# Native Bacillus-Based Probiotic Consortia Suppress Vibrio parahaemolyticus and Restructure Hatchery Water Microbiomes in Shrimp Larval Systems

## TL;DR

Native Bacillus-based probiotics reduce harmful Vibrio bacteria and reshape microbial communities in shrimp hatchery water.

## Contribution

This study demonstrates the efficacy of native Bacillus consortia in suppressing Vibrio parahaemolyticus and restructuring hatchery water microbiomes.

## Key findings

- Probiotic treatments showed high antagonistic activity against Vibrio parahaemolyticus.
- Probiotics increased Bacillus dominance and reduced Vibrio abundance in hatchery water.
- Bacillus dominance was identified as a key driver of antagonistic activity via inferred bioactive functions.

## Abstract

Shrimp aquaculture is constrained by opportunistic bacterial pathogens, particularly Vibrio parahaemolyticus, whose proliferation in hatchery systems is shaped by microbial community structure. We evaluated the antagonistic activity and microbiome effects of two native Bacillus-based probiotic consortia (CN5, RS3) applied alone or combined (MIX) in shrimp larval culture water over 30 days, relative to a no-probiotic control. Treatments were assessed using standardized in vitro inhibition assays, 16S rRNA gene (V3–V4) amplicon sequencing, functional inference, and integrative multivariate and structural modeling. All probiotic treatments showed consistently high antagonistic activity against V. parahaemolyticus, whereas the control showed no inhibition. Amplicon profiling indicated treatment-associated microbiome restructuring, with increased Bacillus dominance and reduced relative abundance of Vibrio spp. under probiotic conditions. Multivariate analyses separated probiotic and control groups, and PLS-SEM identified Bacillus dominance as a central driver of antagonistic activity mediated by inferred bioactive functional potential, while water-quality variables had limited direct effects. Probiotics were administered directly to the culture water once daily after routine water exchange to 1 × 106 CFU mL−1 (CN5 or RS3); MIX was applied 1:1 (v/v) at the same total dose.