Outside of Emma Allen-Vercoe’s office is a bulletin board pinned with her team’s scientific papers since 2013. It’s the academic’s answer to a military uniform grown heavy with medals. But all of that research has come with a side effect: an impressive intimacy with the smells of human digestion.
“This is what we formally call the poopy lab,” she said one morning at the end of January. “Every donor that we use has a distinct aroma, because they have a different profile of microbes in the gut, so it’s like a fine wine — just not quite so fine. I guess this is Eau de Ulcerative Colitis . . . which smells different from Eau de Obesity, and Eau de Healthy Person.”
She’s been working with these gut bacteria for long enough to know what kind of experiment is going on by odor alone. That day, she could pick up notes of short-chain fatty acids; she paused to appreciate a cloud of volatile amines. If this were an obesity experiment, she’d be getting a stronger whiff of butyrate — a bit like rotten cabbage — while a study about premature infants would yield a mild, yogurt-like tang.
What she’s smelling isn’t feces per se. Instead, it’s the mechanical colon that she’s set up in her lab at the University of Guelph, where she is a professor of molecular and cellular biology. She calls it the Robogut. After isolating bacteria from donated human waste, she uses this contraption to see how those microscopic communities shift under different conditions.
Allen-Vercoe’s poopy lab sits on what may seem an unlikely frontier for medical research. The fecal transplant — the use of a slurry of a healthy person’s feces to treat tenacious infections of Clostridium difficile bacteria in a sick patient — has become more and more mainstream among doctors.
Biotech’s response to the fecal transplant has been to try to derive drugs from specific ingredients in dung — and NuBiyota, the company Allen-Vercoe cofounded, is in a race with firms like Seres Therapeutics, Vendanta Biosciences, and Rebiotix to do exactly that. Their argument is that human waste, while it’s been shown to be an effective treatment, is unpredictable stuff, and that we’re better off with medications in which we know every last ingredient.
On the day a reporter visited, Allen-Vercoe had mixed some pre-digested chickpea bits into her usual bacteria feed to see how gut microbes taken from an ulcerative colitis patient would react. The Robogut looks like a giant espresso maker, but one in which no oxygen is allowed. If Allen-Vercoe wants to take a look at the live bugs, she uses a needle to pierce the top of one of the cylinders that bubble with nitrogen. If she wants to study the chemicals they produce instead, she heads straight to the jar where her robot’s feces collects, one dribble at a time.
Her gut-bug-growing services have been in high demand among microbiologists all over the world. Now, though, she has started providing bacteria to a very different group: patients. And that means joining the scrum of businesses all trying to create — and sell — medications that repopulate the microbiome. These companies often start with recurrent Clostridium difficile infections, but they’ve also got their eyes on inflammatory bowel disease, and even certain cancers.
By her own admission, Allen-Vercoe was hardly born for business. She and her husband left England in part because of its obsession with the pub, and they didn’t really consider the United States precisely because the place seemed too obsessed with making a buck. “I couldn’t stand to live in America: the ethos . . . of capitalism, the mentality of dog-eat-dog,” she said.
They ended up in Guelph — a small Canadian city surrounded by farmland, about an hour west of Toronto — and so did NuBiyota. It’s only temporary. For now, there’s nothing but a doorway separating her academic lab from her corporate one. The employees, busy making a first bacterial cocktail for preliminary clinical trials, wander back and forth to manipulate bacteria, their hands stuck in heated, oxygen-free tanks.
But the production will move to an old Pfizer plant outside of New York City for the next phases of the clinical trial, and she’s left the details of running a business to her American partners and investors.
Allen-Vercoe happens to be a master at growing species of bacteria that are notoriously finicky, in part because they thrive in environments without oxygen. That’s a boon if you’re trying to recreate the healthy microbial community of the gut. “People would always say, before I started doing this work, that these microbes were impossible to grow,” she said.
“She is one of the few people in the world that can grow those bacteria in order to characterize them. Her expertise is quite unique,” said Adnane Sellam, an associate professor of microbiology at Université Laval in Quebec City, who has collaborated with Allen-Vercoe to understand the relationship between certain bacteria and yeasts. “Anyone can buy a bioreactor from a company and set it up. But in her case, she’s tinkered. . . to have a similar condition to what we have in the gut.”
Scientists like Sellam see Allen-Vercoe as a “superstar,” and her company has partnered with the pharma giant Takeda — but other details about NuBiyota remain mysterious. The company’s website has nothing but a “contact us” submission form. Trade publications have referred to its operations as stealthy. Noubar Afeyan, founder and CEO of Flagship Pioneering, which helped fund Seres, told STAT he’d never heard of the company. And while Bernat Olle, CEO of Vedanta, could describe (and criticize) the work of other competitors, and had met Allen-Vercoe, he said he didn’t know much about her company.
Allen-Vercoe (pictured) runs a lab that sits on an unlikely cutting edge for medical research. The fecal transplant has become more mainstream among doctors, and biotech is responding.
She herself cheerily declined to describe how NuBiyota is growing and isolating the bacteria that are delivered live, encased in a capsule, to trial participants, though she mentioned that the Robogut has been useful for quality control. The company’s first aim is to treat C. diff (“low-hanging fruit,” she said), and it is now trying it out in a 20-patient phase 1a trial. The company’s mixture is clearly defined, she said, but “there are a lot of microbes here that we’re using that we know nothing about in terms of their effects.”
She’s more than happy focusing on the work in her academic lab, though: Trying to figure out how to keep pig microbiomes diverse. Dropping bacteria into a Petri dish with a chemical that’s commonly used to turn food orange or red, to check if the additive poses a problem to our health. Taking samples of her robot’s “synthetic feces,” to decode the chemical communications among different bacteria.
“It is actually a microbial conversation,” she said, pointing to the grayish-greenish waste that was giving off Eau de Ulcerative Colitis. “And we haven’t yet found the Rosetta stone.”Eric Boodman is a writer for STAT, from which this article was adapted.