Phaeobacter inhibens S4, a promising marine probiotic, protects larval Crassostrea virginica from vibriosis through several mechanisms when administered prophylactically. S4 produces an antimicrobial compound, tropodithietic acid (TDA), which is lethal to the pathogen Vibrio coralliilyticus RE22 and helps exclude it from biofilm formation. S4 also forms strong biofilms, reinforcing its role in niche exclusion. Additionally, it prevents RE22 cell-to-cell communication via quorum quenching, thereby inhibiting the production of virulence factors. Transcriptomic studies reveal that S4 disrupts RE22’s ability to cause larval mortality by downregulating flagellar genes, affecting motility, and impeding the formation of disulfide bonds necessary for proper flagellar protein development. Probiont S4 also primes C. virginica immune genes and restores healthy microbial diversity after UV treatment of hatchery tank water. Given the broad range of probiotic attributes of S4, and the known probiotic potential of a handful other P. inhibens strains in aquaculture, a pangenome of P. inhibens was constructed using 37 unique strains, along with an antiSMASH analysis to explore the distribution of probiotic traits. This analysis also sought to identify other probiotic capabilities within the species.
The pangenome revealed over 11,500 genes, with the core genome containing 3,118 genes, representing 72% of the average genome size of the strains studied. Key genes within the core genome include those responsible for cobalamin (vitamin B12) biosynthesis, biofilm formation, and TDA production. All but one strain possessed a non-ribosomal peptide synthetase (NRPS)-independent siderophore gene cluster, typically located on a plasmid. All strains had at least two homoserine lactone (AHL) clusters potentially involved in quorum signaling and quorum quenching. These findings suggest that all Phaeobacter inhibens strains hold significant potential for probiotic activity, but strain-specific genes may lead to differences in functionality or host specificity.