Effect of Native Bacillus Strains Supplemented in Water on Growth Performance, Resistance to Vibrio parahaemolyticus (AHPND Strain), and Gut Microbiota of White Shrimp (Penaeus vannamei)

Probiotics, especially Bacillus species, have gained attention for their potential to improve growth and strengthen disease resistance in cultured shrimp. This study evaluated the effects of native Bacillus strains on growth performance, disease resistance and gut microbiota of Penaeus vannamei through the rearing water. Bacillus subtilis (BS) and Bacillus cereus (BC) group strain were isolated from pond sediment collected in Chanthaburi, Thailand, in April 2025. Both strains were identified by 16S rRNA gene sequencing, and the sequence data were deposited in the NCBI database under BioProject accession no. PRJNA1513981 (SRX34829739 for B. cereus BUUC2501 and SRX34829740 for B. subtilis BUUC2502). The shrimp were reared in water supplemented with one of four treatments: (a) a negative control (no bacterial addition), (b) a commercial Bacillus spp. product (positive control), (c) B. subtilis, and (d) B. cereus group strain. Treatments were applied every 7 days as three applications on days 7, 14, and 21, with each strain added to the rearing water at a final concentration of approximately 1 × 105 CFU/mL per application; shrimp were then reared until day 28. Shrimp reared with the B. cereus group strain showed numerically higher specific growth rate (SGR) and average daily gain (ADG) than the control; however, after adjusting for a lower initial weight in this group by ANCOVA, these differences were not statistically robust. There was no significant difference in final body weight and feed conversion ratio among groups (p > 0.05). After Vibrio parahaemolyticus (VPAHPND) challenge, the survival rate was the highest in the B. cereus-treated group, showing the highest disease resistance. Alpha diversity of the gut microbiota was not significantly different among groups, whereas beta-diversity analysis (PERMANOVA) showed significant differences in gut microbial community structure among groups, and LEfSe identified the genus Bacillus as a biomarker of the B. cereus group. These results provide proof-of-concept evidence that water-based supplementation with a native B. cereus group strain can enhance disease resistance and increase the relative abundance of Bacillus in the shrimp gut. However, because the B. cereus group includes potentially toxigenic strains, a strain-level safety assessment is required before this approach can be applied in shrimp aquaculture.