Metabolomics in Microbial Genetic Resource Conservation: From Strain Identity to Functional Preservation

The conservation of microbial genetic resources (MGR) is increasingly recognized as a strategic pillar for food security, biotechnology, ecosystem resilience, and climate change adaptation. Traditionally, ex situ conservation efforts have prioritized strain identity, viability, and genetic stability, relying mainly on cryopreservation and lyophilization as long-term storage strategies. However, growing evidence indicates that cellular survival and genomic integrity do not necessarily guarantee the preservation of microbial functionality, as preservation procedures may induce subtle yet biologically relevant metabolic and physiological alterations. In this context, metabolomics emerges as a critical tool for advancing microbial conservation beyond identity-based paradigms toward a framework of functional conservation. By directly capturing the biochemical phenotype, metabolomics provides an integrated readout of microbial physiological state, enabling the assessment of post-preservation metabolic stability, the identification of functionally relevant biomarkers, and the evaluation of preservation-induced metabolic reprogramming. This chapter critically reviews the role of metabolomics in the conservation of microbial genetic resources, highlighting its contributions to functional characterization, post-preservation quality assessment, protocol optimization under quality-by-design principles, and strain prioritization based on functional diversity and resilience. Methodological and conceptual challenges, including standardization, reproducibility, and metabolite identification, are discussed in the context of integrating metabolomics into biobanking and quality assurance frameworks. Finally, future perspectives are outlined, emphasizing the integration of metabolomics with other omics layers, regulatory standards, and predictive approaches to support functional, resilient, and application-oriented microbial conservation under global change.