Abstract

The global prevalence of constipation has been increasing in recent years, posing an urgent need for safer and more effective therapeutic strategies. Given the favorable safety profile and beneficial effects on gut health, probiotics have emerged as a promising means for improving constipation. This study investigated the probiotic potential of Lacticaseibacillus paracasei BGI-N2 (BGI-N2) using integrated genomic and phenotypic analyses. The complete genome of BGI-N2 comprised 3,102,337 bp with a 46.4% GC content and 2,937 coding sequences, including multiple genes related to carbon source fermentation, gastrointestinal tolerance, and antioxidant activities. Furthermore, genomic analysis confirmed the favorable safety profile of BGI-N2. In vitro, this strain showed robust tolerance to extreme gastrointestinal conditions and significant inhibition against common enteropathogens. In constipated zebrafish, it enhanced motility by increasing motilin (MTL) and 5-hydroxytryptamine (5-HT) while decreasing nitric oxide levels. Mechanistically, BGI-N2 upregulated kitla, kitlb, and kitb genes to promote Cajal interstitial cell development, while enhancing 5-HT accumulation through coordinated regulation of biosynthetic genes (tph1a, tph1b, tph2) and the transporter gene (sert). This study provides comprehensive genomic insights for BGI-N2 while establishing a theoretical foundation for understanding host-microbe interactions in intestinal motility disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-026-04831-0.