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

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

The Microbiota Vault takes a holistic approach to preserving Earth’s microscopic diversity.

Jun 1, 2019
Jack Gilbert, Rob Knight, Maria Gloria Dominguez-Bello, and Martin Blaser

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In October 2018, we announced the development of the Microbiota Vault—an international microbiome preservation effort, to be housed somewhere in a very cold former mine or bunker in Northern Europe. The Microbiota Vault represents an opportunity to develop a global, nonprofit, non­governmental organization for the preservation of humanity’s microbial heritage as a way to counter the possible erosion of the microbial diversity associated with our bodies and environments around the world.

Other groups, such as the Global Microbiome Conservancy (GMC), are working to preserve the microbial diversity of our bodies, and samples from such efforts must also be stored in a safe, politically neutral, stable location. As such, the Microbiota Vault is aimed at ensuring that no matter what happens, we can back up our microbial selves for future generations.

Since we initiated the Microbiota Vault effort, the program has expanded to include not just human-associated microbes, which are well covered by the GMC, but also microbes from animals, plants, soils, waters, and other environments. In the tradition of the Earth Microbiome Project, which is producing sequencing data from myriad environmental and human samples, the Microbiota Vault will gather and store samples from many different ecosystems around the world to ensure that the microbial diversity that underpins the health of ourselves and our planet is preserved.

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.