Isolation of a Protease‐Producing Microbacterium From the Intestinal Tract of Ruditapes philippinarum and Its Probiotic Effects

Aquatic probiotics are generally recognized as safe and nontoxic live bacterial preparations, primarily sourced from the culturing environment or directly from aquatic organisms. Upon entering the aquatic environment, these probiotics are capable of colonizing both the surface and internal compartments of aquatic organisms, thereby enhancing their nutrient absorption and immune defense. The intestinal bacteria of aquatic animals represent a significant source of probiotics, as they possess inherent advantages in colonizing the intestinal tracts of their hosts and competing with the established intestinal microbiota. This study was designed to isolate probiotics from Ruditapes philippinarum by screening culturable bacteria harvested from the intestines of healthy clams. Using selective culture media and a protease‐producing test kit, a protease‐producing bacterium that did not form a β‐hemolytic ring on Columbia blood agar plates was successfully isolated and designated as Strain 48. Subsequent morphological analysis, 16S rDNA and whole‐genome sequencing–based molecular identification, and physiological and biochemical profiling confirmed that Strain 48 belonged to the species of Microbacterium forte . Based on the whole‐genome sequencing results, further analyses were conducted to explore its functional potential and saftety‐related genetic characteristics. Immersion bacterial challenge tests revealed that Strain 48 exhibited no toxicity to R. philippinarum at concentrations of 1 × 10 6 , 1 × 10 7 , and 1 × 10 8 CFU/mL. Culture experiments conducted over a 60‐day period demonstrated that the group exposed to Strain 48 at a concentration of 1 × 10 7 CFU/mL exhibited significantly increased weight gain and shell length growth compared to the control group, and lysozyme (LZM) activity was also significantly enhanced ( p < 0.01). Genomic analysis indicated that virulence factors or antibiotic resistance genes (ARGs) associated with mobile genetic elements were absent, which supported the biosafety of Strain 48. Administration of Strain 48 significantly increased LZM activity in the soft tissues of R. philippinarum ( p < 0.01), indicating an enhanced host immune response. Overall, Strain 48 may have the potential to be developed as a probiotic for R. philippinarum .