That gut feeling: Microbes under the microscope

The typical human body is host to trillions of micro-organisms that play a vital role in everything from digesting food to healing skin.

Yet until recently, relatively little was known about the genetic makeup or distribution of organisms in the human biome. Drug developers had few clues about how to put microbes to work in new therapies. And venture capitalists weren’t exactly plowing money into gut bacteria startups.

That’s changing dramatically. Federal funding of the Human Microbiome Project – a five-year-old, $115 million initiative to categorize human microbiota and analyze their role in human health – has helped spur a wave of entrepreneurial activity.

In the last couple of years, VCs have invested tens of millions in companies developing technologies and therapies tied to the human biome. Recently, one particularly ambitious startup – called Seres Health –  emerged from stealth mode with an announcement of an initial microbe-based therapy in clinical trials.

“There’s a lot of activity around this space. It’s been very hot,” said David Berry, Seres’ CEO and a partner at Flagship Ventures, which incubated the company and is the primary backer of its $10.5 million Series A round.

Cambridge, Mass.-based Seres is currently applying biome-related research to develop therapies for a number of diseases, but its most advanced effort is a treatment for Clostridium difficile infection (CDI).

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David Berry

Source: Photo courtesy of Flagship Ventures

David Berry

“The scientific discoveries being made point almost to the notion that the human biome is a new organism that we previously hadn’t been paying attention to.”

David Berry


Flagship Ventures

CDI, a bacterial ailment with symptoms ranging from diarrhea to life-threatening inflammation of the colon, has become an increasingly worrisome disease, as infections, which typically occur after use of antibiotics, have become more frequent and difficult to treat. It’s estimated that 700,000 people are infected each year, resulting in 14,000 deaths.

For Seres, Berry said a distinguishing approach is what the company calls ecobiotic therapeutics — essentially developing cures by identifying how microorganisms are interacting in both healthy and diseased people. The goal is to find the organisms that can be introduced and catalyze a change to bring a sick person back to a healthy state.

For now, most of the activity at microbiome-focused startups is early stage. Seres, incubated by Flagship Ventures, is about 2.5 years along. Second Genome, a San Bruno, Calif.-based startup applying microbiome science to therapeutics, is of similar vintage and is also in growth mode. In June, the company announced it raised the last tranche of an $11.5 million Series A financing led by Advanced Technology Ventures and Morgenthaler Ventures (now known as Canvas Venture Fund).

Among the newest is Ubiome, a San Francisco-based personalized medicine startup that a year ago launched a crowdfunding campaign for a business that will sequence the microbiomes of individuals. (See table for more extensive list of deals.) There are no sizeable microbiome-related exits, nor even much in the way of Series B funding.

The newness makes sense, considering that so much research about the biome is fairly recent and considering the vastness of the subject at hand. It’s estimated that the total number of microbial cells found on peoples’ bodies may exceed the total number of human cells by a factor of 10-to-1. In the past year alone, published research has revealed things about the biome – from the diversity of human foot fungus to the bacterial ecology of the human mouth – that could dramatically alter development of a host of therapies for common and rare ailments.

Public interest in the space is also growing, partly an offshoot of the quantified self movement and partly because many of the findings contain the mix of medical relevance and gross-out factors that makes for a good story.

News about a study in mice linking gut bacteria to obesity, for instance, ranked as the most widely emailed story on the New York Times website shortly after its publication in September (the gross part coming from findings that eating feces from a thin mouse could help catalyze weight loss.)

Studies of the human effectiveness of fecal transplants have also attracted interest, with at least one news site, the memorably named “Power of Poo” devoted to “promoting safe accessible fecal microbiota transplant for all who need it.”

Certainly, it can seem as if startups in the space are leading with their gut. While microbe-based therapies are underway for a host of infections and inflammatory diseases, gut bacteria seems to be the big area of initial focus.

That’s the case, for instance, at Genetic Analysis SA, a Norwegian startup that developed a DNA-based platform technology to identify variations in bacteria that exist in the gut. Enterome, a Paris-based venture-backed starup, is also working on drugs and biomarkers for conditions relating to abnormalities of bacterial composition of the human intestine.

Yet don’t expect gut bacteria to continue to dominate the space. While the high number and diversity of microbes in the gut, combined with promising early research, may be motivating the early wave of startups, there’s plenty of other regions to focus on, from deploying microbes to clear skin infections to improving oral health.

What’s clear, according to Berry, is that these tiny organisms will play an increasingly big role in medical research.   

“The scientific discoveries being made point almost to the notion that the human biome is a new organism that we previously hadn’t been paying attention to,” he said.

Ongoing research, meanwhile, seems to indicate that the organisms of the microbiome play a much greater role in sustaining human health than their hosts had ever expected.

Joanna Glasner is senior editor at VCJ. She can be reached at She tweets at @jglasner.







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