Earth BioGenome Project prioritization: maximizing value to society

The Earth BioGenome Project is scientifically viable and globally coordinated—but success now hinges on strategic policy leadership, sustained funding, and unrestricted data access, asserts Prof. Richard A. Gibbs, Baylor College of Medicine, USA.

DOI: https://doi.org/10.25453/plabs.30157480

Published on September 18th, 2025

In a major push for bio-digitization, the Earth BioGenome Project (EBP) aims to generate a reference genome sequence for each of the 1.67 million described eukaryote species—those organisms with distinct nuclei, including plants, animals, fungi, and protists (1). The potential scientific and societal impact unfolding from the proposed new iteration of the project is vast, including driving solutions for conserving biodiversity, discovering new medicinal resources for human health, and identifying new genetic variation for improving agriculture (2).

Phase I of the EBP is well underway with the generation of the first 2000 EBP-affiliated genomes—a tour de force by current standards and a significant milestone for this mammoth endeavor. Among these genomes are exciting individual stories, and collectively, the generation of the data shows the ultimate feasibility of the project. It is a matter of when, not if, the EBP can succeed. It is now appropriate to plan EBP Phase II, addressing remaining questions as to how the program will be executed, including nuances of governance, sample prioritization, how the data produced should be shared, and, importantly, how the program should be funded (3)

Prior programs, beginning with the Human Genome Project (HGP) (4), tackled many issues related to large-scale sequencing efforts. The EBP has built upon these past lessons in Phase I and now considers the most relevant issues for Phase II. Undoubtedly, additional challenges and policy gaps will emerge with time; we identify some below, proposing further recommendations for a successful path forward.

Safeguarding centralized coordination is necessary for the EBP’s success. The organizational structure of the EBP is a major strength, reflecting a scientific passion for genomes paired with the systematic building of an effective organization. Remarkably, the EBP draws together 60 affiliated projects (https://www.earthbiogenome.org/affiliated-project-networks), working as a global “network of networks”. These individual projects focus on sequencing specific families or clades (e.g., 1,000 Bat Genomes or 10,000 Plant Genomes) or entire countries or continents (e.g., African BioGenome Project or Canada BioGenome Project). Key topics, including technologies, data standards, and data sharing, are tackled regularly in committees, with extensive communication between stakeholders. With this degree of robust organization, it would seem that funding is the most important requirement missing to drive the program to completion, but there are other gaps and potential “potholes” that the EBP needs to be aware of.

Currently, most EBP-affiliated projects are at intermediate stages of data gathering, and their funding status remains uncertain. They are carried out alongside other genome projects that have not yet joined the EBP collective. Local funding that rapidly advances any single project raises the possibility of shifting the center of gravity of the entire program to one or a few regions or species. Continued emphasis on the benefits of centralized coordination is therefore essential for the EBP’s success.

Including sampling for within-species genetic diversity

For Phase II, the EBP wisely plans a shift from species prioritization governed by sample availability and extant funding to a more idealized list based upon ecological and biological principles. A useful addition would be to prioritize sequencing additional individuals from key species to survey genetic diversity. While each reference genome can anchor subsequent studies, additional genomes give essential insight into the genetic variation within a species, which is needed to address key questions in areas such as conservation or agricultural sciences. Additional individuals need not be initially sequenced to the same high standard as the first reference genome, and methods such as pooled very-low-pass sequences from 5 to 10 individuals would provide valuable information. To unlock their maximum societal value, we recommend that these significantly beneficial studies be initiated without delay, rather than awaiting the EBP's full completion.  

Protecting unrestricted data access

The EBP has taken a strong philosophical position of ready data access but a more cautious stance on international declarations of interest and on safeguarding the rights of Indigenous (and other potentially marginalized) populations (5, 6). Moving forward, the EBP must press relentlessly for unrestricted data access. Experience in every other program has shown that even minor impediments to data access slow down and complicate all studies. Obstacles such as protection from bio-piracy should be negotiated ahead of the work, and solutions should not rely on data access restrictions. Unrestricted data access should be a fundamental guiding principle of the EBP.  

Securing political support for stable long-term funding

Support for the ongoing sequencing is the critical ingredient for the program. So far, the EBP has gained momentum from the affiliated projects that have relatively stable support. Ideally, there would be an international agreement that participation would be coupled to base-level funding, supporting the Phase II inspiration of a centralized $0.5 billion Foundational Impact Project (FIF) (3). There is no simple way in which this can be achieved. Only the persistent demonstration of the value of the ongoing data to address the precarious state of the planet, coupled with meaningful dialogue with those in political leadership positions, can hope to deliver this funding.

Communication between scientists, administrators, and politicians is essential to convey the real economic and social benefits of the EBP. Often, projects and visions fail because those who control funds are unconvinced of the return on investment for the required work. To date, the EBP has largely engaged scientists; even more communication with industry leaders and savvy politicians should continue to be a priority.

The complete EBP is an enormous project beyond the scope of current methods and resources to complete the program. But this is exactly the position of the HGP in the late 1980s (7). We are all amazed at the technological improvements that have been driven by the practical work being performed by genome scientists—most importantly, the concomitant cost savings—over the last 3 decades. The future is hard to predict, but there is every reason to be optimistic about vastly reduced costs, and EBP proponents should emphasize this at every opportunity to garner political and societal support to ensure long-term success.

Conclusion 

A new world where all eukaryotes are digitally cataloged should be welcomed. There will surely be unexpected challenges to ethics, policy, and science, as is the case for all other aspects of digital monitoring, but we should not shy away from these challenges. The reason is simple: the health of the planet is at stake. The expansion of humanity and the challenges of climate change and encroachment on natural habitats mean that we cannot simply rely on nature to take care of itself. We need to actively assist, and to do so effectively, we need every possible tool that we can manufacture. Achieving a complete digital understanding of all these species, including a robust measure of their genetic diversity and other tools to study and safeguard biological processes, represents a critical priority for humanity.

To unlock the maximum societal value of this ambitious endeavor, the EBP must safeguard its centralized coordination, integrate early and efficient assessment of within-species genetic diversity, protect unrestricted data access, and secure stable, long-term political support. These strategic imperatives, drawing parallels to the transformative success of projects like the Human Genome Project, will empower the EBP to deliver the essential knowledge and tools needed to navigate the planet’s most pressing biological challenges and secure a healthier future.

Copyright statement 

Copyright: © 2025 [author(s)]. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in Frontiers Policy Labs is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.     

Generative AI statement 

The author declares that no generative AI was used in the creation of this article.

References

1. Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, et al. Earth BioGenome Project: sequencing life for the future of life. Proc Natl Acad Sci (2018) 115(17):4325–33. doi: 10.1073/pnas.1720115115

2. Richards S. It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet (2015) 31(7):411-21. doi: 10.1016/j.tig.2015.04.007

3. Blaxter M, Lewin HA, Di Palma F, Challis R, da Silva M, Durbin R, et al. The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life. Front Sci (2025) 3:1514835. doi: 10.3389/fsci.2025.1514835

4. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature (2004) 431(7011):931-45. doi: 10.1038/nature03001

5. Sherkow JS, Barker KB, Braverman I, Cook-Deegan R, Durbin R, Easter CL, et al. Ethical, legal, and social issues in the Earth BioGenome Project. Proc Natl Acad Sci USA (2022) 119 (4) e2115859119. doi: 10.1073/pnas.2115859119

6. Mc Cartney AM, Head MA, Tsosie KS, Sterner B, Glass JR, Paez S, et al. Indigenous peoples and local communities as partners in the sequencing of global eukaryotic biodiversity. npj biodivers (2023) 2(1):8. doi: 10.1038/s44185-023-00013-7

7. Gibbs RA. The Human Genome Project changed everything. Nat Rev Genet (2020) 21(10):575-6. doi: 10.1038/s41576-020-0275-3