She soon realized she needed to broaden her scope.

An electron microscope image of Clostridioides difficile. Science Source

Momentary mom guilt

Eighteen months ago, “a big pharma company actually came to us and said, ‘Well, we know how you’re discovering what’s wrong in the microbiomes of cancer patients. We think you could be that impactful in infants,’” Culler says. 

At that time, her infant daughter was just six months old. “I got very emotional, to be honest, because I was like, here I am, this leading expert in this space, and I’m overlooking a problem that a pharma company is telling me I should look at,” she says.

Culler is, by any standard, a microbiome expert. A brainy kid who chose chemical engineering over a career as a violinist, she launched her career engineering microbes to make renewable chemicals through fermentation. On her off hours, she brewed beer and made wine with colleagues. These days, she’s more easily found at the zoo with her daughter, or wine tasting with friends, but her passion for microbes hasn’t waned.

After a month spent poring over data on infant microbiomes, Culler’s research team concluded that many modern babies are growing up without a small set of key bacteria. Lack of access to diverse diets, Caesarian sections (which can deprive a newborn of the normal microbiome “seeding” from their mother’s vaginal canal), antibiotics, and the need for formula instead of breast milk can limit infants’ exposure to key sources of bacteria that colonize the gut, oral, and other microbiota as the baby’s immune system develops. 

At Persephone, scientists began to map the infant microbiome as samples poured in. “We found out—very concerning—that over half of U.S. infants do not have the right microbes,” Culler says. 

It’s not necessarily a birth parent’s fault. First, what people who are pregnant don’t have, babies can’t receive. Meanwhile, antibiotics can wipe out bacteria, and C-sections have the unfortunate side effect of limiting babies’ contact with the birth canal, where they normally pick up a parent’s bacteria. Other drugs, like proton pump inhibitors that reduce stomach acid and even medical procedures that alter digestive motility, can have an impact, Ajami says. With or without medical interference, microbiomes are dynamic ecosystems that change over our lifetimes. Even a person’s genetics factor into determining how their microbiome behaves. 

Culler admits these are hurdles to developing microbiome-based therapies. She plans to genetically engineer the bacteria that Persephone Bioscience’s team flag as therapeutic targets to ensure they are able to colonize a recipient’s gut. “Synthetic biology [combined] with genetic engineering would allow us to control how these microbes function, what they produce, and how much they produce,” she says.

“Strain-level variation is something that we don’t really know enough about, probably, in the microbiome world,” says Anna Seekatz, a Clemson University microbiologist who is not involved in Persephone’s work. “But conducting these types of clinical studies, which it seems that this company is doing, and really trying to understand some of that diversity is a good start.”

Early microbiome-based therapies

Part of the promise of microbiome-based therapies is their poster-child success in curing deadly Clostridioides difficile. An invasion of C. diff causes violent diarrhea and colon inflammation, but it can be cured when people with recurrent infections receive an infusion of new bacterial strains via Rebyota or Vowst, another fecal transplant therapy approved by the FDA last year. These two therapies basically move bacteria from a donor’s gut to a recipient’s. So far, scientists can’t predict when or why it works. Sometimes, the first transplant fails, yet a second transplant nudges a person toward recovery. 

Unfortunately, fecal transplant therapies still largely rely on a steady supply of stool from a stable of healthy donors. Of dozens of clinical trials currently underway, some target microbiome-based therapies for specific conditions like graft versus host disease and ulcerative colitis. Culler is among those hoping to map the human microbiome to reveal scalable, synthetic solutions. Experts like Ajami say the success of fecal transplants for C. diff is “a blessing and a curse.” 

“The curse part came from an understanding—or maybe the illusion—that the solution was translatable across all the diseases where we saw microbiome dysbiosis, or some sort of disruption, which didn’t end up being as true or as efficacious,” he says. 

Microbiomes that predict cancer or speed recovery

At Persephone, baby poo sampling has ended, but people with cancer and those in remission can participate in another Persephone initiative called Poop for the Cure. Culler is currently halfway through the Argonaut clinical trial, which uses fecal and blood samples to shed light on why some cancers respond to various therapies.

The trial, which runs until 2025, is an observational study of 5,000 people, including four groups with 1,000 people, each with advanced lung, breast, pancreatic, or colorectal cancers. Approximately half the people in the study are from minoritized groups, Culler says, to ensure that patterns identified between treatment success and microbiome composition are broadly applicable.

Babies born to Amish families in Pennsylvania have more diverse gut microbiomes than non-Amish infants.

For colorectal cancers, scientists are also collecting tissue samples gathered during colonoscopies and surgeries to remove cancerous portions of the colon. By comparing tissue from high- and low-risk people, Culler hopes her team can delineate microbiome differences that could predict who will develop colorectal cancer.

Just like the babies who lack the “right” microbes, people with cancer might be missing needed bacteria, too. “We find that in the place of those ‘right’ microbes, the same microbes these advanced-stage cancer patients have, we think, are connected to why they don’t respond to treatment, bacteria that cause inflammation, bacteria that have been associated with causing cancer, and pathogens,” Culler says.

If personalized microbiome therapies are possible, they will be more complex to develop for adults than for infants. Babies have about 40 bacterial strains in their microbiome. The supplement Culler is developing for infants is a uniform set of eight bacteria her team has identified as crucial to infant health. She envisions an over-the-counter supplement, a kind of sachet that could be sprinkled into breast milk or formula. 

“What I like about that is that they’re trying to identify [the mixture] of bacteria that actually naturally exist in the gut,” says Seekatz, pointing out that most probiotics on the shelf today may not even be strains typical to the gut. 

Leen Kawas, co-founder of the investment firm Propel Bio Partners and an investor in both Vowst’s manufacturer and Persephone, agrees. “There has been a significant gap in developing products, probiotics, that are based on data, guided by data, and basically [support] the actual needs for the current patient population,” she says. “Like anything else, our gut microbiome continues to shift.”

Rebyota. International Society of Microbiota

Why some bacteria stick around

The science around how and whether bacteria establish in our microbiota is complex and controversial. In the simpler infant microbiome, Culler says she’s selected bacteria already present in babies from Amish and old-order Mennonite groups, as well as hunter-gatherers in Africa and Europe. Those bacteria are not present in up to half of babies born today, and infants born to Amish families in Pennsylvania, for example, have more diverse gut microbiomes than non-Amish infants. Scientists believe this is because people in Amish communities rarely use prescription drugs or feed babies formula, and often have livestock as well as multiple pets.

Yet whether the changes to typical infant microbiota are truly a loss, as opposed to a simple shift, Seekatz says, is still an open question.

When it comes to commercial bacterial strains available today, Culler says, “What we’ve discovered is they’re just not relevant anymore. They don’t even exist in the human population, and they’ve lost some of their functionality. They don’t seem to consume breast milk sugars as much anymore.” The bacteria Culler and her team have identified are also primed to feed on certain sugars found in milk, which Culler hopes makes them better able to colonize baby microbiota. 

For adults, who have somewhere in the ballpark of 400 strains in their microbiota, Culler believes genetic engineering may be necessary to ensure that her theoretical therapeutics deliver bacteria that truly “stick” in the microbiome. It could prove a challenging task. Even when a bacteria colonizes the gut and becomes established there, each person’s microbiome has a unique composition, and bacteria can behave unpredictably.

“One thing that is sort of overlooked with some of these microbiome therapeutics and what has proved to be really challenging in the field is their interactions with other bacteria in the gut,” says Seekatz. “That’s maybe one of the reasons that even if you get colonization… you don’t actually get the product that you actually want.” 

Rather than microbiome-only approaches, Seekatz feels hopeful about approaches that, like Culler’s, incorporate a genetic approach to help identify not only which bacteria, but what gene activity, could be therapeutic. “Potentially, a lot of times it’s going to come down to identifying the actual genes that are important rather than just the bacterium,” she says. 

Whether Culler’s approach is successful won’t be apparent for years. In the meantime, Ajami still has hope for better outcomes for people with cancer through microbiome-based therapies he says are “very early stages, but in my opinion, extremely promising.” For longevity seekers interested in both preventing disease and, perhaps, perfecting an already healthy microbiome, the outcomes, if still farther off and hard to predict, hint at a host of intriguing possibilities.

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