On Apr. 17, 2023, a new initiative led by Jennifer Doudna and Jill Banfield at the Innovative Genomics Institute was announced. The Audacious Project, an initiative housed at TED, encourages the world’s greatest change makers to dream bigger.

The research initiative, “Engineering the Microbiome with CRISPR to Improve our Climate and Health,” will receive $70 million in funding from donors, making it the largest scientific project funded through The Audacious Project to date.

It involves a close collaboration across three University of California (UC) campuses — the Innovative Genomics Institute (IGI) at UC Berkeley, UC Davis, and UC San Francisco — that capitalizes on the strengths of each institution.

The two project leaders have a unique connection: Doudna is best known for her groundbreaking work developing CRISPR genome editing, for which she received the Nobel Prize in Chemistry in 2020; Banfield studied microbial communities for decades and first introduced Doudna to CRISPR systems in bacteria, at a fortuitous meeting at a UC Berkeley café in 2006. Now, they’re bringing their specialties together to develop a new toolkit to address global problems in climate and human health by applying CRISPR genome editing to complex microbial communities known as “microbiomes.”

Though invisible to the naked eye, microbes — bacteria, fungi, viruses, and other microscopic organisms — are everywhere. They account for the vast majority of life’s diversity and they shape the world in significant but often overlooked ways. While scientists have historically studied microbes individually, they commonly live in complex communities, or microbiomes, in the environment around us, and on and even in our bodies. In fact, there are more microbial cells in our body than human cells, and we depend on them for a variety of functions — but when out of balance, microbiomes can also create problems instead.

Currently, the tools we have to address problem-causing microbiomes are blunt. Antibiotics wipe out whole populations of beneficial and harmful bacteria, probiotics have limited impact, and fecal transplants have shown some promise in specific areas, but face concerns with safety and acceptance.

The IGI team is developing a revolutionary new approach to precisely control microbiomes by building on two state-of-the-art methods pioneered by Doudna and Banfield that have both developed significantly over the past decade: CRISPR genome editing and genome-resolved metagenomics. Less than 1 percent of microbial species can be cultured in the lab, but genome-resolved metagenomics removes the need to grow individual species one-by-one by  providing a detailed map of all organisms in a microbiome and the functions of their genes. Banfield and collaborators used these techniques in a 2016 paper in Nature Microbiology to develop a new, clearer picture of the tree of life, showing just how much of the tree is dominated by unseen microbes.