Opinion: New Repository Will Hold the World’s Microbial Riches

If we can provide that knowledge and sufficient resources, the stored microbes could one day be used to repopulate and revive damaged ecosystems across the globe.

Earth’s microbiota—and its collective genomes, the microbiome—comprises bacteria, viruses, fungi, protozoa, and other micro-eukaryotic colonizers, organisms that inhabit all environments on our planet. Microbiomes support human health through direct and indirect association with our bodies, but they also affect the health of soils and waterways. Soils, rivers, lakes, and oceans are critical to feeding the ever-growing human population, and microorganisms are central to ensuring the ongoing fertility and fecundity of these environments. Understanding and quantifying how the smallest life-forms have enabled the vast diversity of the entire biosphere is key, and ongoing investigations in microbial ecology and physiology are resulting in explosive discoveries.

Simultaneously with this line of inquiry, researchers are studying how we can leverage microorganisms, translating their potential into practical solutions for the health of humans and the environment. To do this, we need not only to have viable collections that can be mined to access every aspect of microbial physiology, but also to have examples of intact microbial ecosystems: for example, maintaining whole soil and sediment samples, with the biological matrices intact, will be of immense value.

To preserve global microbiota diversity, we must limit the ecological damage to extant environments. Much of this can be accomplished by better stewardship of our ecosystems. In human medicine, this means managing clinical practice, such as the use of antibiotic therapy, to prevent the devastation of the human microbiome. In agriculture, it means determining how to manage soil health through reducing tillage and artificial fertilizers and limiting the use of pesticides and herbicides, which are known to damage the soil microbiome. But even if such tactics are highly successful, they will likely only diminish the pace of the decline. Ideally, we should strive to preserve the current state of microbiome affairs in both agriculture and medicine.

We also need to examine ways to accelerate restoration efforts for damaged ecosystems. Designing consortia of bacteria that feed one another and can create a self-sustaining ecosystem when integrated into the human body presents a solution to rebuilding a damaged ecosystem. Similarly, efforts to create agricultural probiotics that can improve the resilience, resistance, and productivity of crops and animal stock are showing promise. However, the more we learn about these ecosystems, and the more sophisticated our technologies become, the more we will need access to the existing diversity of microbial life to augment current products, which tend to oversimplify real-world microbial communities.

The Microbiota Vault will be built from both existing research collections and new exploratory efforts from groups around the world. Better connecting existing regional collections will promote regional capacity building and collaborative research. The vault needs buy-in from scientists, philanthropists, NGOs, politicians, and multinational entities, and we need to ensure that the collections are viable. Moreover, the data collected from each sample should adhere to recording standards, such as those provided by the Genomic Standards Consortium, so that they can actually enable future preservation and restoration efforts.

If we are to restore an environment from a sample stored underground near the Arctic, we need to understand not only how the microscopic environment functions, but also as much as possible about the physicochemical and biological character of the environment from which that sample was collected. If we can provide that knowledge and sufficient resources, the stored microbes could one day be used to repopulate and revive damaged ecosystems across the globe.

Jack Gilbert is a professor of pediatrics at the University of California, San Diego. Rob Knight is the founding Director of the Center for Microbiome Innovation and a professor of pediatrics and computer science & engineering at UC San Diego. Maria Gloria Dominguez-Bello is Henry Rutgers Professor of Microbiome and Health at Rutgers University. Martin Blaser is Henry Rutgers Chair of the Human Microbiome at Rutgers University.