Screening and functional characterization of indigenous probiotic bacteria from shrimp gut and aquaculture water for sustainable shrimp farming

The excessive use of antibiotics in shrimp aquaculture has accelerated the emergence of antimicrobial resistance and contributed to environmental deterioration, highlighting the urgent need for sustainable disease management strategies. Probiotics represent an eco-friendly alternative capable of improving shrimp growth performance, immunity, and resistance to pathogenic infections. This study aimed to isolate, screen, and functionally characterize indigenous probiotic bacteria from shrimp gut and aquaculture water. Gut samples from healthy shrimps of Litopenaeus vannamei and aquaculture water samples were collected from shrimp farms in the Mumbai-Konkan region and processed aseptically. A total of twelve bacterial isolates were evaluated for probiotic attributes including acid tolerance (pH 3), bile tolerance (0.3%), salt tolerance (up to 6% NaCl), catalase activity, antimicrobial activity against shrimp-associated pathogens (Vibrio spp. ATCC 33866, Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Salmonella typhi ATCC 14028). and antibiotic susceptibility profiles. Four isolates (SG1, SG2, AQW1, AQW4) exhibited high survival under acid and bile stress, while SG1, SG2, AQW1 and AQW4 demonstrated broad-spectrum antimicrobial activity against all tested pathogens. Antibiotic susceptibility profiling indicated that six isolates exhibited acceptable sensitivity patterns, supporting their biosafety and suitability for probiotic development. Notably, antimicrobial activity persisted following pH neutralization, suggesting inhibitory metabolites beyond organic acids. Based on combined functional performance, promising isolates were identified by 16S rRNA gene sequencing as Priestia flexa, Alcaligenes faecalis, Bacillus megaterium and Lactiplantibacillus plantarum. These indigenous strains possess key probiotic characteristics and represent promising candidates for sustainable shrimp aquaculture; however, in vivo validation is required before commercial application.