microbiome vault
Chris DeGraw/Digital Trends Graphic

The Norweigian archipelago Svalbard is home to ice caves, sled dogs, and even polar bears, but what it’s arguably most known for is the Global Seed Vault, an enormous seed bank built directly into the side of a frozen mountain. The idea is that if the world suffers some kind of devastating catastrophe that wipes out other gene banks, Svalbard’s vault would act as a backup and allow humanity to repopulate the world with important plant species, such as staple crops and medicinal herbs.

But seeds aren’t the only part of the natural world that we might want to keep backups of. Recently, scientists have begun to consider the benefits of building a similar doomsday vault for important microbes — a Noah’s Ark for bacteria, if you will.

When Dr. Maria Gloria Dominguez-Bello, a microbiologist at Rutgers University, heard about the seed storage, the parallels jumped out at her, she told Digital Trends. “It was so obvious, and I became very interested in the idea of doing something like that for the microbiome,” she said.

Your microbiota and you

Microbiota are all the microorganisms — including bacteria, viruses, and fungi — found in a particular environment, like the skin or gastrointestinal tract. The microbiome refers to those microorganisms and their genes. Many factors influence the mix of these microbes inside the gut, including both hereditary and environmental components. Research about how microbiota influence human health is still relatively new, but they are thought to play roles in the immune system, enzyme synthesis, and digestion of complex carbohydrates.

Some researchers are studying the ways in which the microbiota of people in industrial areas differ from those in rural or remote areas. Diet, pollution, medication, sanitation, and other markers of urban environments could manifest these changes in the microorganisms. While studies have shown that such differences exist, it’s not yet fully clear that these alterations are driving increases in chronic conditions, such as diabetes or heart disease.

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Yet Dominguez-Bello is worries that as microbiota research matures, its practitioners might be losing out on valuable data from indigenous populations with more traditional lifestyles and diverse microbiota. “By the time we know better– if we don’t preserve now, we won’t have it,” she said.

In case of emergency

Having worked in both her native Venezuela and Puerto Rico, Dominguez-Bello knows firsthand the hazards that political unrest and climate threats pose to sample collections. In 2012, she moved to New York University, where, after only a month, Hurricane Sandy hit. She and her team had to go into the lab with headlamps to rescue the samples. “I lived, in my own skin, how vulnerable our individual collections are,” she said.

After contacting the researchers involved in the Svalbard project, Dominguez-Bello started assembling scientists in her own field to look at the potential of creating a microbiota vault. In mid-June of this year, a feasibility study from two independent agencies, EvalueScience and Advocacy, found the proposal to be “of high significance and potential.” Dominguez-Bello sees the study’s completion as moving the project from the gestational to newborn phase. The next steps are to form several committees dedicated to outreach and philanthropy; finalize the vault’s location, funding, technical issues; improve education and international relations; and other areas.

arctic-world-data-archive-global-seed-vault
Global Crop Diversity Trust/Flickr

There already exist a number of microorganism collections all over the world, including the American Gut Project, Asia Microbiota Bank, and the Million Microbiome of Humans Project. One major step will be persuading the stewards of such banks to hand over samples for backup storage. Another goal is to encourage the creation of more local collections, particularly of indigenous groups.

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“The local collections are extremely important because the local collections are the live collections,” said Dominguez-Bello. These samples could be used for research and collaboration, with extra material prepared for long-term storage in the vault. One day, the vault could potentially hold hundreds of thousands of samples, but the pilot program would start with a few thousand.

The vault’s participants have started making contacts in several countries, including Peru, Bolivia and Indonesia. “And the way we are planning to do it is through education,” said Dominguez-Bello.

“This is more than microbiology”

The plan is to partner with universities in various countries to teach local scientists about the microbiome, why such collections are needed, and how to collect and preserve samples. “This is more than microbiology,” said Dominguez-Bello. “This is also anthropology and ethics.” By connecting with local experts, foreign universities would potentially have an easier time figuring out laws and permits, as well as communicating with indigenous groups. The first 10-day course was scheduled for Peru, but that was pre-COVID-19.

Local medical teams or anthropologists will also be familiar with an area’s unique challenges, like whether electricity is reliable enough to keep samples cool. Long-term preservation presents different challenges than live samples. The feasibility study acknowledged that there’s much about prepping microorganisms for such storage that researchers don’t understand. Some methods could preserve certain organisms while killing off others.

Two potential methods for the vault are cryopreservation, with liquid nitrogen, and lyophilization, or freeze drying. While liquid nitrogen is the gold standard, Dominguez-Bello said freeze dried samples wouldn’t require electricity, if they were stored in a cold enough area. The microbiota vault’s organizers are considering either Switzerland or Norway, or potentially both locations. The feasibility study’s authors suggested freeze-dried samples could potentially be kept in the Svalbard seed vault.

Ethical issues

Unlike with a vault full of seeds, there are ethical and privacy concerns that come along with collecting and retaining human samples. Laws in both the countries where collections are stored and procured may vary. For example, some countries — including Switzerland and Norway — are part of the Nagoya Protocol, an international agreement that attempts to equitably share the benefits that come from genetic research. Whether microbiota samples fall under this agreement is still under debate.

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Regardless, Dominguez-Bello believes any institution that hopes to profit from these microbiota samples — for example, by creating a new probiotic — has a responsibility to the communities that donated relevant samples. “There is an ethical obligation with the people that were the source of those bacteria,” she said. For example, researchers might help rebuild schools or provide medical equipment, based on an area’s needs. “You do have to do something for the good, for the well-being of their community as a whole,” she said.

The vault will also have to balance openly sharing data while maintaining privacy, not just of individuals but potentially of whole communities. When populations are small enough, even giving a person’s age can make them identifiable.

At the same time, the vault is meant to foster a network, encouraging collaboration between researchers. “I think this is very closely linked to educating not only our students — the future generation of scientists of the U.S. or France or Switzerland or Sweden or Norway or or Portugal — but also” in countries with minimal access to laboratories and equipment, said Dominguez-Bello, who added that we must “expand the scientific community to incorporate them. I think the microbiome is a perfect arena to do that.”

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