Startup aims to make allies of human gut’s microbes

Suzanne Kreiter/Globe staff
Vedanta scientist Brian Klein opened the “library” of pure isolates of bacteria in a minus-80 degrees celsius freezer.

It sounds like a preposterous idea: Collect a sample of every type of bacteria that lives in the human gut. But that’s the goal of Bernat Olle, an MIT-trained chemical engineer. Over the past three years, the Cambridge biotech startup he runs, Vedanta Biosciences Inc., has assembled a menagerie of some 60,000 bacteria types.

They came from the digestive systems of 220 healthy people who donated fecal samples in countries from the Netherlands to Papua New Guinea. Now they live in suspended animation in ice-caked freezers kept at minus-80 degrees Celsius, poised to one day be used in drugs.

Vedanta is one of dozens of startups across the globe that hope to make medicines based on the latest insights about the trillions of bacteria, fungi, and other microbes that live inside and on our bodies. Together, they make up what it known as the human microbiome. A growing body of research suggests that this invisible world plays an important and overlooked role in maintaining our health — so important, in fact, that collectively it might even be considered another organ.


On Wednesday, about 250 biotech leaders from around the world will come to Boston for a three-day conference to discuss the prospect of developing drugs that change a person’s microbiome to treat diseases. Disorders that may stem from an imbalance of bacteria in the digestive system, researchers believe, range from the not-so-surprising (inflammatory bowel disease) to the unexpected (Parkinson’s disease).

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“We now know that if the composition of the microbes in your gut is not the right one, this may make you more likely to develop a condition,” said Olle, the 39-year-old Catalonia-born chief executive of Vedanta. “If you can go back and reestablish the right composition, then you could help those patients.”

Scientists have known about microbes since at least the 17th century, when Antonie van Leeuwenhoek, the Dutch scientist and father of microbiology, examined scrapings from his mouth. Looking at the specimen under a microscope he made, he spotted tiny organisms — “animalcules,” he called them.

In the late 1800s, the German-Austrian pediatrician Theodor Escherich gathered scientific evidence that microorganisms are part of the normal human system. Escherichia coli (E. coli), the bacteria that bear his name, for example, live in the intestines of healthy people and are harmless in most varieties.

But it wasn’t until the past decade or so, as a result of research like a massive project by the National Institutes of Health to sequence the genomes of such organisms, that scientists began to get a deeper understanding of the breadth and importance of microbes. Indeed, there appear to be at least as many microorganism cells in the body as human cells.


These microbes, research suggests, may help you digest food, regulate weight, fight off infections, and even affect your mood by influencing the production of serotonin, a neurotransmitter.

“We used to think of microbes mostly as disease-causing bacteria,” said Mike Bonney, chief executive of Kaleido Biosciences, a Bedford startup that is doing clinical trials for a drug to treat urea cycle disorders by targeting gut chemistry. “Over the last 10 years, we’ve come to the appreciation that the vast majority of bacteria and other microbes that have co-evolved with humans are actually there for beneficial purposes.”

Bonney called the subject “one of the hottest areas of medicine that has evolved over the last six or seven years.”

How hot? Consider that the first “Microbiome Movement — Drug Development Summit” in Boston in 2016 drew 113 attendees, fewer than half the number expected starting Wednesday at the Seaport Hotel & World Trade Center, according to organizers.

Among the scheduled speakers are Natalia Palacios, a public health professor at the University of Massachusetts Lowell who recently received a $2.1 million grant from the NIH to study the relationship between gut bacteria and Parkinson’s disease.


Research shows that people with Parkinson’s, a disorder of the central nervous system, experience constipation and gastrointestinal problems years before they show symptoms like tremors and impaired balance.

A team led by Palacio plans to sequence the genes of gut bacteria of people in the early stage of Parkinson’s and compare them with those of healthy people. If people with early Parkinson’s have a distinctive bacterial pattern, she said, doctors might be able to diagnose the disease earlier and intervene with drugs sooner.

All told, more than 150 drug makers globally are working on potential medicines for various disorders that could be linked to the human microbiome, and they have invested more than $2 billion in research, said Mo Langhi, an organizer of this week’s microbiome conference.

The Food and Drug Administration has yet to approve a medicine that targets the microbiome.

The drugs in development are a far cry from over-the-counter probiotic supplements that supposedly promote gut health but, in the view of some scientists, are of questionable value.

Vedanta, which is affiliated with PureTech Health, a Boston-based biotech, is deploying what Olle calls “consortia’’ of live bugs that he hopes will work together to treat disorders ranging from inflammatory bowel disease to cancer.

Later this year, Vedanta plans to start mid-stage clinical trials of a medicine for Clostridium difficile infection, a potentially deadly disorder that often afflicts elderly people taking antibiotics in health care facilities. A single beige capsule contains eight strains of live bacteria — 100 million of each — in freeze-dried powder.

Kaleido, a startup created by Flagship Pioneering, a venture capital firm, isn’t introducing live bugs; rather, it’s creating a synthetic compound to change the function of the microbiome.

It has a drug in early clinical trials to treat urea cycle disorders, a group of diseases that make it hard for the body to remove waste products.

One thing everyone agrees on is that the effort to develop drugs that change the microbiome is in its infancy. Scientists at Vedanta are still discovering new human gut bacteria and don’t know how many there actually are in the world.

Olle, the CEO, said he believes the 60,000 types of bacteria his company has in freezers account for most of the common bugs, but beyond that he’s just not sure.

“It’s almost like Christopher Columbus gets to Puerto Rico and then tries to figure out how big America is,” he said. “You’re going to need a few more expeditions to figure it out.”

Jonathan Saltzman can be reached at