By Ross Youngs, 
November 26, 2025.

Microbiome Metabolic Fingerprinting: The Critical Control Layer for Deep Space Survival and Terrestrial Health (D2)

The two defining challenges of the coming century—reversing the decline in pharmaceutical R&D productivity on Earth and enabling sustainable human habitation in space—are usually treated as separate problems. In reality, they share a common dependency: access to and control over microbiome-derived chemistry. For approximately 3.8 billion years, microbes have acted as Earth’s primary chemists, producing vast repertoires of small molecules that mediate ecological interactions, host physiology, and system resilience. Yet current analytical workflows suggest that 90–95% of microbiome-derived small molecules remain structurally uncharacterized “dark matter.”This blind spot limits our ability to design robust closed-loop life support systems, maintain astronaut health, exploit in situ resources in space, and reverse the productivity crisis in drug discovery known as Eroom’s Law.

This article formalizes Industrial-Scale Microbiome Mining (ISMM) as a dual-use platform. First, we argue that ISMM addresses the microbial dark-matter access problem, enabling a finite-priors hybrid model that can reverse Eroom’s Law by improving late-stage success rates. Second, we show that ISMM-AI-derived microbiome metabolic fingerprinting provides a critical control layer for closed-loop life support, food systems, biomining, and human health in space, where phenotypic drift and unmonitored metabolic shifts can threaten mission viability. We conclude that industrial-scale microbiome mining is not an optional adjunct to space biomanufacturing; it is foundational infrastructure for sustainable human activity beyond Earth and for the next generation of network-level therapeutics on Earth. From this perspective, the barrier to sustainable human presence beyond Earth is not primarily rocketry or materials science; it is our incomplete grasp of microbiome-derived chemistry. Mastering that chemistry through ISMM is therefore not an optional research direction but a strategic necessity—for reversing Eroom’s Law on Earth and for keeping humans alive, healthy, and adaptive as they move outward into the solar system.

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