Scientists want to build a Noah’s Ark for the human microbiome

Our bodies host a vast
ecosystem of bacteria, viruses and fungi. Just as scientists are beginning to
understand how this microbiome supports human health, hallmarks of modern life such
as antibiotics and processed foods may be pushing many of our microbial
residents toward extinction.

Now an international team of
scientists wants to safeguard humanity’s long-term health by creating a Noah’s Ark
for microbes. Taking inspiration from the Svalbard Global Seed Vault, which protects the world’s crop diversity from
natural or human-made disasters, the team proposes to create the Microbiota
Vault to preserve human microbiome
collections that may one day be used to prevent disease.

The project is both possible and prudent, a team of independent experts at two Switzerland-based
firms, EvalueScience and advocacy. reports June 11.  “If we are just at the beginning of really
understanding and elucidating what is the role of the microbiota, it is of
course precautionary to at least safeguard part of this diversity before it
just goes away,” says Dominik Steiger, chief operating officer of EvalueScience,
which is based in Zurich.

Studies, mostly in animals,
suggest that a missing microbe or a dearth of microbial diversity may
contribute to a wide range of health conditions, from obesity and inflammatory bowel disorders to C. difficile infection and Lou Gehrig’s disease.

Researchers suspect that
many modern practices contribute to the decline of our beneficial microbial partners,
including being born by cesarean section, eating a low-fiber diet
and overusing antibiotics.

Global Seed Vault
The Svalbard Global Seed Vault on Norway’s Svalbard archipelago protects the world’s crop diversity from natural or human-made disasters. Scientists are now proposing a Microbiota Vault to similarly safeguard the future of the human microbiome.RelaxedPace/iStock/Getty Images Plus

“Rural peoples are
urbanizing and traditional peoples living in savannas and in jungles are moving
to cities,” says Maria Gloria Dominguez-Bello, a microbiologist at Rutgers
University in New Brunswick, N.J., and a leader of the Microbiota Vault
initiative. “What we see is that we are losing [microbiome] diversity, and in
parallel there is a correlation with increase in chronic diseases.”

Dominguez-Bello has worked
with local researchers in Venezuela, Bolivia, Peru and Brazil to collect and study
stool samples from indigenous populations in those countries. In 2017, she and her
colleagues published a study in Science that
shows that the more industrialized a society, the less diverse
its microbiome. The gut diversity of
people in the United States is almost half that of the most isolated
Amerindians living in South America, she says.

Dominguez-Bello’s research
collections have been in jeopardy many times, from
political unrest when her lab was based in Venezuela to Hurricane Sandy
after she’d moved her lab to New York University.

So the idea for the Microbiota Vault, first proposed in a 2018 Science paper, is that microbiome collections, many of which like
Dominguez-Bello’s already exist in research or health facilities all over the
world, would be maintained locally, as well as stored in a backup vault in a
politically stable location. The feasibility report recommends Switzerland or
Norway, possibly even alongside or within the Svalbard Global Seed Vault.

The report also suggests
that specimens could be preserved by cryopreservation, cooling them to very low
temperatures. As a backup, researchers should also consider using a less tested
freeze-drying technique known as lyophilization.

The initiative, run as a
global nonprofit, would encourage the development of more microbiome
collections by creating courses to train researchers across the globe to
collect samples from indigenous populations in their regions. In a pilot phase,
Dominguez-Bello plans to host a course in Lima, Peru with collaborators from
local universities, but the timing is uncertain due to the coronavirus pandemic.

Funding for such an
initiative would likely originally come from research entities and philanthropic
organizations but could grow to include a larger portion of government funding
once the project becomes more established, says Steiger.

“The Microbiota Vault really
seems like it has huge potential to benefit human health,” says Matthew Kelly,
a pediatrician and global health specialist at Duke University, who is not
involved with the initiative. But Kelly cautions that the ethics of the project
are complex, and researchers will need to clearly communicate with indigenous
communities about the benefits, if any, to their participation in this
research.

Ethics will be a major
component of the courses, says Dominguez-Bello. In a 2016 opinion piece in Nature Microbiology, she and coauthors
state that any commercialization resulting from samples collected
from indigenous peoples “should be
done with the highest ethical standards, respect for native cultures, and
involving a mediator of their choice, familiarized with financial systems and
terms, who can defend their interests.”

Many indigenous communities
also recognize the potential health benefit of banking their microbes, as they
too are moving toward industrialization, she says.