Whose Microbes? Building Ethical Foundations for Microbiome Preservation

The Microbiota Vault Initiative, recently highlighted in Nature Communications, proposes an ambitious and timely effort to preserve microbial diversity for the benefit of future generations. While the goals are admirable, this framework is best understood as the beginning of a deeper and necessary conversation about ethics in microbiome science. As microbiome researchers, ethicists, and global health stakeholders, we are at a crossroads where we must balance innovation with introspection.

The Vault, as described by Mooser et al. (2025), outlines a compelling plan to safeguard microbial biodiversity through cryopreservation, drawing inspiration from the Svalbard Global Seed Vault (Fowler, 2008). Given the continuing loss of microbial diversity associated with urbanization, dietary changes, antibiotic use, and modern sanitation (Blaser and Falkow, 2009), the proposal is both timely and forward-looking.

Yet even promising proposals must be stress-tested by ethical questions. These are not critiques but invitations to broaden the dialogue so that the science of preservation is paired with the ethics of protection.

Context is Key

One key consideration is how the Vault plans to manage the eventual reintroduction of preserved microbes into human populations, agricultural systems, or natural ecosystems. Microbes do not act in isolation. They function as part of dynamic, interdependent communities that are shaped by host biology, environmental pressures, microbial competitors, and available nutrients (Coyte and Rakoff-Nahoum, 2019). A microbe that contributes to health or balance in one context may behave very differently in another. For instance, Prevotella copri is associated with beneficial metabolic effects in high-fiber diets, but in some industrialized populations it has been linked to inflammation and autoimmune risk, including rheumatoid arthritis (Scher et al., 2013). These opposing effects reflect the importance of ecological context.

Studies in fecal microbiota transplantation further illustrate how unpredictable microbial behavior can be. Even when donors are screened and microbial communities appear beneficial, outcomes in recipients can vary widely. Some patients experience dramatic symptom relief, while others see little change or even adverse effects. These differences often depend on subtle host factors, microbial interactions, and ecological compatibility that remain poorly understood (Smillie et al., 2018). There is limited guidance on how the Vault plans to assess ecological risk or adapt to emerging insights about microbial complexity. Without a strategy for long-term oversight, the act of preservation risks creating downstream consequences that are difficult to reverse.

Preservation, in this case, is not just about freezing strains but must be about maintaining the integrity of ecosystems, relationships, and trust.

Function Over Identity

Another point worth discussing is the assumption that microbial loss is always harmful. In some cases, this may be true. But other microbes carry both potential benefits and documented risks. For example, Helicobacter pylori has been associated with immune training and reduced allergy risk (Blaser and Chen, 2008). At the same time, it is a known cause of ulcers and gastric cancer (IARC, 1994). Similarly, Bifidobacterium infantis plays a key role in the infant gut by helping break down human milk oligosaccharides and shaping immune development. However, this species naturally declines as we age. Its disappearance in adults likely reflects normal microbiome maturation rather than a deficiency (Sela and Mills, 2010; Turroni et al., 2012). These examples suggest that a focus on microbial function, rather than ancestral identity, may provide a more nuanced foundation for deciding what to preserve or reintroduce.

The notion that ancestral microbes are inherently superior risks romanticizing a past that may not reflect present-day realities. As human environments, diets, and exposures evolve, so too do our microbiomes—sometimes in ways that confer new benefits, such as reduced inflammation or enhanced pathogen resistance. Attempting to reverse these changes could disrupt adaptations that are now beneficial. Additionally, microbial ecosystems often exhibit functional redundancy, meaning multiple species can perform similar roles. The loss of one taxon doesn’t necessarily equate to a loss of function. Yet the paper doesn’t examine whether these so-called “missing microbes” are truly irreplaceable or if current microbial communities already compensate for their absence.

From Depositor Sovereignty to Shared Governance

The paper also highlights the rich microbial diversity found in Indigenous and rural communities. These communities often have more complex and less industrially disrupted microbiomes due to lifestyle, diet, and environmental exposure (Schnorr et al., 2014), making them invaluable scientifically and commercially. Therefore in order to protect these populations complex discussions about how samples from these communities will be managed must be asked. How will long-term consent be maintained? What role will communities play in deciding how and when their samples are used in the future? How will benefits be shared fairly and transparently? Were community members informed in linguistically and culturally appropriate ways, or if future use cases (such as reintroduction or commercialization) were transparently discussed.

It is evident that the Vault has taken into account some of the ethical concerns that come along with microbiome research and do mention “depositor sovereignty,”. This concept offers a promising starting point, but there is little indication that community leaders or Indigenous scholars helped to shape the Vault’s governance. History has shown that meaningful engagement must go beyond consultation. It requires shared ownership, co-authorship, and long-term partnership (Harding et al., 2012; TallBear, 2013). There is support for young scientists from these communities to travel to symposia and conferences but there is no evidence of structural inclusion of Indigenous scientists, ethicists, or community leaders in actual decision-making roles. Were these communities involved in protocol design, authorship, or sample governance? Without their meaningful participation in shaping the initiative, references to equity risk being performative rather than substantive.

Microbial Samples Are Not Culturally Neutral

Additionally, the implicit assumption that biological materials like stool, skin microbes, or even DNA are culturally neutral commodities is deeply problematic. In many Western biomedical frameworks, these materials are often viewed as resources to be extracted, banked, and studied with minimal emotional or cultural weight. But this view is not universal. Across many Indigenous and traditional knowledge systems, bodily materials are not just biological, they are sacred, relational, and often carry ancestral or spiritual significance. For instance, in some Native American communities, hair, blood, or tissue samples are considered extensions of the person and the community, making their collection or storage without permission an act of violation rather than scientific utility.

Microbial samples, such as stool or skin swabs, may seem innocuous in a laboratory context. However, from a relational or cosmological perspective, these can be seen as carrying a person’s essence or energy. In Māori communities, for instance, bodily substances are considered tapu (sacred) and must be handled according to strict cultural protocols. Disregarding these beliefs can result in spiritual harm and fractured relationships, even if the research aims are well-intended.

Therefore, preserving microbial samples must be done with the engagement of community knowledge holders, recognition of sovereignty over biospecimens, and flexible governance structures that allow for withdrawal, co-ownership, or culturally specific restrictions on use.

Looking forward

In sum, the Microbiota Vault is a promising and ambitious step toward preserving microbial life in an era of rapid ecological and biomedical change. But like the microbes it seeks to protect, its strength will depend on the ecosystems it builds around it scientific, cultural, and ethical. Preservation must be paired with participation. Innovation must walk hand-in-hand with accountability. As this initiative grows, the opportunity lies not only in what is frozen for the future, but in how we build frameworks of trust, inclusion, and shared stewardship today. The conversation is just beginning, and the microbiome community has a chance to shape it with care.

References

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