Mapping microbiome manufacturing

Why making microbiome drugs will require reinventing bacterial manufacturing

Microbiome companies have been squeezed by the scarcity of contract manufacturers willing to work with tough bacterial strains. While contractors are starting to engage, it could take a big clinical win for them to fully take the plunge.

Manufacturing is one of the biggest bottlenecks faced by microbiome companies. Despite decades of experience growing bacteria to produce biologics, the biotech industry is ill-equipped to produce live bacterial therapies.

One reason is that manufacturers have historically had little concern for the state of the bacteria, so long as enough protein product is made.

“You don’t really care how fit the cells are, how many of them are dead or alive at the end of the process, it’s really just about yield from the protein perspective,” said Aoife Brennan, CEO and CMO of Synlogic Inc., which is using synthetic biology to engineer live microbial therapeutics.

The lack of manufacturing capacity is especially acute for companies developing intestinal microbiome strains, which represent the lion’s share of the field. This is because many gut microbes require low-oxygen culture conditions and produce hard-to-kill spores that readily contaminate other cultures.

“It’s a new class of therapeutics, no one’s really done it before,” said Duncan Peyton, CEO of 4D pharma plc., which is developing products based on single microbiome strains.

“I think manufacturers will move when they start to say, ‘there’s a real base of business there’.”

Wende Hutton, Canaan Partners

Some companies have responded to the challenge by building capabilities to manufacture in-house.

Others are waiting for more proof-of-concept data before investing in infrastructure, and are outsourcing to the few contract manufacturing organizations (CMOs) willing to accommodate live microbiome therapies.

Mark Smith, CEO of Finch Therapeutics Group Inc., said the short supply of CMOs that can handle gut microbes has created “long lead times and high prices,” though that is partly because the field is still in its infancy.

“Our expectation is that over time, the market

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