Jennifer Doudna’s Innovative Genomic Institute has received $70 million to explore a bold idea: combating climate change and other emergencies by modifying the microbial communities that live outside and inside us.

Bacteria are the true masters of the planet, for better or worse. Besides affecting our health in many ways, they are responsible for much of the methane emissions. This gas traps heat far more than carbon dioxide and is produced in large quantities by microbes that proliferate in environments associated with human activities (farms, landfills, rice paddies). The good news is that methane is short-lived, so reducing its emissions would have a rapid and substantial effect on global warming. What tools do we have at our disposal to try to pursue such an ambitious goal?

The philanthropists who have joined the Audacious Project under the TED umbrella have decided to bet $70 million on a frontier approach that uses the CRISPR genome editing platform but is not merely correcting the DNA of one organism at a time. It is called microbiome editing and applies to the ensemble of genomes of microbial communities, which would be edited in their natural environment without the need to isolate the strains to be treated. Take livestock farming, which causes 15% of global emissions. Much of the blame does not lie with cattle as such, but rather with the methanogenic microbes they harbour in their stomachs.

To reduce ruminants’ burping, the scientific community has postulated various stratagems, from seaweed based dietary supplements to the administration of methane-inhibitors. But to have a global effect, practical, cost-effective and lasting strategies would be needed, possibly implemented in a ‘one-shot’ mode, with a single early intervention on each calf. This is precisely the bold idea proposed by the Innovative Genomic Institute (founded in Berkeley by the co-inventor of CRISPR) and developed in collaboration with other Californian universities (Davis and San Francisco).

The proof of concept of microbiome editing was published two years ago in Nature Microbiology by Doudna and Jill Banfield, who is considered the founder of metagenomics (the science that studies environmental samples in which genomes of known and unknown microorganisms are mixed). Two systems were then used as models: a natural soil microbiome and the intestinal microbiome of a child.

The alliance between the two scientists continues under the double challenge of environmental and health in the new project entitled ‘Engineering microbiomes with CRISPR to improve our climate and health’. As far as climate is concerned, in a nutshell, the aim is to perfect the technologies needed to edit the microbes living in the rumen of cattle and make them produce less methane. And as for health, what do Doudna and Banfield have in mind?

The microbes that live in our bodies, from the skin to the gut, not forgetting the respiratory airways, affect a myriad of conditions including allergies, obesity, cardiovascular disease, neurological disorders. Antibiotics are double-edged weapons because they also affect beneficial bacteria, probiotics have limited effects, and faecal transplants still arouse some mistrust.

The first test bed for microbiome editing should be asthma, which affects 300 million children worldwide, many of them in low- and middle-income countries. It is currently possible to treat its symptoms, but there is no cure. The hope for the future is to be able to intervene in the composition of the intestinal flora, inhibiting the production of certain inflammatory compounds.

Beyond the Audacious Project, however, there is a whole microbial world whose potential has only just begun to be investigated with the tools of editing. The fields of application are countless, as Nature Biotechnology notes in its June editorial: sustainable production of useful substances, biomeremediation of contaminated areas, fertilising microbes instead of synthetic nitrogen.