Are we ready for consumer microbiome testing?

With $15.5 million more in the bank, San Francisco startup uBiome is on a mission to scale and diversify its consumer gut bacteria tests into clinically actionable diagnostics.

Intestines Sketch with Guts Bacteria

Some people collect stamps. uBiome has a different area of interest.

Since 2012, the San Francisco, California, startup has received and analyzed nearly 100,000 stool samples from customers trying to understand the unique population of microorganisms that call their body ‘home.’ 

It’s now preparing to scale-up and diversify its testing options, with the help a $15.5 million Series B funding round that was announced in early November.

An alum of the Y Combinator, uBiome has grand plans. But is the microbiome science really there?

It certainly wasn’t when the company launched as a citizen science crowdfunding project on Indiegogo.

In a phone interview, co-founder and CEO Jessica Richman said uBiome has grown rapidly in its space, filling a healthcare void.

“When we started out, we thought let’s get some microbiomes together and see what we learn,” Richman said. “Four years later, we literally have a clinical lab that’s unique in the entire world. And it’s real. Doctors can order this test and give it to their patients.”

In many ways, the company operates like a humble, gut bacteria version of 23andMe.

It sells an all-in-one kit, with savvy packaging and marketing. The user collects a sample at home and mails it in for testing.

At the lab, uBiome extracts and sequences the specimen’s unique mix of DNA, generating the raw data for the report.

Things get much more complicated from there.

The scientific community doesn’t understand a lot about the human genome. It knows even less about the human microbiome. When the company started out there were very few definitive guidelines on what species had a good, bad, neutral or mixed effect. 

To understand what it all meant, Richman said the company began its own research journey. The team trawled through academic literature, recording papers that linked certain microorganisms to health or disease. An emphasis was placed on human studies, to avoid confusing the data with the countless preliminary reports that relied on mouse models.

As more and more customers submitted their stool samples for analysis, uBiome began to build its own database of information. By applying those findings to the scientific literature, uBiome was able to generate some of the first approximate ranges for levels of  bacteria that were good or bad.

Over time, customers have received an increasingly well-informed report, which identifies microorganisms down to the genus level. Some individuals have chosen to submit multiple samples to compare the before and after effects of antibiotics, lifestyle changes, pregnancy and more.

Customers also receive an approximate report of how their microbiome compares to that of an ‘average’ healthy individual. Where it differs, advice is given on how to positively influence the composition through specific dietary changes, probiotics, and more.

uBiome is now preparing for its next phase of testing, with greater validation and the input of the medical community.

In October 2016, it announced the launch of SmartGut, which it pitches as the first sequencing-based clinical microbiome test. The company also announced the accreditation of its fully automated lab by the College of American Pathologists (CAP), a rare feat for any science company.

At this point, Richman said the company is moving away from the 23andMe consumer model. SmartGut, for example, is ordered through a licensed medical professional and aims to deliver clinically actionable results.

Potentially hazardous strains are flagged for follow-up medical care. The test also identifies certain bacteria that are associated with chronic diseases, such as Type 2 diabetes, irritable bowel syndrome (IBS) and Crohn’s disease.

“Our focus is on being the leading microbial genomics company,” Richman said, channeling leaders in human genome analysis, such as Foundation Medicine and Counsyl. There are no immediate plans to sell the data acquired through customer testing.

It has been a busy four years for Richman.

“We went from crazy crowdfunding campaign to actual bulletproof clinic test, legally performed in a clinical lab run by medical professionals.”

By maturing in the public sphere, Richman said the company has helped to challenge the norms for how science products and services are created.

The company will need to stay on its toes as the science around the microbiome continues to change. Its potential to improve health, however, does appear solid.

Photo: TLFurrer, Getty Images