Articel Content
Stockpiling bacteria.
Text: Samuel Schlaefli
Our health is highly dependent on the presence of a diverse community of microorganisms in the body, but the diversity of this “microbiome” is in rapid decline. An international research consortium is therefore planning to build a vault
for the long-term conservation of particularly valuable microbial communities.
It sounds like something out of a James Bond film: In a decommissioned army bunker in a remote Swiss valley, millions of small containers of bacteria, viruses, fungi and archaea are stored at temperatures as low as –196°C, behind meter-thick walls and with strict security measures. Every day, new microorganisms from all over the world are added to the collection — a stool sample containing intestinal bacteria from the Maasai people in the Serengeti, for example, or a piece of fermented cabbage with bacteria from South Korea. Over time, this gives rise to an archive of microbial communities from around the world that are considered particularly worthy of conservation. This archive doesn’t actually exist yet, but it is the long-term vision of an international initiative known as the Microbiota Vault.
Working behind the scenes on this major project is a core team of 19 researchers from the USA and Europe, including pioneers in the field of microbiome research, with support from around 40 academics from four continents. Following a feasibility study that assessed Norway and Switzerland as potential locations for the construction of the microbiome vault, Switzerland was selected in summer 2021. This was coupled with the idea of using a decommissioned army bunker as the site for the vault.
A microcosm of species extinction
The human body is inhabited by around 40 billion microbial cells, including bacteria, viruses and fungi. Many of these cells form part of the intestinal flora, but dense colonies of microorganisms can also be found on the surface of the skin and the mucous membranes of body orifices. Everyone has their own individual microbiome, which varies depending on what we eat and the environment in which we live.
“Today, we know from research that the microbiome assumes core functions relating to metabolism, the uptake of vitamins and the immune system, for example,” says Adrian Egli, research group leader at the Department of Biomedicine of the University of Basel and Head of Clinical Bacteriology and Mycology (the study of fungi) at University Hospital Basel.
Egli says that current studies also suggest a relationship with autoimmune diseases such as multiple sclerosis (MS), as well as metabolic diseases and excess weight. Even in the treatment of intestinal cancer using the latest drugs, it has become clear that treatment success is highly dependent on the microbial environment of the tumor. Researchers therefore hope that a better understanding of the microbiome will open up new treatment possibilities and that healthy microorganisms can be put to targeted use.
This is becoming less and less likely, however, as potentially valuable bacteria, fungi and viruses are lost on a daily basis. The diversity of the microbiome is in rapid decline,” says Egli. “This decline is probably something to do with our diet and lifestyle, environmental factors, the use of antibiotics, and climatic conditions.” Analyses have shown that the microbiome in the intestines of hunter-gatherers in the Amazon rainforest of Venezuela is twice as diverse as that of healthy people in cities in the USA.
This is where the Alpine vault comes into play. “What we have in mind is a kind of backup storage facility,” says Egli, who is part of the Swiss research team that plans to lay the groundwork for construction of the Microbiota Vault over the course of a two-year pilot phase. “Otherwise, data analyses may one day show that, although a certain bacterium would have been useful for cancer treatment, it is no longer to be found anywhere in the world.” Egli compares the project with the Global Seed Vault in Svalbard, where over a million seeds are kept in the permafrost of Spitzbergen in order to conserve global plant diversity for future generations and scientific research despite dramatic species extinction.
A wealth of data for bioinformatics
Work during the pilot phase is focusing on legal and technical aspects of the project. The diversity of intestinal flora is particularly high in the populations of rural areas of Africa, Asia and South America. Accordingly, the team wants to explore how difficult it is to bring stool samples from these countries for storage in Switzerland and the ethical challenges that this poses. There are also questions about the ideal forms of preservation and storage with a view to conserving the original microbiological diversity of a sample.
The precursor to the vault is currently found in Egli’s laboratory at the University of Basel, where hundreds of stool samples are already stored in conventional laboratory freezers. By the end of the pilot phase, this collection is expected to grow to 2,000 samples. The focus is currently on samples taken from humans, but other microbial communities from foodstuffs, plants and animals will be added at a later stage. One unique feature of the project is that the genetic make-up of the microorganisms in each sample is deciphered using next-generation sequencing, producing data that allows the researchers to compare individual genetic features of microorganisms in the microbiome. One day, the aim is for this wealth of digital information to be made freely available to the global scientific community for further computer-based analyses.
Research infrastructure for future generations
Once the pilot phase is completed, the initiators anticipate investments of several million francs. “The construction process is anything but trivial,” says Egli. “We’re looking for a safe location where the vault can be supplied with power reliably. At the same time, the site must also be easily accessible for the transport of samples.”
The costs are currently being met by a number of universities and foundations, which are set to be joined by other globally active foundations when it comes to funding the construction and long-term operation of the facility. Egli expects that it will take at least 10 years for the microbe vault to enter routine operation. “My own microbiome research probably won’t even benefit from it,” he says — but that does nothing to dampen his motivation. Rather, he is fascinated by the opportunity to establish research infrastructure that will one day benefit generations of scientists.
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