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Human Health, Sustainability, Innovation

Manipulating the Microbiome in Plants and Humans

We humans contain multitudes in our microbiome alone – there are trillions of microbial organisms living on and within our human bodies. Plants, similarly, are populated by massive colonies of microbes. All this creates vast potential to improve both our personal health and our agriculture.

What are biomes and microbiomes?

A biome is a specific physical environment and the community of organisms inhabiting it.

Thus, a biome may be as big as the Earth itself. Or it may be an immense but subsidiary environment in the planetary context, like the Taiga (or boreal forest) that covers the world’s sub-Arctic northern landscapes with coniferous forests. Or it may be small like the artificial biomes that microbiologist Clair Folsome began creating in 1967, which fitted inside one-liter wine bottles and supported communities of microorganisms.

Our gut’s surface area, unwound, would be about 3,000 square feet, or an area slightly larger than a tennis court.

Environments that support communities of microorganisms – or microbiomes – exist throughout nature. In fact, each of the seven-and-a-half-billion humans now living on the planet is one, although human microbiomes are much bigger than those Folsome created. Our gut’s surface area, unwound, would be about 3,000 square feet, or an area slightly larger than a tennis court; every human individual has an estimated population of 30 trillion-odd microflora – bacteria, viruses, and fungi – that play important roles in a wide range of our biological processes, including our pathogen resistance and immune function regulation.

The human microbiome is effectively an organ

So important is the human microbiome to our health that it makes sense to consider it an organ. Specific microflora populations differ from individual to individual, so it may be possible to use microbiomes for identification purposes, much as we now use fingerprints. Nevertheless, individuals’ microflora populations function in strikingly consistent ways. That’s true not only for healthy people, but also for patients whose microflora suffer dysbiosis: an imbalance or maladaption of the microbiome. This makes it possible to target the microbiome to treat a wide variety of diseases.

Flagship Pioneering has been a leader in understanding microbiome functioning, and in creating companies – Seres, Evelo, Kaleido, and Indigo Agriculture – aimed at drugging or using microbiomes in new ways. One example is a drug from Seres Therapeutics named SER-109, now in clinical trials, a microbiome therapeutic to prevent Clostridium difficile infection, one of the three top antibiotic-resistant bacterial threats in the United States. The U.S. Food and Drug Administration (FDA) has given SER-109 the agency’s Breakthrough Therapy and Orphan Drug designations.

Plant Microbiomes

The Earth’s human population is expected to reach around 10 billion by 2050. To feed that many people, in the face of increasing drought, herbicide, and pesticide resistance, we will need more nutritious crops that can be grown in more environmentally sustainable ways. Fortunately, the potentials of the microbiome are not limited to human therapeutics.

Commensal, symbiotic microorganisms have been found to exist in and on all species of plants studied. Indigo Agriculture now possesses the world’s largest plant microbiome database and has already brought its first four commercial products to market: Indigo Cotton, Indigo Wheat, Indigo Corn, and Indigo Soy. The company coats its specially-developed microbes over its seeds’ surfaces to improve factors like drought tolerance and insect resistance, then markets those seeds to farmers while contracting to pre-purchase the resulting crops, which it then sells on to food companies, grain mills, and commodity traders.

During 2016, Indigo’s marketed its first product, Indigo Cotton, which demonstrated average yield gains of 11 percent in 2017 and then 14 percent yield gains the next year. During 2017, Indigo Wheat showed average yield gains of 15.7 percent, while Indigo Corn has had yield increases of up to 77 percent. In 2018, the company introduced Indigo Rice to the market.

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