The expanding ecosystem of microbiome startups

More funding and another powerful pharma backer have entered the microbiome space, showing that at least some investors and pharma execs believe the field can begin converting preclinical ideas into valid human therapies.

Finch Therapeutics

Somerville, Massachusetts-based Finch Therapeutics announced a new agreement with Takeda Pharmaceuticals on Wednesday, a solid endorsement of its sophisticated bioinformatics platform.

Along with oncology and central nervous system disorders, gastrointestinal diseases are one of Takeda’s three therapeutic pillars. As part of the deal, Takeda will pay an upfront $10 million for exclusive worldwide rights to FIN-524, an investigational drug for ulcerative colitis, and any follow-on products for irritable bowel diseases (IBDs). Ulcerative colitis is a form of IBD in which the immune system attacks the lining of the large intestine.

Finch’s science taps into the high-potential, highly-unpalatable concept of a fecal transplant. It involves transferring a microbiota rich stool sample from a healthy individual into someone with severe gut dysbiosis.

It’s a smart approach, given how little we know about the many thousands of microbial strains that occupy our guts. Instead of adding them to a therapy one-by-one, scientists can take a sample ecosystem that is already known to work. Finch then has a feedback loop in place to determine how patients responded to the different donor cultures.

“By working from clinically annotated datasets of donor and patient microbiota before and after fecal transplantation, we can look for the patterns in changes to the patients’ microbiota associated with targeted clinical outcomes,” said Finch CEO Mark Smith in an email forwarded by a company representative.

It underscores how variable our microbiomes are, whether we’re healthy, sick, or somewhere in between.

Smith cited a 70-patient randomized control trial of fecal transplants performed at McMaster University (Moayyedi et al, 2015). Five donors were used in the study, but just one, Donor B, had a demonstrably large therapeutic effect. Without Donor B, the study would have failed.

Just how much Kombucha was Donor B drinking? And how do we learn from the strength of that participant’s microbiota? Finch is working to answer the latter.

Azitra

While gut bacteria and the microbiome are often used interchangeably, our microscopic citizens really populate our entire body, including the skin. That’s the target for Farmington, Connecticut-based Azitra.

Azitra announced on Wednesday that it had closed a $2.9 million Series A venture round led by Bios Partners. With earlier seed funding, including from Peter Thiel’s Breakout Labs program, the startup has raised $3.75 million to date.

Rather than brewing a complex bacterial concoction, Azitra has identified one key bacteria strain for its lead candidate, AZT-01, to be applied as a cream to affected skin. In its cross-hairs for treatment are eczema, rare genetic skin diseases, and more everyday cosmetic applications such as dry skin.

In an email forwarded by a company representative, Azitra Cofounder and CSO Travis Whitfill said the microbial treatment isn’t just a band-aid — it could address an underlying cause.

“Studies have repeatedly shown that these patients have an imbalanced microbiome, and in the case of eczema, they often have an overgrowth of Staph aureus. There is also evidence that our strain of bacteria can kill some strains of Staph aureus, which is one of the reasons we chose it as a chassis,” Whitfill said.

Applied topically, the good bacteria can colonize the area and begin correcting the dysbiosis.

Photo: spawns, Getty Images