From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic

A key bottleneck in microbiome engineering is ensuring the long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of host dependency offers a potential solution. The Ruegeria strain B4 of the population MC10, identified by such signatures, has shown persistent colonization in corals. To understand the putative mechanisms behind this, we characterized its functional profile using an integrated multi-omics approach, comparing it to non-candidate Ruegeria strains isolated from the same coral colony and compartment (mucus). This controlled for host genotype and microenvironment, both of which influence colonization outcomes. We show that MC10s genome is uniquely enriched for host-interaction functions, such as siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, which were confirmed phenotypically by enhanced siderophore production and biofilm formation. Subsequent proteomic analysis showed that the MC10-B4 proteome underwent a "motility-to-sessility" reprogramming upon exposure to host metabolites, a response distinct from its non-candidate sympatric relatives. Our findings suggest an evolutionary shift toward host dependency, marked by genomic decay on one hand and compensated by the gain and expression of functions that enable stable colonization on the other. MC10s functional profile, particularly its sensitivity to oxidative stress, would likely have excluded it from conventional probiotic screens that prioritize robust in vitro performance. This validates an evolution-guided approach that prioritizes innate colonization potential over pre-defined in vitro functionalities, informing the rational design of next-generation probiotics.