‘Microbial Noah’s Ark’ to preserve the diversity of human microbiota

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By Stephen Daniells

- Last updated on GMT

Related tags microbiota microbiome Probiotics

A new biobank known as the Microbiota Vault recently received the go ahead to move on to the pilot stage: The ultimate goal is to gather beneficial microorganisms from human populations whose microbiomes are uncompromised by antibiotics, processed diets and other ill effects of modern society.

Increased industrialization after the Second World War has been accompanied by a dramatic increases in metabolic disease, cognitive diseases, and immune diseases, and there is a school of thought that the common underlying factor in all of this is a shift in our gut microbiota, or to put it another way, a loss of diversity. This was perhaps most famously summarized by Prof Martin Blaser in his book, Missing Microbes​.

Prof Blaser, who is the Henry Rutgers Chair of the Human Microbiome at Rutgers University, is one of the leaders of the Microbiota Vault​, along with Maria Gloria Dominguez-Bello (Rutgers) and Professors Rob Knight and Jack Gilbert at the University of California at San Diego.

Outlining their proposal for the Vault in 2018 in the journal Science​, the four researchers wrote: “A global repository of human-associated microbes should back up existing research collections, similar in principle to the inspiring example of the Seed Vault established in the permafrost of Svalbard Island in Norway to preserve the natural biodiversity of plants. We owe future generations the microbes that colonized our ancestors for at least 200,000 years of human evolution. We must begin before it is too late.”


Speaking to NutraIngredients-USA from San Diego, Prof Gilbert explained that there’s a relationship we need to understand between the bacteria we appear to be losing, and our health.

People living in urbanized societies have lost a substantial part of their microbiota diversity; the gut flora of most Americans, for example, is half as diverse as that of hunter-gatherers in isolated Amazonian villages.

 “There are a number of efforts around the world to get hold of microbes and store them, both fecal samples and to collect samples from non-industrialized societies. So, people that have not necessarily got into the full scale of multi-generational development that we see in Europe, America, and China.

“So, hunter gatherer populations, or people living in a more holistic environment, like the study in Nature Medicine that looked at Travellers in Ireland​. They have a very diverse microbiome and a very healthy immune system probably because they are not living in a highly processed and highly manipulated world.”

“The Microbiota Vault is there to maintain them, and to keep a catalog of organisms that are potentially important for our health.”


A feasibility study was performed by two independent Swiss firms, commissioned by the Seerave Foundation, Gebert Rüf Foundation, Rutgers University, Calouste Gulbenkian Foundation, Kiel University, UC San Diego School of Medicine, Canadian Institute for Advanced Research, and Bengt E. Gustafsson Symposium Foundation, affiliated with Karolinska Institutet.

The study found that the Microbiota Vault initiative has great significance and potential, and that its leaders should establish a pilot project that would include installing infrastructure to store microbes in a site such as Norway or Switzerland and collaborations for collecting samples with developing countries.

In a press release, Dr Dominguez-Bello stated: “We look forward to taking the next steps toward a pilot project with the goal of testing the legal and logistical framework of the Microbiota Vault. We’ll also start capacity building by creating dedicated courses at Rutgers and universities in Peru and other developing countries.”

When fully operational, the Microbiota Vault would be a global backup store for all microbial samples, the originals of which would remain within local collections in the countries of origin.

“This should be a globally-relevant resource,” ​explained Prof Gilbert. “We want to make sure that this material is not just locked up inside one organization’s or one country’s purview but is made available to the rest of the world.”

The characterization of samples stored in the Microbiota Vault would be available in a transparent and open access fashion, enabling researchers across the globe and optimizing use of information and use of the specimens in the local collections.

Reintroducing lost microbes

The researchers also hope that it may be possible one day to prevent disease by reintroducing lost microbes.

“If you look at probiotics at the moment, the vast majority of them are bacteria that are found in food, not bacteria that are found in the human body,” ​said Prof Gilbert. “There are a few available that are ‘human’ microbes, but not many. And most of those food bacteria aren’t necessarily the right ones to stimulate our immune system.

“We are interested in making sure we can get human-associated bacteria out, but we’re not at the stage where we’re ready to commercialize those kinds of products yet. We don’t know if they’re effective, we don’t know how to deliver them, we don’t know what dosing, so we need to capture those resources now and make sure they’re available for the future when our research and development processes get to the stage where we can effectively use that resource.

“But hopefully we’ll be able to culture up some of those bugs, figure out ways of developing a probiotic formulation or maybe even capitalizing on the kind of chemistry those bugs produce and isolating that chemistry and using that as a drug.”

Source: Science​ 
2018: Volume 362, Issue 6410, Pages 33-34, doi: 10.1126/science.aau8816
“Preserving microbial diversity”
Authors: M.G. Dominguez Bello, R. Knight, J.A. Gilbert, M.J. Blaser

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