Startup Indigo wants to use bacteria to create hardy super-crops

In a Cambridge greenhouse with a spectacular view of the Charles River, one startup is making a bet on the next great revolution in plant science.

Soy plants sun themselves under skylights year-round in this balmy space, ground zero for Indigo, a two-year-old company that is cultivating hardy super-crops by changing the bacteria and fungi that live in them.

Just as the emerging medical field around the so-called human microbiome seeks to fight disease by adjusting the balance of bacteria in the body, Indigo’s goal is to manipulate the composition of bacteria in plants to grow healthier crops that ultimately produce more nutritious food.

On Thursday, the company revealed the first details about its products: Seeds bathed in custom-crafted cocktails of bacteria and fungi that would make crops hardier or more drought resistant, potentially attacking big problems like world famine or the global food supply in a dramatically new way.

Indigo — called Symbiota at its launch — was conceived and funded by VentureLabs, the startup unit within Cambridge company Flagship Ventures, in 2014. It was rebranded Indigo on Thursday. The company also announced that Roger Beachy, executive director of the World Food Center at the University of California at Davis would join the company as chief scientific officer.

In the last two years, with $56 million in funding led by Flagship, the company has grown its research team to about 60 people, sequenced the genomes of 40,000 microbes, and conducted field tests on three continents with wheat, corn, cotton, soy, and chickpea crops.

The idea is that crop seeds coated with a custom-crafted brew of bacteria and fungi can better resist high temperatures or drought conditions. The results so far: a 10 percent increase in crops yields across the board.

“If we’re right, this is an innovation that is going to create tens of billions of dollars a year in revenue,” Indigo chief executive David Perry said. “From a farmer’s perspective we can improve their profitability. From a consumer’s perspective we can improve the healthfulness of the food and the environment in which it is grown.”

Indigo intends to sell its first products this year, Perry said, to its target customer: large agribusinesses first in the United States, followed by South America, Australia, and Western Europe.

In the last decade, a flood of research has revealed a universe of bacteria that thrive in our guts and organs. It turns out they influence every aspect of health, from digestion to mental health, and a new wave of bacteria-based therapies are being funded and developed to fight off illness by rebalancing the body’s native flora.

By comparison, research into the plant microbiome is about ten years behind, said Indigo founder and chief technology officer Geoffrey von Maltzahn. But the principles are similar.

Von Maltzahn previously founded Seres Therapeutics, a Cambridge biotech that developed a pill to treat a bacterial intestinal condition. Last summer, Seres went public and raised more than $133 million in its initial public offering. Last month, Seres signed a multimillion dollar partnership with the health science arm of Swiss food giant Nestle.

Von Maltzahn founded Indigo with the goal of training that expertise on one of humanity’s basic needs: food. “We don’t talk about agriculture a lot in these zip codes but it is objectively at the very top of challenges — from an environmental perspective and the perspective on our own health,” he said.

Indigo is able to capitalize on a handful of new technologies that have only recently matured. For one, the team deploys machine learning algorithms — powerful data crunchers — to analyze results from gene sequencing and field tests to predict which combinations of microbes suit which crop under what conditions. The plummeting cost of sequencing technology is also key. “Two years ago it was too expensive to do what we’re doing,” Perry said.

The advances pioneered by companies like Seres was the final piece of the puzzle. “You basically couldn’t do this today unless you were deeply borrowing from the insights that have been coming through from the human microbiome side of things,” von Maltzahn said.

The idea that bacteria and fungi co-exist with plants is not new. Teenagers are introduced to the concept in high school biology class.

But scientists were previously unaware of the scale to which microbes proliferate within plants — not just in their roots, but studded throughout the cellular layers of the leaves, stems, fruits.

“It’s an incredible renaissance in our thinking about how to approach plant microbiology,” said Betsy Arnold, a professor of plant microbiology at the University of Arizona who has been studying the relationship between bacteria and plants for two decades. Like research into the human/bacteria relationship, much of plant microbe research until recently had focused on disease.

Arnold instead looked at plants that survived in extreme conditions — the one sapling in a field, say, that thrived through a hot spell or drenching rain — to find the tricks they used to outlast heat or drought. What they found was that in many cases there were strains of bacteria or fungi that gave them that ability.

Arnold is partnering with Indigo on a handful of research projects. The company reimburses the Arnold lab for sample-collecting excursions in various parts of the world and has access to the microbes collected during those trips. Arnold is also a member of the company’s scientific advisory board.

Christopher Udry, a Yale University professor who studies agriculture in the developing world, said that farmers there see much more than a 10 percent change in yield from season to season depending on factors such as rainfall. Indigo’s 10 percent bump, if reliable, could make a real difference.

One big challenge will be to introduce farmers to the new technology and convince them that it is a good idea, Udry said. He said that poor farmers would find it a financial strain and risk to make such a large investment in a new technology at the very beginning of the season, compared to investing in a technology that was applied further along.

As with agricultural technologies that arrived before Indigo, there is likely to be skepticism, even worry, about its environmental impact. The company says it is merely using bacteria that has always been present in hardy plants and that the process is safe.

But Udry said, “We need to have a scientific consensus regarding the potential environmental consequences of any such new technology.”