A multi-omics analysis reveals the response mechanism of Weissella confusa ZJU.2 to gastric acid and bile salts

Stress response pathways are critical for probiotic survival, promoting survival through adaptive changes in genes and proteins. However, the underlying stress response mechanisms of probiotics, especially Weissella confusa, are poorly understood. We have employed whole genome sequencing to assemble and annotate the W. confusa ZJU.2 genome, probing in parallel the proteome and transcriptome changes under the treatment of gastric acid and bile salts through a multi-omics approach. Stringent filtering reveals that significant upregulation of alanine, aspartate and glutamate metabolism and glycolysis/gluconeogenesis pathway are critical for gastric acid and bile salt tolerance in W. confusa ZJU.2. Concomitantly, the conjoint transcriptome and proteome analysis showed that the polysaccharide biosynthesis protein WP_039968605.1 plays an important role in gastric acid and bile salt tolerance. Parallel reaction monitoring (PRM) and Real-time quantitative polymerase chain reaction (RT-qPCR) analysis were used to demonstrate the reliability of the results. Moreover, we found that W. confusa ZJU.2 may have hypoglycemic effects through an in vivo zebrafish chip model and in vitro alpha-glucosidase activity assay. Collectively, this study provides a valuable multi-omics resource for the study of stress response mechanisms of Weissella and lays a solid foundation for its broader functional activity applications.