Introduction

Microbial ecosystems underpin life on Earth, yet they are increasingly imperiled by human activities, including unsustainable agricultural practices and overuse of antibiotics. These disturbances disrupt microbial networks essential for environmental stability, biodiversity, and animal and human health, contributing to the global rise of chronic diseases and ecosystem degradation. As future restoration efforts will depend on the microbial diversity preserved today, proactive measures are urgently required. In this Perspective, we focus on one such initiative, the Microbiota Vault Initiative (MVI), a not-for-profit non-governmental organization that we have developed to address the urgent need. Inspired by the Svalbard Global Seed Vault (SGSV), the MVI shares a vision of safeguarding diversity, although its goals and implementation differ substantially. Unlike the SGSV, which provides backup for existing seed banks with well-documented restoration outcomes, the MVI proactively archives microbiota across human, animal, and environmental domains in anticipation of future unknown needs in restoration efforts.

The MVI embodies an integrative One Health approach by safeguarding microbial biodiversity critical to human and animal health, plant resilience, and environmental functions such as soil fertility, nutrient cycling, climate regulation, and pathogen resistance. By fostering equitable collaboration, honoring diverse knowledge systems, and ensuring depositor sovereignty, the MVI provides a culturally attuned framework for mitigating microbial loss (Table 1). Coordinated action through this initiative offers a timely opportunity to protect health, biodiversity, and ecosystem resilience through the lens of One Health, underscoring the deep interdependence of microbial diversity, environmental integrity, and well-being across species.

Table 1 Core priorities of the Microbiota Vault
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There is broad recognition of the essential role that naturally evolved microbes play in ecosystems, including in humans1,2,3,4. Human activities have disrupted these evolutionary connections in host-associated microbiomes [humans1,2,3,4, animals5,6,7, and plants8,9,10] and have been associated with an alarming rise in chronic diseases such as allergic, autoimmune, and metabolic disorders4,11,12,13,14,15. The loss of microbial diversity extends to environmental ecosystems16,17,18, jeopardizing agricultural systems and environmental resilience.

The loss of crucial microbes in both human and environmental contexts represent a growing but often overlooked crisis. In human health, several key examples illustrate how modernization disrupts the coevolved microbial partnerships19,20. The decline in prevalence of Bifidobacterium longum subsp. infantis—a bacterium that evolved to digest human milk oligosaccharides and support infant immune development—in industrialized societies has been associated with increased risks of allergies, diabetes, and other immune conditions21,22. This decline, likely due to increased use of Cesarean sections, formula feeding, and antibiotics, has become so severe that some pediatricians now recommend probiotic supplementation23. Similarly, the decrease of Helicobacter pylori and Treponema succinifaciens24 from gut microbiomes in industrialized countries shows broader implications of urbanization. While H. pylori’s reduction has decreased stomach ulcers, its absence correlates with increased rates of allergic asthma and metabolic disorders20, highlighting the complex roles that these co-evolved microbes have in human health. In environmental systems, the thawing of Arctic permafrost threatens unique cold-adapted microorganisms like Methanoflorens stordalenmirensis, which helps regulate methane emissions25, and various Acidobacteria species crucial for carbon cycling. The loss of these environmental microbes creates a dangerous feedback loop: as climate change kills off permafrost microbes, their absence accelerates the release of greenhouse gases, further warming the planet26,27. These parallel losses in both human and environmental microbiomes demonstrate how changes caused by human activity can disrupt microbial ecosystems that evolved over millions of years, with cascading effects on both human and planetary health. Just as we strive to preserve endangered macro-organisms, urgent global efforts are needed to understand and preserve microbial diversity.

While much microbial biodiversity and mechanisms underlying sustaining natural ecosystems and health remain to be discovered, viewed through the lens of One Health, it is our obligation to future generations to preserve this microbial diversity28. The concept of preserving Earth’s microbial heritage draws parallels to seed banks, which safeguard plant genetic diversity. Similarly, the MVI is a non-profit organization that operates as a public charity (www.microbiotavault.org). Its primary aim is to support local collections to preserve microbial biodiversity globally, including environmental, plant, animal, and human-associated microbiota.

The microbiota vault initiative: a framework for safeguarding microbial ecosystems

The goal of the MVI is to foster an inclusive, global effort to preserve microbial specimens while fostering extramural research. It is intentionally non-commercial and based on an equitable framework that is designed to address the urgent need for microbial preservation amidst global biodiversity loss. Inspired by the Svalbard Global Seed Vault (www.croptrust.org), the initiative prioritizes microbial biodiversity preservation, fostering the creation of local collections and offering secure cryogenic storage of microbiomes from diverse human and environmental sources (Fig. 1).

Fig. 1: Conceptual framework of the microbiota vault.
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The Microbiota Vault educates scientists and promotes the creation of Local Collections for preservation and research. These local collections can request that the Microbiota Vault preserve a safe backup of their specimens, maintaining all rights over their deposits; they have the option to request sequencing for open access under the license of their choice, and the MV will publish on its webpage a database of the deposited specimens, including metadata, links to sequences, and contact information about depositors. Those in the global community interested in doing research can then contact the depositor from the Local Working Collection. For the use of data derived from the Microbiota Vault, explicit acknowledgments to the specific Local Working Collection and to the Microbiota Vault will be required.

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The MVI acts at the request and on behalf of sovereign depositors, and worldwide local collections, to preserve backup copies of specimens of human, animal, plant, or environmental origin. These samples are not accessible to anyone other than the depositors, or their registered agent. Additionally, upon request by the depositing collections, the Microbiota Vault may sequence microbial DNA (or RNA), depositing in open-access databases under the Creative Commons license of their choice (https://creativecommons.org/licenses/). This helps depositors define the terms of their collaborations29 and foster global research connections, leading to global capacity strengthening in microbiome research. The MVI does not engage in discovery research, therapeutic development, patenting, profit generation, or the assertion of material or intellectual property rights over its collections. Instead, it focuses on building a collaborative, multidisciplinary network. Through initiatives such as the annual Global Microbiome Network Symposia (GloMiNe), the MVI brings together researchers, public health professionals, legal experts, anthropologists, sociologists, and other stakeholders to engage in dialogue around microbiome science, research ethics, standardization, and equitable access and benefit-sharing.

Equity, ethics, education, and global collaboration

The MVI is committed to educating and preserving microbial diversity while ensuring adequate representation of all people. The initiative fully supports multilateral efforts within the Global Biodiversity Framework towards equitable sharing of benefits from the use of biological materials or their data30,31. The initiative is deeply committed to equity and ethical engagement with local communities, including Indigenous peoples who hold and protect critical microbiome knowledge and biodiversity29,32. The MVI acknowledges that decisions regarding the common good and the future of traditional communities should be made by the communities themselves. Its framework aims to support the development of equitable and inclusive approaches to sovereignty and governance in microbiome research.

As a non-profit organization, the MVI operates under its bylaws and global policies to maximize inclusion, providing fiduciary oversight and educating prospective depositors on ethical research practices, access and benefit-sharing requirements under the Nagoya Protocol, and standardized methods for metadata design.

A cornerstone of the MVI outreach efforts is the annual GloMiNe symposium. These events bring together scientists from diverse disciplines—microbiology, anthropology, ethics, public health, and bioinformatics—to share knowledge, discuss microbial biodiversity conservation, and strengthen local research capacity. Over four years, these symposia have fostered interdisciplinary collaboration and contributed to the establishment of a global microbiome network (Table 2).

Table 2 The annual Global Microbiome Network (GloMiNe) symposia are co-organized by the local host institution and the Microbiota Vault
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In addition to symposia, the Microbiota Vault supports capacity strengthening through mentoring for scientists from low- and middle-income countries, who thanks to collaborating with the Digital Sequence Information Scientific Network (DSI) are offered travel grants to their meetings, further advancing global equity in microbiome research. As part of its global advocacy efforts, the MVI has engaged with United Nations delegations, coordinating educational screenings to highlight the importance of the microbiome, and presented at the UN COP24 conference in Cali, Colombia.

The microbiota vault launch phase

The MVI has just concluded its Launch Phase, refining a model for the interaction between a globally coordinated fundraising initiative and locally operated biobanks. Backup collections are deposited with a contractual legal framework in which Deposit Agreements are signed between depositors and the Microbiota Vault. During this initial phase, Local Working Collections from Benin, Brazil, Ethiopia, Ghana, Laos, Thailand, and Switzerland deposited 1204 human fecal specimens and 190 fermented food samples. These deposits required navigating complex local and global regulations for exporting samples to Switzerland, where they are housed securely in cryo-storage (−80 °C) at the Institute of Medical Microbiology, University of Zurich.

The MVI Launch Phase also enabled the development of standardized protocols for sample collection, preservation, transport, metadata development, and data annotation. For metadata, the Microbiota Vault has adopted minimum information about any (x) sequence (MIxS) standards, a modular framework developed by the international scientific community, which offers flexibility to accommodate additional sample types such as environmental or wildlife specimens33. Best practices emerging from this phase include robust traceability of samples, equitable biobanking frameworks, standardized metadata, harmonized storage protocols, advanced biobanking systems, and quality control adhering to the recommendations of the Swiss Biobanking Platform (https://swissbiobanking.ch/).

Future perspective

The MVI’s Launch Phase focused on human-associated microbiomes and fermented food microbes. To support broader ecological goals, it will expand to include environmental microbiota from threatened ecosystems. This aligns with a One Health framework by preserving microbes vital to environmental and planetary health, and by providing a framework for fostering research and strengthening local capacities. While reintroducing preserved microbes remains speculative, and functional restoration from frozen specimens is unproven, preservation offers a valuable opportunity for future research. Indeed, the application of “microbiome therapy” in humans34, animals35,36, and environmental ecosystems37,38, is promising. Stored samples may one day support fundamental microbiological research, ecosystem restoration, or biotechnological advances.

Around the world, other groups of scientists have independently recognized the need to conserve microbial communities through specimen preservation. Among them, the Global Microbiome Conservancy stands out as a research-driven effort actively collecting and studying human microbial samples from diverse geographic regions. While most other initiatives are also research-oriented (Table 3), they align closely with the Microbiota Vault Initiative (MVI) and offer complementary strengths that create opportunities for future collaboration. By partnering with and receiving specimens from local microbial collections, the MVI and similar efforts help safeguard regional ecosystems while advancing education, capacity strengthening, and inclusive governance. In particular, the MVI empowers local stakeholders through depositor sovereignty and strict standards for metadata and preservation protocols.

Table 3 Initiatives for the preservation of microbiome specimens
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